{"entity": "label", "iuid": "31324019cd27487fb30cf7d8497d141d", "timestamp": "2026-09-11T19:30:22.750Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/label/Vicente%20Pelechano.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/label/Vicente%20Pelechano"}}, "value": "Vicente Pelechano", "created": "2020-10-09T14:02:26.475Z", "modified": "2026-09-11T13:23:23.857Z", "accounts": [{"entity": "account", "iuid": "43d414f3d1d04ea19ac969a8df4ed4a6", "timestamp": "2026-09-11T19:30:22.750Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:30.148Z", "created": "2024-08-16T10:03:01.443Z", "modified": "2026-09-11T13:23:23.990Z"}, {"entity": "account", "iuid": "59d7e928268c4c5c9d866673716a8f2d", "timestamp": "2026-09-11T19:30:22.750Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se"}}, "email": "christopher.erdmann@scilifelab.uu.se", "name": "Christopher Erdmann", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-08-16T11:57:32.037Z", "created": "2024-08-16T10:02:45.342Z", "modified": "2026-09-11T13:23:24.200Z"}, {"entity": "account", "iuid": "a2ab8ad8cd1b4af2970553a4874f9a76", "timestamp": "2026-09-11T19:30:22.750Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/account/vicent.pelechano%40scilifelab.se.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/account/vicent.pelechano%40scilifelab.se"}}, "email": "vicent.pelechano@scilifelab.se", "name": "Vicent Pelechano", "orcid": null, "role": "curator", "status": "enabled", "login": "2024-11-26T08:27:06.812Z", "created": "2020-10-09T14:03:03.499Z", "modified": "2026-09-11T13:23:24.256Z"}], "publications_count": 77, "publications": [{"entity": "publication", "iuid": "1ff970d64d8f4acdaffe257ebbbadf21", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ff970d64d8f4acdaffe257ebbbadf21.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ff970d64d8f4acdaffe257ebbbadf21"}}, "title": "The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans.", "authors": [{"family": "Stevens", "given": "Irene", "initials": "I", "orcid": "0000-0003-3823-1499", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89f8823541844106b92311e5cd7ec22a.json"}}, {"family": "Silao", "given": "Fitz Gerald", "initials": "FG"}, {"family": "Huch", "given": "Susanne", "initials": "S", "orcid": "0000-0003-3956-7197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0b94cf87e4243efa8e6229f49403d0f.json"}}, {"family": "Liu", "given": "Honglian", "initials": "H", "orcid": "0000-0001-6771-9421", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87cc9eafc4d54c479686bd44b6c48d18.json"}}, {"family": "Ryman", "given": "Kicki", "initials": "K"}, {"family": "Carvajal-Jimenez", "given": "Adriana", "initials": "A"}, {"family": "Ljungdahl", "given": "Per O", "initials": "PO"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2024-11-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "29012", "issn-l": "2045-2322"}, "abstract": "Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5'P mRNA degradation intermediates, we establish that co-translational mRNA decay occurs in C. albicans and characterize how in vivo 5\u00b4-3\u00b4 exonuclease degradation trails the last translating ribosome. Thus, the study of the 5' Phosphorylated mRNA degradome (5PSeq) offers a simple and affordable way to measure ribosome dynamics and identify codon specific ribosome stalls in response to drugs and amino acid deprivation. Building upon this, we combine RNA-Seq and 5PSeq to study the early response of sensitive and resistant C. albicans isolates to fluconazole. Our results highlight that transcriptional responses, rather than changes in ribosome dynamics, are the main driver of Candida resistance to fluconazole.", "doi": "10.1038/s41598-024-80435-w", "pmid": "39578617", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-024-80435-w"}], "notes": [], "created": "2024-11-26T08:29:39.804Z", "modified": "2026-09-11T13:23:24.743Z"}, {"entity": "publication", "iuid": "74dc476cd8cc45d1a9b37d20fc070d79", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/74dc476cd8cc45d1a9b37d20fc070d79.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/74dc476cd8cc45d1a9b37d20fc070d79"}}, "title": "The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.", "authors": [{"family": "Turnbull", "given": "Kathryn", "initials": "K", "orcid": "0000-0002-0899-974X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02a543194bb94a0e89f62e7288cc2036.json"}}, {"family": "Paternoga", "given": "Helge", "initials": "H", "orcid": "0000-0001-8335-3239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dead4106bf4c4cfbbd1243f24dac0f23.json"}}, {"family": "von der Weth", "given": "Esther", "initials": "E"}, {"family": "Egorov", "given": "Artyom A", "initials": "AA", "orcid": "0000-0001-5578-5384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db620b86e13e45618e7cad6a06cd474e.json"}}, {"family": "Pochopien", "given": "Agnieszka A", "initials": "AA"}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Nersisyan", "given": "Lilit", "initials": "L"}, {"family": "Margus", "given": "T\u00f5nu", "initials": "T"}, {"family": "Johansson", "given": "Marcus J O", "initials": "MJO"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c2d78750ccb42239a7363f99f58dcc5.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}], "type": "journal article", "published": "2024-10-28", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "19", "pages": "12005-12020", "issn-l": "0305-1048"}, "abstract": "The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.", "doi": "10.1093/nar/gkae748", "pmid": "39217469", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC11514491"}, {"db": "pii", "key": "7747204"}], "notes": [], "created": "2024-11-26T08:29:41.203Z", "modified": "2026-09-11T13:23:24.905Z"}, {"entity": "publication", "iuid": "b2f48a7e4c764756947e6674ebeaed51", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b2f48a7e4c764756947e6674ebeaed51.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b2f48a7e4c764756947e6674ebeaed51"}}, "title": "Comparison of Xrn1 and Rat1 5' \u2192 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay.", "authors": [{"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE", "orcid": "0000-0002-1992-513X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac4f5d4d6cd54c1bbafeec15e97e5c49.json"}}, {"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Moreno-Garc\u00eda", "given": "Jorge", "initials": "J"}, {"family": "Bassot", "given": "Claudio", "initials": "C"}, {"family": "Barba-Aliaga", "given": "Marina", "initials": "M"}, {"family": "de Campos-Mata", "given": "Leire", "initials": "L", "orcid": "0000-0003-1998-4014", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cb488200bfe47c5b1d1b1c17a46f193.json"}}, {"family": "Choder", "given": "Mordechai", "initials": "M"}, {"family": "D\u00edez", "given": "Juana", "initials": "J"}, {"family": "Piazza", "given": "Ilaria", "initials": "I"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Yeast", "issn": "1097-0061", "volume": "41", "issue": "7", "pages": "458-472", "issn-l": "0749-503X"}, "abstract": "The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' \u2192 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger RNA (mRNA) decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes to the nucleus. Xrn1 is 30% identical to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes, a process referred to as \"cotranslational mRNA decay.\" The division of labor between the two enzymes is still enigmatic and serves as a paradigm for the subfunctionalization of many other paralogs. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the physical segregation of the two paralogs plays roles in their specific functions. However, reversing segregation is not sufficient to fully complement the Xrn1 function. Specifically, cRat1 can partially restore the cell volume, mRNA stability, the proliferation rate, and 5' \u2192 3' decay alterations that characterize xrn1\u0394 cells. Nevertheless, cotranslational decay is only slightly complemented by cRat1. The use of the AlphaFold prediction for cRat1 and its subsequent docking with the ribosome complex and the sequence conservation between cRat1 and Xrn1 suggest that the tight interaction with the ribosome observed for Xrn1 is not maintained in cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve phenotypes, which indicates that lack of the C-terminal is not responsible for partial complementation. Overall, during evolution, it appears that the two paralogs have acquired specific characteristics to make functional partitioning beneficial.", "doi": "10.1002/yea.3968", "pmid": "38874348", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2024-11-26T08:29:42.638Z", "modified": "2026-09-11T13:23:24.916Z"}, {"entity": "publication", "iuid": "7450274bf80a45959f3ae8a23a23dcce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7450274bf80a45959f3ae8a23a23dcce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7450274bf80a45959f3ae8a23a23dcce"}}, "title": "Cellular energy regulates mRNA degradation in a codon-specific manner.", "authors": [{"family": "Tomaz da Silva", "given": "Pedro", "initials": "P", "orcid": "0000-0001-6320-4885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4c2e93d144149d98e9d67a716b057a3.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Theodorakis", "given": "Evangelos", "initials": "E"}, {"family": "Martens", "given": "Laura D", "initials": "LD"}, {"family": "Y\u00e9pez", "given": "Vicente A", "initials": "VA"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Gagneur", "given": "Julien", "initials": "J", "orcid": "0000-0002-8924-8365", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d003f1d4e07f407b9c2ce0f40db1d53d.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "20", "issue": "5", "pages": "506-520", "issn-l": "1744-4292"}, "abstract": "Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated remains poorly understood. Here we show that codon optimality associates with up to 2-fold change in mRNA stability variations between human tissues, and that its effect is attenuated in tissues with high energy metabolism and amplifies with age. Mathematical modeling and perturbation data through oxygen deprivation and ATP synthesis inhibition reveal that cellular energy variations non-uniformly alter the effect of codon usage. This new mode of codon effect regulation, independent of tRNA regulation, provides a fundamental mechanistic link between cellular energy metabolism and eukaryotic gene expression.", "doi": "10.1038/s44320-024-00026-9", "pmid": "38491213", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC11066088"}, {"db": "pii", "key": "10.1038/s44320-024-00026-9"}], "notes": [], "created": "2024-11-26T08:29:43.838Z", "modified": "2026-09-11T13:23:25.004Z"}, {"entity": "publication", "iuid": "482d0f069b40487e9349bec0aab986dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/482d0f069b40487e9349bec0aab986dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/482d0f069b40487e9349bec0aab986dd"}}, "title": "The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae.", "authors": [{"family": "Cuevas-Berm\u00fadez", "given": "Abel", "initials": "A"}, {"family": "Mart\u00ednez-Fern\u00e1ndez", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Garrido-Godino", "given": "Ana I", "initials": "AI", "orcid": "0000-0002-7389-1372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7683c79eb2a94be1b118e80b275b94a7.json"}}, {"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Pe\u00f1ate", "given": "Xenia", "initials": "X"}, {"family": "Mart\u00edn-Exp\u00f3sito", "given": "Manuel", "initials": "M"}, {"family": "Guti\u00e9rrez", "given": "Gabriel", "initials": "G"}, {"family": "Govind", "given": "Chhabi K", "initials": "CK"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Navarro", "given": "Francisco", "initials": "F", "orcid": "0000-0002-4180-422X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2abed56af56f41fcb118d39f21b9a8e5.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms", "issn": "1876-4320", "pages": "194995", "volume": "1867", "issue": "1", "issn-l": "1874-9399"}, "abstract": "The tripartite interaction between the chromatin remodeler complex RSC, RNA polymerase subunit Rpb5 and prefoldin-like Bud27 is necessary for proper RNA pol II elongation. Indeed lack of Bud27 alters this association and affects transcription elongation. This work investigates the consequences of lack of Bud27 on the chromatin association of RSC and RNA pol II, and on nucleosome positioning. Our results demonstrate that RSC binds chromatin in gene bodies and lack of Bud27 alters this association, mainly around polyA sites. This alteration impacts chromatin organization and leads to the accumulation of RNA pol II molecules around polyA sites, likely due to pausing or arrest. Our data suggest that RSC is necessary to maintain chromatin organization around those sites, and any alteration of this organization results in the widespread use of alternative polyA sites. Finally, we also find a similar molecular phenotype that occurs upon TOR inhibition with rapamycin, which suggests that alternative polyadenylation observed upon TOR inhibition is likely Bud27-dependent.", "doi": "10.1016/j.bbagrm.2023.194995", "pmid": "37967810", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S1874-9399(23)00090-1"}], "notes": [], "created": "2023-11-23T09:13:48.750Z", "modified": "2026-09-11T13:23:25.086Z"}, {"entity": "publication", "iuid": "9d67dfa80487430897db6cd86901138a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9d67dfa80487430897db6cd86901138a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9d67dfa80487430897db6cd86901138a"}}, "title": "Targeting MYC induces lipid droplet accumulation by upregulation of HILPDA in clear cell renal cell carcinoma.", "authors": [{"family": "Sainero-Alcolado", "given": "Lourdes", "initials": "L", "orcid": "0000-0002-9406-6478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2fd18f4ec7d64556a55e1b1ac58f1a76.json"}}, {"family": "Garde-Lapido", "given": "Elisa", "initials": "E", "orcid": "0009-0001-5321-1253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/629c0c3b04da41c8ad4ad5f81765b46c.json"}}, {"family": "Snaebj\u00f6rnsson", "given": "Marteinn Thor", "initials": "MT"}, {"family": "Schoch", "given": "Sarah", "initials": "S"}, {"family": "Stevens", "given": "Irene", "initials": "I", "orcid": "0000-0003-3823-1499", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89f8823541844106b92311e5cd7ec22a.json"}}, {"family": "Ruiz-P\u00e9rez", "given": "Mar\u00eda Victoria", "initials": "MV"}, {"family": "Dyrager", "given": "Christine", "initials": "C", "orcid": "0000-0003-4647-9769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57d602cf9db24839a0b437e3e97705f8.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Axelson", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-7749-5043", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11870c1e339d421aa2e4823c72231a2b.json"}}, {"family": "Schulze", "given": "Almut", "initials": "A"}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M", "orcid": "0000-0001-6376-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44b0383f17264df8a5c09f385a09b97b.json"}}], "type": "journal article", "published": "2024-02-13", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "121", "issue": "7", "pages": "e2310479121", "issn-l": "0027-8424"}, "abstract": "Metabolic reprogramming is critical during clear cell renal cell carcinoma (ccRCC) tumorigenesis, manifested by accumulation of lipid droplets (LDs), organelles that have emerged as new hallmarks of cancer. Yet, regulation of their biogenesis is still poorly understood. Here, we demonstrate that MYC inhibition in ccRCC cells lacking the von Hippel Lindau (VHL) gene leads to increased triglyceride content potentiating LD formation in a glutamine-dependent manner. Importantly, the concurrent inhibition of MYC signaling and glutamine metabolism prevented LD accumulation and reduced tumor burden in vivo. Furthermore, we identified the hypoxia-inducible lipid droplet-associated protein (HILPDA) as the key driver for induction of MYC-driven LD accumulation and demonstrated that conversely, proliferation, LD formation, and tumor growth are impaired upon its downregulation. Finally, analysis of ccRCC tissue as well as healthy renal control samples postulated HILPDA as a specific ccRCC biomarker. Together, these results provide an attractive approach for development of alternative therapeutic interventions for the treatment of this type of renal cancer.", "doi": "10.1073/pnas.2310479121", "pmid": "38335255", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC10873620"}], "notes": [], "created": "2024-11-26T08:29:45.281Z", "modified": "2026-09-11T13:23:25.099Z"}, {"entity": "publication", "iuid": "919c6fe71cdf4d7ea3e7b7223aa3508e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/919c6fe71cdf4d7ea3e7b7223aa3508e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/919c6fe71cdf4d7ea3e7b7223aa3508e"}}, "title": "RNA Pol II Assembly Affects ncRNA Expression.", "authors": [{"family": "Garrido-Godino", "given": "Ana I", "initials": "AI", "orcid": "0000-0002-7389-1372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7683c79eb2a94be1b118e80b275b94a7.json"}}, {"family": "Gupta", "given": "Ishaan", "initials": "I"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Navarro", "given": "Francisco", "initials": "F", "orcid": "0000-0002-4180-422X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2abed56af56f41fcb118d39f21b9a8e5.json"}}], "type": "journal article", "published": "2023-12-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "1", "issn-l": null}, "abstract": "RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.", "doi": "10.3390/ijms25010507", "pmid": "38203678", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC10778713"}, {"db": "pii", "key": "ijms25010507"}], "notes": [], "created": "2024-11-26T08:29:47.844Z", "modified": "2026-09-11T13:23:25.114Z"}, {"entity": "publication", "iuid": "76699bd557614e69bccb6e73592cd4a7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76699bd557614e69bccb6e73592cd4a7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76699bd557614e69bccb6e73592cd4a7"}}, "title": "Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs.", "authors": [{"family": "Tayyab", "given": "Muhammad", "initials": "M", "orcid": "0000-0002-4372-504X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fbced44ff6847fab3b50a830f44abc4.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "van Riel", "given": "Gijs", "initials": "G"}, {"family": "Liu", "given": "Shujing", "initials": "S", "orcid": "0000-0002-5783-4204", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efd66c143bda4ad68ba21cd6e2319e15.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Scharfe", "given": "Curt", "initials": "C", "orcid": "0000-0001-6322-2039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/151a81585ba4445793d52cf41934b10e.json"}}, {"family": "Griffin", "given": "Peter", "initials": "P"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Javanmard", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-6297-392X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1208a771a4fa451d92a74c76aa6032b2.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-09-08", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "36", "pages": "eadi4997", "issn-l": "2375-2548"}, "abstract": "Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, \u03b2-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).", "doi": "10.1126/sciadv.adi4997", "pmid": "37672583", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC10482329"}], "notes": [], "created": "2023-11-23T09:13:47.169Z", "modified": "2026-09-11T13:23:25.167Z"}, {"entity": "publication", "iuid": "c0cf16af36db4481865c4c6ccffb5d75", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0cf16af36db4481865c4c6ccffb5d75.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0cf16af36db4481865c4c6ccffb5d75"}}, "title": "Atlas of mRNA translation and decay for bacteria.", "authors": [{"family": "Huch", "given": "Susanne", "initials": "S", "orcid": "0000-0003-3956-7197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0b94cf87e4243efa8e6229f49403d0f.json"}}, {"family": "Nersisyan", "given": "Lilit", "initials": "L", "orcid": "0000-0001-8525-420X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c77363d1fa7f4ea6b50c22590c23a163.json"}}, {"family": "Ropat", "given": "Maria", "initials": "M"}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Wu", "given": "Mengjun", "initials": "M"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Valeriano", "given": "Valerie D", "initials": "VD", "orcid": "0000-0002-4396-346X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c444998f561a43e8a8a8295b5ead218b.json"}}, {"family": "Vardazaryan", "given": "Nelli", "initials": "N", "orcid": "0000-0002-7972-8912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dabc3fd207b54423bf21dcbee3ca03ee.json"}}, {"family": "Huerta-Cepas", "given": "Jaime", "initials": "J", "orcid": "0000-0003-4195-5025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c8c00b0396840c480fa3f57a376ce00.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-05-22", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276"}, "abstract": "Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.", "doi": "10.1038/s41564-023-01393-z", "pmid": "37217719", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-023-01393-z"}], "notes": [], "created": "2023-05-29T07:36:18.693Z", "modified": "2026-09-11T13:23:25.240Z"}, {"entity": "publication", "iuid": "b286c12a79af41768be6da62ae5271c8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b286c12a79af41768be6da62ae5271c8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b286c12a79af41768be6da62ae5271c8"}}, "title": "A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-\u03baB signaling.", "authors": [{"family": "Altea-Manzano", "given": "Patricia", "initials": "P", "orcid": "0000-0002-7075-2051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc925e104e4b4ffda45d0b7eb0bed274.json"}}, {"family": "Doglioni", "given": "Ginevra", "initials": "G", "orcid": "0000-0002-9470-4476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/167294e97bcf475db6219c085d91f517.json"}}, {"family": "Liu", "given": "Yawen", "initials": "Y"}, {"family": "Cuadros", "given": "Alejandro M", "initials": "AM", "orcid": "0000-0002-5900-5143", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/234d712891214dfbbde12ea56006b555.json"}}, {"family": "Nolan", "given": "Emma", "initials": "E"}, {"family": "Fern\u00e1ndez-Garc\u00eda", "given": "Juan", "initials": "J", "orcid": "0000-0003-3422-3627", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb950bd644874146a9d1dc8f8227e459.json"}}, {"family": "Wu", "given": "Qi", "initials": "Q", "orcid": "0000-0002-5901-8438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee1b2a31dd1b43b8af053286423ecf04.json"}}, {"family": "Planque", "given": "M\u00e9lanie", "initials": "M"}, {"family": "Laue", "given": "Kathrin Julia", "initials": "KJ"}, {"family": "Cidre-Aranaz", "given": "Florencia", "initials": "F"}, {"family": "Liu", "given": "Xiao-Zheng", "initials": "XZ", "orcid": "0000-0002-8452-6848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc53423116764d08b9a705fd0a3c6632.json"}}, {"family": "Marin-Bejar", "given": "Oskar", "initials": "O", "orcid": "0000-0002-6889-6566", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec5e4afab030414198c01b69f34e37c5.json"}}, {"family": "Van Elsen", "given": "Joke", "initials": "J", "orcid": "0000-0002-7349-043X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f7560e6f8f94bc5b76d15736b67b7da.json"}}, {"family": "Vermeire", "given": "Ines", "initials": "I", "orcid": "0000-0003-3366-7410", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4d49d566b5247b89001d79c64d1b1c7.json"}}, {"family": "Broekaert", "given": "Dorien", "initials": "D", "orcid": "0000-0002-9777-1607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f21d3c32c3e947e7bbc04f9a7dd463a9.json"}}, {"family": "Demeyer", "given": "Sofie", "initials": "S", "orcid": "0000-0002-8193-5734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87b5193f78094e76ba09965287fa555e.json"}}, {"family": "Spotbeen", "given": "Xander", "initials": "X"}, {"family": "Idkowiak", "given": "Jakub", "initials": "J"}, {"family": "Montagne", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Demicco", "given": "Margherita", "initials": "M", "orcid": "0000-0002-9396-3281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/262c2c679dc34e1085822ed3dcfdf689.json"}}, {"family": "Alkan", "given": "H Furkan", "initials": "HF"}, {"family": "Rabas", "given": "Nick", "initials": "N"}, {"family": "Riera-Domingo", "given": "Carla", "initials": "C", "orcid": "0000-0001-7277-234X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a208ccdba4eb4f6dbf8993e989115066.json"}}, {"family": "Richard", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0003-4353-3619", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10489c1570014490a694b956f0b31706.json"}}, {"family": "Geukens", "given": "Tatjana", "initials": "T"}, {"family": "De Schepper", "given": "Maxim", "initials": "M"}, {"family": "Leduc", "given": "Sophia", "initials": "S"}, {"family": "Hatse", "given": "Sigrid", "initials": "S", "orcid": "0000-0002-6764-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/239722ea0fc24415b277ac974df7d5b3.json"}}, {"family": "Lambrechts", "given": "Yentl", "initials": "Y", "orcid": "0000-0002-9013-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4371ed18359541869b8c6b7333146ebe.json"}}, {"family": "Kay", "given": "Emily Jane", "initials": "EJ"}, {"family": "Lilla", "given": "Sergio", "initials": "S", "orcid": "0000-0003-3142-7640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a5956d3819947df8122ec1601025bbc.json"}}, {"family": "Alekseenko", "given": "Alisa", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Geldhof", "given": "Vincent", "initials": "V"}, {"family": "Boeckx", "given": "Bram", "initials": "B"}, {"family": "de la Calle Arregui", "given": "Celia", "initials": "C", "orcid": "0000-0002-4627-2963", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb32d4a0bd1543f5b57eaf754ecd31f3.json"}}, {"family": "Floris", "given": "Giuseppe", "initials": "G", "orcid": "0000-0003-2391-5425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/748c63dfe15b4711a498bbd88ec7b383.json"}}, {"family": "Swinnen", "given": "Johannes V", "initials": "JV", "orcid": "0000-0002-7720-5077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a93abc364bf44a0afc7ca6648e48f89.json"}}, {"family": "Marine", "given": "Jean-Christophe", "initials": "JC"}, {"family": "Lambrechts", "given": "Diether", "initials": "D", "orcid": "0000-0002-3429-302X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/000c5cebe4004ee289be1979ff1ecda4.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Mazzone", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-8824-4015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4bb29c0c042446bae12282bc0923cc4.json"}}, {"family": "Zanivan", "given": "Sara", "initials": "S", "orcid": "0000-0002-9880-9099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b30d0f0cade4acca44a4a38fcf64345.json"}}, {"family": "Cools", "given": "Jan", "initials": "J", "orcid": "0000-0001-6626-5843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c076c535fa3d483088f4ecb649f64f2c.json"}}, {"family": "Wildiers", "given": "Hans", "initials": "H", "orcid": "0000-0001-8990-7837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f87f05ea445475c973704a31cd81027.json"}}, {"family": "Baud", "given": "V\u00e9ronique", "initials": "V", "orcid": "0000-0002-4090-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b7ec92cacb442749cee18c474e4573d.json"}}, {"family": "Gr\u00fcnewald", "given": "Thomas G P", "initials": "TGP", "orcid": "0000-0003-0920-7377", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7d1c5a1b0c94ede884388c2e86503f1.json"}}, {"family": "Ben-David", "given": "Uri", "initials": "U", "orcid": "0000-0001-7098-2378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b88b311ac57b45afb37e8ba5e253191a.json"}}, {"family": "Desmedt", "given": "Christine", "initials": "C", "orcid": "0000-0002-5223-5579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7a7cb14a2ab4c55a3a23ed8e4323395.json"}}, {"family": "Malanchi", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-4867-3311", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b2a177fdd084ba88486b18ca508d231.json"}}, {"family": "Fendt", "given": "Sarah-Maria", "initials": "SM", "orcid": "0000-0001-6018-9296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5269066243ec45129407a6340bb437cc.json"}}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "4", "issue": "3", "pages": "344-364", "issn-l": null}, "abstract": "Metabolic rewiring is often considered an adaptive pressure limiting metastasis formation; however, some nutrients available at distant organs may inherently promote metastatic growth. We find that the lung and liver are lipid-rich environments. Moreover, we observe that pre-metastatic niche formation increases palmitate availability only in the lung, whereas a high-fat diet increases it in both organs. In line with this, targeting palmitate processing inhibits breast cancer-derived lung metastasis formation. Mechanistically, breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a-dependent manner. Concomitantly, lysine acetyltransferase 2a expression is promoted by palmitate, linking the available acetyl-CoA to the acetylation of the nuclear factor-kappaB subunit p65. Deletion of lysine acetyltransferase 2a or carnitine palmitoyltransferase 1a reduces metastasis formation in lean and high-fat diet mice, and lung and liver metastases from patients with breast cancer show coexpression of both proteins. In conclusion, palmitate-rich environments foster metastases growth by increasing p65 acetylation, resulting in a pro-metastatic nuclear factor-kappaB signaling.", "doi": "10.1038/s43018-023-00513-2", "pmid": "36732635", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s43018-023-00513-2"}], "notes": [], "created": "2023-05-29T07:36:16.305Z", "modified": "2026-09-11T13:23:25.268Z"}, {"entity": "publication", "iuid": "e89bfdd27dad4213a6aebdbd3e2d26d6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e89bfdd27dad4213a6aebdbd3e2d26d6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e89bfdd27dad4213a6aebdbd3e2d26d6"}}, "title": "Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.", "authors": [{"family": "Allen", "given": "George", "initials": "G"}, {"family": "Weiss", "given": "Benjamin", "initials": "B"}, {"family": "Panasenko", "given": "Olesya O", "initials": "OO", "orcid": "0000-0002-0990-7472", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9636da2224704c03b3d57ee729c69a99.json"}}, {"family": "Huch", "given": "Susanne", "initials": "S"}, {"family": "Villanyi", "given": "Zoltan", "initials": "Z"}, {"family": "Albert", "given": "Benjamin", "initials": "B"}, {"family": "Dilg", "given": "Daniel", "initials": "D"}, {"family": "Zagatti", "given": "Marina", "initials": "M"}, {"family": "Schaughency", "given": "Paul", "initials": "P"}, {"family": "Liao", "given": "Susan E", "initials": "SE", "orcid": "0000-0002-8380-7824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c59cf03d13c4e79bee9d0c9c031df92.json"}}, {"family": "Corden", "given": "Jeff", "initials": "J"}, {"family": "Polte", "given": "Christine", "initials": "C"}, {"family": "Shore", "given": "David", "initials": "D", "orcid": "0000-0002-9859-143X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b48fc8ed9cd4943956574edbcbbaf8a.json"}}, {"family": "Ignatova", "given": "Zoya", "initials": "Z", "orcid": "0000-0002-9478-8825", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9ff2bcc30ed4068a6c0b628f086a844.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Collart", "given": "Martine A", "initials": "MA", "orcid": "0000-0001-6955-1773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a30c470c8f9d497eb85b4a4e902446f6.json"}}], "type": "journal article", "published": "2023-02-20", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "24", "issue": "1", "pages": "30", "issn-l": "1474-7596"}, "abstract": "The Ccr4-Not complex is mostly known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics has been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after the disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts.\n\nIn this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impacts mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion.\n\nOur results reveal that mRNA solubility defines the dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.", "doi": "10.1186/s13059-023-02871-7", "pmid": "36803582", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC9940351"}, {"db": "pii", "key": "10.1186/s13059-023-02871-7"}], "notes": [], "created": "2023-05-29T07:36:21.663Z", "modified": "2026-09-11T13:23:25.314Z"}, {"entity": "publication", "iuid": "18ed7dda17774ed28651b0abac78c7f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/18ed7dda17774ed28651b0abac78c7f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/18ed7dda17774ed28651b0abac78c7f7"}}, "title": "Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.", "authors": [{"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Zeis", "given": "Patrice", "initials": "P", "orcid": "0000-0001-7615-2201", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9cd91e9e23f74093903c94117303a485.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Alekseenko", "given": "Alisa", "initials": "A"}, {"family": "F\u00fcrst", "given": "Eliska", "initials": "E", "orcid": "0000-0001-7101-5347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/322dcf90ca3249e5bcf75bc6fcf8c9df.json"}}, {"family": "Sanchez", "given": "Yerma Pareja", "initials": "YP"}, {"family": "Lin", "given": "Gen", "initials": "G", "orcid": "0000-0001-9969-8418", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28ac170431ce4b8cb65ea783ecdb5154.json"}}, {"family": "Tekkedil", "given": "Manu M", "initials": "MM"}, {"family": "Piazza", "given": "Ilaria", "initials": "I"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-02-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "910", "issn-l": "2041-1723"}, "abstract": "Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.", "doi": "10.1038/s41467-023-36586-x", "pmid": "36801853", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC9936472"}, {"db": "pii", "key": "10.1038/s41467-023-36586-x"}], "notes": [], "created": "2023-05-29T07:36:20.218Z", "modified": "2026-09-11T13:23:25.379Z"}, {"entity": "publication", "iuid": "9be1ae6123ae437e8fde8d91b37b6931", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9be1ae6123ae437e8fde8d91b37b6931.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9be1ae6123ae437e8fde8d91b37b6931"}}, "title": "OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.", "authors": [{"family": "Alekseenko", "given": "Alisa", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "4", "issue": "2", "pages": "lqac048", "issn-l": null}, "abstract": "Detection of low-frequency DNA variants (below 1%) is becoming increasingly important in biomedical research and clinical practice, but is challenging to do with standard sequencing approaches due to high error rates. The use of double-stranded unique molecular identifiers (dsUMIs) allows correction of errors by comparing reads arising from the same original DNA duplex. However, the implementation of such approaches is still challenging. Here, we present a novel method, one-pot dsUMI sequencing (OPUSeq), which allows incorporation of dsUMIs in the same reaction as the library PCR. This obviates the need for adapter pre-synthesis or additional enzymatic steps. OPUSeq can be incorporated into standard DNA library preparation approaches and coupled with hybridization target capture. We demonstrate successful error correction and detection of variants down to allele frequency of 0.01%. Using OPUSeq, we also show that the use of enzymatic fragmentation can lead to the appearance of spurious double-stranded variants, interfering with detection of variant fractions below 0.1%.", "doi": "10.1093/nargab/lqac048", "pmid": "35769342", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC9235115"}, {"db": "pii", "key": "lqac048"}], "notes": [], "created": "2022-11-25T19:21:46.596Z", "modified": "2026-09-11T13:23:25.428Z"}, {"entity": "publication", "iuid": "e927581965e9438ab317c64fa56dfb6c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e927581965e9438ab317c64fa56dfb6c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e927581965e9438ab317c64fa56dfb6c"}}, "title": "Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics.", "authors": [{"family": "Crowe-McAuliffe", "given": "Caillan", "initials": "C"}, {"family": "Murina", "given": "Victoriia", "initials": "V"}, {"family": "Turnbull", "given": "Kathryn Jane", "initials": "KJ"}, {"family": "Huch", "given": "Susanne", "initials": "S"}, {"family": "Kasari", "given": "Marje", "initials": "M", "orcid": "0000-0002-2177-3753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed7c29af0b0e450197585fe3220fd834.json"}}, {"family": "Takada", "given": "Hiraku", "initials": "H"}, {"family": "Nersisyan", "given": "Lilit", "initials": "L"}, {"family": "Sundsfjord", "given": "Arnfinn", "initials": "A"}, {"family": "Hegstad", "given": "Kristin", "initials": "K", "orcid": "0000-0002-1314-0497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af03b1cbe6c34e94b38e43a75871d0b1.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c2d78750ccb42239a7363f99f58dcc5.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1860", "issn-l": "2041-1723"}, "abstract": "PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall translating ribosomes when certain amino acids are present at a defined position in the nascent polypeptide chain. These proteins are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria, and are thought to confer resistance by binding to the ribosome and dislodging the bound antibiotic. However, the mechanistic basis of this resistance remains unclear. Here we refine the PoxtA spectrum of action, demonstrate alleviation of linezolid-induced context-dependent translational stalling, and present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome. PoxtA perturbs the CCA-end of the P-site tRNA, causing it to shift by \u223c4 \u00c5 out of the ribosome, corresponding to a register shift of approximately one amino acid for an attached nascent polypeptide chain. We postulate that the perturbation of the P-site tRNA by PoxtA thereby alters the conformation of the attached nascent chain to disrupt the drug binding site.", "doi": "10.1038/s41467-022-29274-9", "pmid": "35387982", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC8987054"}, {"db": "pii", "key": "10.1038/s41467-022-29274-9"}], "notes": [], "created": "2022-11-25T19:21:44.833Z", "modified": "2026-09-11T13:23:25.480Z"}, {"entity": "publication", "iuid": "54639014665c40669d8135cf7676d4bc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/54639014665c40669d8135cf7676d4bc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/54639014665c40669d8135cf7676d4bc"}}, "title": "Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A.", "authors": [{"family": "Allen", "given": "George E", "initials": "GE"}, {"family": "Panasenko", "given": "Olesya O", "initials": "OO"}, {"family": "Villanyi", "given": "Zoltan", "initials": "Z"}, {"family": "Zagatti", "given": "Marina", "initials": "M"}, {"family": "Weiss", "given": "Benjamin", "initials": "B"}, {"family": "Pagliazzo", "given": "Lucile", "initials": "L"}, {"family": "Huch", "given": "Susanne", "initials": "S"}, {"family": "Polte", "given": "Christine", "initials": "C"}, {"family": "Zahoran", "given": "Szabolcs", "initials": "S"}, {"family": "Hughes", "given": "Christopher S", "initials": "CS"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Ignatova", "given": "Zoya", "initials": "Z"}, {"family": "Collart", "given": "Martine A", "initials": "MA"}], "type": "journal article", "published": "2021-08-31", "journal": {"title": "Cell Reports", "issn": "2211-1247", "volume": "36", "issue": "9", "pages": "109633", "issn-l": null}, "abstract": "In this work, we show that Not4 and Not5 from the Ccr4-Not complex modulate translation elongation dynamics and change ribosome A-site dwelling occupancy in a codon-dependent fashion. These codon-specific changes in not5\u0394 cells are very robust and independent of codon position within the mRNA, the overall mRNA codon composition, or changes of mRNA expression levels. They inversely correlate with codon-specific changes in cells depleted for eIF5A and positively correlate with those in cells depleted for ribosome-recycling factor Rli1. Not5 resides in punctate loci, co-purifies with ribosomes and Rli1, but not with eIF5A, and limits mRNA solubility. Overexpression of wild-type or non-complementing Rli1 and loss of Rps7A ubiquitination enable Not4 E3 ligase-dependent translation of polyarginine stretches. We propose that Not4 and Not5 modulate translation elongation dynamics to produce a soluble proteome by Rps7A ubiquitination, dynamic condensates that limit mRNA solubility and exclude eIF5A, and a moonlighting function of Rli1.", "doi": "10.1016/j.celrep.2021.109633", "pmid": "34469733", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S2211-1247(21)01076-7"}], "notes": [], "created": "2021-12-02T18:34:55.652Z", "modified": "2026-09-11T13:23:25.541Z"}, {"entity": "publication", "iuid": "002a0e0d9c4e46248181462770e15535", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/002a0e0d9c4e46248181462770e15535.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/002a0e0d9c4e46248181462770e15535"}}, "title": "Sample-to-answer COVID-19 nucleic acid testing using a low-cost centrifugal microfluidic platform with bead-based signal enhancement and smartphone read-out.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG", "orcid": "0000-0001-5958-5232", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fef4d913e9e74505a000d8d8488cb62b.json"}}, {"family": "Akhtar", "given": "Ahmad S", "initials": "AS", "orcid": "0000-0002-4560-4735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f3dc0fe88bd41f2a435b2c0a7d46238.json"}}, {"family": "Pinto", "given": "In\u00eas F", "initials": "IF", "orcid": "0000-0002-9714-4742", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47785e08c3f84b7ebdcbf4b8b979ef21.json"}}, {"family": "Lapins", "given": "Noa", "initials": "N"}, {"family": "Barrett", "given": "Donal", "initials": "D"}, {"family": "Sandh", "given": "Gustaf", "initials": "G"}, {"family": "Yin", "given": "Xiushan", "initials": "X"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Russom", "given": "Aman", "initials": "A", "orcid": "0000-0002-0242-358X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8939625551d5409aac4593329e2a6578.json"}}], "type": "journal article", "published": "2021-08-07", "journal": {"title": "Lab Chip", "issn": "1473-0189", "volume": "21", "issue": "15", "pages": "2932-2944", "issn-l": null}, "abstract": "With its origin estimated around December 2019 in Wuhan, China, the ongoing SARS-CoV-2 pandemic is a major global health challenge. The demand for scalable, rapid and sensitive viral diagnostics is thus particularly pressing at present to help contain the rapid spread of infection and prevent overwhelming the capacity of health systems. While high-income countries have managed to rapidly expand diagnostic capacities, such is not the case in resource-limited settings of low- to medium-income countries. Aiming at developing cost-effective viral load detection systems for point-of-care COVID-19 diagnostics in resource-limited and resource-rich settings alike, we report the development of an integrated modular centrifugal microfluidic platform to perform loop-mediated isothermal amplification (LAMP) of viral RNA directly from heat-inactivated nasopharyngeal swab samples. The discs were pre-packed with dried n-benzyl-n-methylethanolamine modified agarose beads used to selectively remove primer dimers, inactivate the reaction post-amplification and allowing enhanced fluorescence detection via a smartphone camera. Sample-to-answer analysis within 1 hour from sample collection and a detection limit of approximately 100 RNA copies in 10 \u03bcL reaction volume were achieved. The platform was validated with a panel of 162 nasopharyngeal swab samples collected from patients with COVID-19 symptoms, providing a sensitivity of 96.6% (82.2-99.9%, 95% CI) for samples with Ct values below 26 and a specificity of 100% (90-100%, 95% CI), thus being fit-for-purpose to diagnose patients with a high risk of viral transmission. These results show significant promise towards bringing routine point-of-care COVID-19 diagnostics to resource-limited settings.", "doi": "10.1039/d1lc00266j", "pmid": "34114589", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2021-12-02T18:31:50.594Z", "modified": "2026-09-11T13:23:25.560Z"}, {"entity": "publication", "iuid": "13391e75d3544426839d9f0c58723541", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/13391e75d3544426839d9f0c58723541.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/13391e75d3544426839d9f0c58723541"}}, "title": "Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.", "authors": [{"family": "Garrido-Godino", "given": "A I", "initials": "AI", "orcid": "0000-0002-7389-1372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7683c79eb2a94be1b118e80b275b94a7.json"}}, {"family": "Gupta", "given": "I", "initials": "I", "orcid": "0000-0001-8934-9919", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/873bb3fa7657413da1e432cfd3c700c2.json"}}, {"family": "Guti\u00e9rrez-Santiago", "given": "F", "initials": "F"}, {"family": "Mart\u00ednez-Padilla", "given": "A B", "initials": "AB"}, {"family": "Alekseenko", "given": "A", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Steinmetz", "given": "L M", "initials": "LM"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "J E", "initials": "JE", "orcid": "0000-0002-1992-513X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac4f5d4d6cd54c1bbafeec15e97e5c49.json"}}, {"family": "Pelechano", "given": "V", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Navarro", "given": "F", "initials": "F", "orcid": "0000-0002-4180-422X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2abed56af56f41fcb118d39f21b9a8e5.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "RNA Biol", "issn": "1555-8584", "issn-l": "1547-6286", "volume": "18", "issue": "8", "pages": "1206-1220"}, "abstract": "Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.", "doi": "10.1080/15476286.2020.1839229", "pmid": "33094674", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC8244751"}], "notes": [], "created": "2020-11-28T17:34:48.540Z", "modified": "2026-09-11T13:23:25.568Z"}, {"entity": "publication", "iuid": "05de871990a14e28881934e2086bb024", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05de871990a14e28881934e2086bb024.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05de871990a14e28881934e2086bb024"}}, "title": "Simultaneous detection of SARS-CoV-2 and pandemic (H1N1) 2009 virus with real-time isothermal platform.", "authors": [{"family": "Yu", "given": "Lin", "initials": "L", "orcid": "0000-0001-6802-7494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be8d88789ed743178f16202e95c73023.json"}}, {"family": "Wang", "given": "Jingyao", "initials": "J"}, {"family": "Li", "given": "Xuelong", "initials": "X"}, {"family": "Mao", "given": "Lingling", "initials": "L"}, {"family": "Sui", "given": "Yi", "initials": "Y", "orcid": "0000-0002-2898-7877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1a78e868d1a4d6cb90c27460f329dc7.json"}}, {"family": "Chen", "given": "Weihua", "initials": "W"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Guo", "given": "Xing", "initials": "X"}, {"family": "Yin", "given": "Xiushan", "initials": "X"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Heliyon", "issn": "2405-8440", "volume": "7", "issue": "7", "pages": "e07584", "issn-l": "2405-8440"}, "abstract": "The recent ongoing outbreak of novel coronavirus SARS-CoV-2 (known as COVID-19) is a severe threat to human health worldwide. By press time, more than 3.3 million people have died from COVID-19, with many countries experiencing peaks in infections and hospitalizations. The main symptoms of infection with SARS-CoV-2 include fever, chills, coughing, shortness of breath or difficulty breathing, fatigue, muscle or body aches and pains. While the symptoms of the pandemic (H1N1) 2009 virus have many similarities to the signs and transmission routes of the novel coronavirus, e.g., fever, cough, sore throat, body aches, headache, chills and fatigue. And a few cases of serious illness, rapid progress, can appear viral pneumonia, combined with respiratory failure, multiple organ function damage, serious people can die. Therefore, there is an urgent need to develop a rapid and accurate field diagnostic method to effectively identify the two viruses and treat these early infections on time, thus helping to control the spread of the disease. Among molecular detection methods, RT-LAMP (real-time reverse transcription-loop-mediated isothermal amplification) has some advantages in pathogen detection due to its rapid, accurate and effective detection characteristics. Here, we combined the primers of the two viruses with the fluorescent probes on the RT-LAMP detection platform to detect the two viruses simultaneously. Firstly, RT-LAMP method was used respectively to detect the two viruses at different concentrations to determine the effectiveness and sensitivity of probe primers to the RNA samples. And then, the two virus samples were detected simultaneously in the same reaction tube to validate if testing for the two viruses together had an impact on the results compared to detecting alone. We verified the detection efficiency of three highly active BST variants during RT-LAMP assay. We expect that this assay can effectively and accurately distinguish COVID-19 from the pandemic (H1N1) 2009, so that these two diseases with similar symptoms can be appropriately differentiated and treated.", "doi": "10.1016/j.heliyon.2021.e07584", "pmid": "34307953", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC8280398"}, {"db": "pii", "key": "S2405-8440(21)01687-X"}], "notes": [], "created": "2021-12-02T18:34:54.428Z", "modified": "2026-09-11T13:23:25.583Z"}, {"entity": "publication", "iuid": "97204b9cb60b402fa448fb45427381e3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/97204b9cb60b402fa448fb45427381e3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/97204b9cb60b402fa448fb45427381e3"}}, "title": "Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.", "authors": [{"family": "Kubik", "given": "Slawomir", "initials": "S"}, {"family": "Marques", "given": "Ana Claudia", "initials": "AC"}, {"family": "Xing", "given": "Xiaobin", "initials": "X"}, {"family": "Silvery", "given": "Janine", "initials": "J"}, {"family": "Bertelli", "given": "Claire", "initials": "C"}, {"family": "De Maio", "given": "Flavio", "initials": "F"}, {"family": "Pournaras", "given": "Spyros", "initials": "S"}, {"family": "Burr", "given": "Tom", "initials": "T"}, {"family": "Duffourd", "given": "Yannis", "initials": "Y"}, {"family": "Siemens", "given": "Helena", "initials": "H"}, {"family": "Alloui", "given": "Chakib", "initials": "C"}, {"family": "Song", "given": "Lin", "initials": "L"}, {"family": "Wenger", "given": "Yvan", "initials": "Y"}, {"family": "Saitta", "given": "Alexandra", "initials": "A"}, {"family": "Macheret", "given": "Morgane", "initials": "M"}, {"family": "Smith", "given": "Ewan W", "initials": "EW"}, {"family": "Menu", "given": "Philippe", "initials": "P"}, {"family": "Brayer", "given": "Marion", "initials": "M"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Si-Mohammed", "given": "Ali", "initials": "A"}, {"family": "Chuisseu", "given": "Josiane", "initials": "J"}, {"family": "Stevens", "given": "Richard", "initials": "R"}, {"family": "Constantoulakis", "given": "Pantelis", "initials": "P"}, {"family": "Sali", "given": "Michela", "initials": "M"}, {"family": "Greub", "given": "Gilbert", "initials": "G"}, {"family": "Tiemann", "given": "Carsten", "initials": "C"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Willig", "given": "Adrian", "initials": "A"}, {"family": "Xu", "given": "Zhenyu", "initials": "Z"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Clin. Microbiol. Infect.", "issn": "1469-0691", "volume": "27", "issue": "7", "pages": "1036.e1-1036.e8", "issn-l": "1198-743X"}, "abstract": "Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping.\n\nWe established and used a sequencing data analysis workflow that reliably identifies and removes technical artefacts; such artefacts can result in miscalls when using alternative pipelines to process clinical samples and synthetic viral genomes with an amplicon-based genotyping approach. We evaluated the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination.\n\nWe found that at least 1000 viral genomes are necessary to confidently detect variants in the SARS-CoV-2 genome at frequencies of \u226510%. The broad applicability of our recommendations was validated in over 200 clinical samples from six independent laboratories. The genotypes we determined for clinical isolates with sufficient quality cluster by sampling location and period. Our analysis also supports the rise in frequencies of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was facilitated by travel during the summer of 2020.\n\nWe present much-needed recommendations for the reliable determination of SARS-CoV-2 genome sequences and demonstrate their broad applicability in a large cohort of clinical samples.", "doi": "10.1016/j.cmi.2021.03.029", "pmid": "33813118", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S1198-743X(21)00164-6"}, {"db": "pmc", "key": "PMC8016543"}], "notes": [], "created": "2021-12-02T18:34:52.871Z", "modified": "2026-09-11T13:23:25.647Z"}, {"entity": "publication", "iuid": "42e064225e8f462999fc48a3f212c295", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/42e064225e8f462999fc48a3f212c295.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/42e064225e8f462999fc48a3f212c295"}}, "title": "Application of high-throughput 5'P sequencing for the study of co-translational mRNA decay.", "authors": [{"family": "Zhang", "given": "Yujie", "initials": "Y"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}], "type": "journal article", "published": "2021-06-18", "journal": {"title": "STAR Protoc", "issn": "2666-1667", "volume": "2", "issue": "2", "pages": "100447", "issn-l": null}, "abstract": "mRNA degradation is connected to the translation process up to the degree that 5'-3' mRNA degradation follows the last translating ribosome. To study 5'-3'co-translational mRNA decay and the associated ribosome dynamics, here we present an improved high-throughput 5'P degradome RNA sequencing protocol (HT-5Pseq). We exemplify its application in Saccharomyces cerevisiae, but in principle, it could be applied to any other eukaryotic organism. HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. For complete details on the use and execution of this protocol, please refer to Zhang and Pelechano (2021).", "doi": "10.1016/j.xpro.2021.100447", "pmid": "33870233", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S2666-1667(21)00154-4"}, {"db": "pmc", "key": "PMC8044721"}], "notes": [], "created": "2021-12-02T18:33:41.256Z", "modified": "2026-09-11T13:23:25.655Z"}, {"entity": "publication", "iuid": "0f9b522f5c7e488fae7a585a9ef303e5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0f9b522f5c7e488fae7a585a9ef303e5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0f9b522f5c7e488fae7a585a9ef303e5"}}, "title": "Using TIF-Seq2 to investigate association between 5\u00b4 and 3\u00b4mRNA ends.", "authors": [{"family": "Li", "given": "Bingnan", "initials": "B"}, {"family": "Marques", "given": "Sueli", "initials": "S"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}], "type": "journal article", "published": "2021-05-28", "journal": {"title": "Meth. Enzymol.", "issn": "1557-7988", "volume": "655", "pages": "85-118", "issn-l": "0076-6879"}, "abstract": "The development of high-throughput technologies has revealed pervasive transcription in all genomes that have been investigated so far. This has uncovered a highly interleaved transcriptome organization involving thousands of overlapping coding and non-coding RNA isoforms that challenge our traditional definitions of genes and functional regions of the genome. In this chapter, we discuss the application of an improved Transcript Isoform Sequencing approach (TIF-Seq2) able to concurrently determine the start and end sites of individual RNA molecules. We exemplify its use for the investigation of the human transcriptome and show how it is especially well suited to discriminate between overlapping molecules and accurately define their boundaries.", "doi": "10.1016/bs.mie.2021.03.017", "pmid": "34183135", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S0076-6879(21)00130-0"}], "notes": [], "created": "2021-12-02T18:34:50.325Z", "modified": "2026-09-11T13:23:25.673Z"}, {"entity": "publication", "iuid": "3e3213fffbd449ba9410298238eb3a2f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3213fffbd449ba9410298238eb3a2f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3213fffbd449ba9410298238eb3a2f"}}, "title": "High-throughput 5\u2032P sequencing enables the study of degradation-associated ribosome stalls", "authors": [{"family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal-article", "published": "2021-05-00", "journal": {"title": "Cell Rep Methods", "issn": "2667-2375", "issn-l": null, "volume": "1", "issue": "1", "pages": "100001"}, "abstract": "RNA degradation is critical for gene expression and mRNA quality control. mRNA degradation is connected to the translation process up to the degree that 5'-3' mRNA degradation follows the last translating ribosome. Here, we present an improved high-throughput 5'P degradome RNA-sequencing method (HT-5Pseq). HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. We investigate in vivo ribosome stalls focusing on translation termination. By comparing ribosome stalls identified by ribosome profiling, disome-seq and HT-5Pseq, we find that degradation-associated ribosome stalls are often enriched in Arg preceding the stop codon. On the contrary, mRNAs depleted for those stalls use more frequently a TAA stop codon preceded by hydrophobic amino acids. Finally, we show that termination stalls found by HT-5Pseq, and not by other approaches, are associated with decreased mRNA stability. Our work suggests that ribosome stalls associated with mRNA decay can be easily captured by investigating the 5'P degradome.", "doi": "10.1016/j.crmeth.2021.100001", "pmid": "35474692", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC9017187"}, {"db": "pii", "key": "S2667-2375(21)00001-1"}], "notes": [], "created": "2021-12-02T18:38:13.745Z", "modified": "2026-09-11T13:23:25.681Z"}, {"entity": "publication", "iuid": "b07323c92b2a46a7abf1df532fe692c2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b07323c92b2a46a7abf1df532fe692c2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b07323c92b2a46a7abf1df532fe692c2"}}, "title": "Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples.", "authors": [{"family": "Alekseenko", "given": "Alisa", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Pareja-Sanchez", "given": "Yerma", "initials": "Y", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Strandback", "given": "Emilia", "initials": "E"}, {"family": "Ampah-Korsah", "given": "Henry", "initials": "H", "orcid": "0000-0002-8363-1697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5f166b865a7483c88415aa9c607d039.json"}}, {"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0ab87a8712f4ad886da61c1edcf679f.json"}}, {"family": "Zuniga-Veliz", "given": "Silvia", "initials": "S"}, {"family": "Klenov", "given": "Alexander", "initials": "A"}, {"family": "Malloo", "given": "Jayshna", "initials": "J"}, {"family": "Ye", "given": "Shenglong", "initials": "S"}, {"family": "Liu", "given": "Xiyang", "initials": "X"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faaf7145e4044091a2fed9069f56b92e.json"}}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "Sandh", "given": "Gustaf", "initials": "G"}, {"family": "Yin", "given": "Xiushan", "initials": "X", "orcid": "0000-0001-8124-7387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10f57a1b340547ebb74092bd2c6acdfe.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2021-01-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "1820", "issn-l": "2045-2322"}, "abstract": "RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.", "doi": "10.1038/s41598-020-80352-8", "pmid": "33469065", "labels": {"Simon Els\u00e4sser": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-80352-8"}, {"db": "pmc", "key": "PMC7815738"}], "notes": [], "created": "2021-12-02T18:33:50.940Z", "modified": "2026-09-11T13:23:25.692Z"}, {"entity": "publication", "iuid": "cf6ea628345547a7b49907972c7d4710", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cf6ea628345547a7b49907972c7d4710.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cf6ea628345547a7b49907972c7d4710"}}, "title": "A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae.", "authors": [{"family": "Rodr\u00edguez-Gal\u00e1n", "given": "Olga", "initials": "O"}, {"family": "Garc\u00eda-G\u00f3mez", "given": "Juan J", "initials": "JJ"}, {"family": "Rosado", "given": "Iv\u00e1n V", "initials": "IV"}, {"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "M\u00e9ndez-Godoy", "given": "Alfonso", "initials": "A"}, {"family": "Pillet", "given": "Benjamin", "initials": "B"}, {"family": "Alekseenko", "given": "Alisa", "initials": "A"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Kressler", "given": "Dieter", "initials": "D"}, {"family": "de la Cruz", "given": "Jes\u00fas", "initials": "J"}], "type": "journal article", "published": "2021-01-11", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "49", "issue": "1", "pages": "206-220", "issn-l": "0305-1048"}, "abstract": "Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5' region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.", "doi": "10.1093/nar/gkaa1200", "pmid": "33330942", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "6039917"}, {"db": "pmc", "key": "PMC7797049"}], "notes": [], "created": "2021-12-02T18:34:51.600Z", "modified": "2026-09-11T13:23:25.705Z"}, {"entity": "publication", "iuid": "856d0f7884314572804afd4810432a40", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/856d0f7884314572804afd4810432a40.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/856d0f7884314572804afd4810432a40"}}, "title": "Improved computational analysis of ribosome dynamics from 5\u2032P degradome data using fivepseq", "authors": [{"family": "Nersisyan", "given": "Lilit", "initials": "L", "orcid": "0000-0001-8525-420X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c77363d1fa7f4ea6b50c22590c23a163.json"}}, {"family": "Ropat", "given": "Maria", "initials": "M"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal-article", "published": "2020-11-24", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "issn-l": null, "volume": "2", "issue": "4", "pages": null}, "abstract": null, "doi": "10.1093/nargab/lqaa099", "pmid": "33575643", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-11-28T17:36:30.801Z", "modified": "2026-09-11T13:23:25.742Z"}, {"entity": "publication", "iuid": "127ab2b4417f4ac0ace77e0f2c278dbc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc"}}, "title": "TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Marques", "given": "Sueli", "initials": "S", "orcid": "0000-0003-3368-4392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36fa155444764068a6515a6ec93a7a2e.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "18", "pages": "e104"}, "abstract": "Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.", "doi": "10.1093/nar/gkaa691", "pmid": "32816037", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "5894951"}, {"db": "pmc", "key": "PMC7544212"}], "notes": [], "created": "2020-11-08T15:50:59.020Z", "modified": "2026-09-11T13:23:25.817Z"}, {"entity": "publication", "iuid": "aed3c1e3d03b42278b08c1b74653acde", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aed3c1e3d03b42278b08c1b74653acde.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aed3c1e3d03b42278b08c1b74653acde"}}, "title": "The RNA exosome shapes the expression of key protein-coding genes.", "authors": [{"family": "Wu", "given": "Mengjun", "initials": "M"}, {"family": "Karadoulama", "given": "Evdoxia", "initials": "E"}, {"family": "Lloret-Llinares", "given": "Marta", "initials": "M"}, {"family": "Rouviere", "given": "Jerome Olivier", "initials": "JO"}, {"family": "Vaagens\u00f8", "given": "Christian Skov", "initials": "CS"}, {"family": "Moravec", "given": "Martin", "initials": "M"}, {"family": "Li", "given": "Bingnan", "initials": "B"}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Wu", "given": "Guifen", "initials": "G"}, {"family": "Gockert", "given": "Maria", "initials": "M"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Jensen", "given": "Torben Heick", "initials": "TH", "orcid": "0000-0001-5127-1239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f63375fe0a24f95b0b6bb6674d7a3b1.json"}}, {"family": "Sandelin", "given": "Albin", "initials": "A", "orcid": "0000-0002-7109-7378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9618b5e69c14c6e9df631a8abfcd77c.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "15", "pages": "8509-8528"}, "abstract": "The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify \u223c2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3' end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.", "doi": "10.1093/nar/gkaa594", "pmid": "32710631", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "5876282"}, {"db": "pmc", "key": "PMC7470964"}], "notes": [], "created": "2020-11-08T15:50:45.945Z", "modified": "2026-09-11T13:23:25.872Z"}, {"entity": "publication", "iuid": "a0e9da26436a4b199e959d5a7e39b2de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0e9da26436a4b199e959d5a7e39b2de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0e9da26436a4b199e959d5a7e39b2de"}}, "title": "Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.", "authors": [{"family": "Liang", "given": "Shuo", "initials": "S"}, {"family": "Ezerskyte", "given": "Monika", "initials": "M"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Dreij", "given": "Kristian", "initials": "K"}], "type": "journal article", "published": "2020-08-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "13513"}, "abstract": "The transcriptional error rate can be significantly increased by the presence of DNA lesions that instruct mis-insertion during transcription; a process referred to as transcriptional mutagenesis (TM) that can result in altered protein function. Herein, we determined the effect of O6-methylguanine (O6-meG) on transcription and subsequent transactivation activity of p53 in human lung H1299 cells. Levels of TM and effects on transactivation were determined genome wide by RNA-seq. Results showed that 47% of all p53 transcripts contained an uridine misincorporation opposite the lesion at 6 h post transfection, which was decreased to 18% at 24 h. TM at these levels reduced DNA binding activity of p53 to 21% and 80% compared to wild type p53, respectively. Gene expression data were analysed to identify differentially expressed genes due to TM of p53. We show a temporal repression of transactivation of > 100 high confidence p53 target genes including regulators of the cell cycle, DNA damage response and apoptosis. In addition, TM repressed the transcriptional downregulation by p53 of several negative regulators of proliferation and differentiation. Our work demonstrates that TM, even when restricting its effect to an individual transcription factor, has the potential to alter gene expression programs and diversify cellular phenotypes.", "doi": "10.1038/s41598-020-70412-4", "pmid": "32782319", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-70412-4"}, {"db": "pmc", "key": "PMC7419513"}], "notes": [], "created": "2020-11-08T15:50:53.280Z", "modified": "2026-09-11T13:23:25.914Z"}, {"entity": "publication", "iuid": "628acc9a259749108bdcc1dbc54e598a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/628acc9a259749108bdcc1dbc54e598a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/628acc9a259749108bdcc1dbc54e598a"}}, "title": "Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform.", "authors": [{"family": "Yu", "given": "Lin", "initials": "L"}, {"family": "Wu", "given": "Shanshan", "initials": "S"}, {"family": "Hao", "given": "Xiaowen", "initials": "X"}, {"family": "Dong", "given": "Xue", "initials": "X"}, {"family": "Mao", "given": "Lingling", "initials": "L"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Chen", "given": "Wei-Hua", "initials": "WH"}, {"family": "Yin", "given": "Xiushan", "initials": "X"}], "type": "letter", "published": "2020-07-01", "journal": {"title": "Clin. Chem.", "issn": "1530-8561", "issn-l": "0009-9147", "volume": "66", "issue": "7", "pages": "975-977"}, "abstract": null, "doi": "10.1093/clinchem/hvaa102", "pmid": "32315390", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "5823294"}, {"db": "pmc", "key": "PMC7188121"}], "notes": [], "created": "2020-11-08T15:49:47.909Z", "modified": "2026-09-11T13:23:25.981Z"}, {"entity": "publication", "iuid": "a80d534b3097447888f8c79c3323f9e7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a80d534b3097447888f8c79c3323f9e7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a80d534b3097447888f8c79c3323f9e7"}}, "title": "Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.", "authors": [{"family": "Thomas", "given": "Quentin Angelo", "initials": "QA", "orcid": "0000-0002-3522-5125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6fa033a00e46d0b068dcdebd13a25e.json"}}, {"family": "Ard", "given": "Ryan", "initials": "R", "orcid": "0000-0002-9070-9747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b7dd13a6df4e1aa77fced747dc0f2a.json"}}, {"family": "Liu", "given": "Jinghan", "initials": "J", "orcid": "0000-0001-7816-4791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c1e737ce8d9491192727f16ede2e359.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B"}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Marquardt", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1709-2717", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c0e928664724466ad7e558bef348c86.json"}}], "type": "journal article", "published": "2020-05-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "2589"}, "abstract": "RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.", "doi": "10.1038/s41467-020-16390-7", "pmid": "32444691", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16390-7"}, {"db": "pmc", "key": "PMC7244574"}], "notes": [], "created": "2020-11-08T15:50:38.178Z", "modified": "2026-09-11T13:23:26.014Z"}, {"entity": "publication", "iuid": "5ae608853bc545c9b08e1b8c6a0abab9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae608853bc545c9b08e1b8c6a0abab9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae608853bc545c9b08e1b8c6a0abab9"}}, "title": "Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.", "authors": [{"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Hennig", "given": "Bianca P", "initials": "BP", "orcid": "0000-0002-7733-8160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c64ef90520aa408c8c2ed17fae8fd95c.json"}}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}}, {"family": "Piazza", "given": "Ilaria", "initials": "I", "orcid": "0000-0001-5895-6134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5258dce396444d9a8f5e5bc2fd13b282.json"}}, {"family": "Pareja Sanchez", "given": "Yerma", "initials": "Y", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}}, {"family": "Chabbert", "given": "Christophe D", "initials": "CD", "orcid": "0000-0001-7851-4640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/490051f9ae674750a4dd3ee10c27b2b0.json"}}, {"family": "Adjalley", "given": "Sophie H", "initials": "SH", "orcid": "0000-0002-5666-7088", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0ba3a91cf9b4039a83e915d1698e581.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Genome Res", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "29", "issue": "12", "pages": "1974-1984"}, "abstract": "Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site (TSS) usage, chromatin organization, and posttranscriptional consequences in Saccharomyces cerevisiae We show that TSSs of chromatin-sensitive internal cryptic transcripts retain comparable features of canonical TSSs in terms of DNA sequence, directionality, and chromatin accessibility. We define the 5' and 3' boundaries of cryptic transcripts and show that, contrary to RNA degradation-sensitive ones, they often overlap with the end of the gene, thereby using the canonical polyadenylation site, and associate to polyribosomes. We show that chromatin-sensitive cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Finally, we confirm the presence of the predicted polypeptides by reanalyzing N-terminal proteomic data sets. Our work suggests that a fraction of chromatin-sensitive internal cryptic promoters initiates the transcription of alternative truncated mRNA isoforms. The expression of these chromatin-sensitive isoforms is conserved from yeast to human, expanding the functional consequences of cryptic transcription and proteome complexity.", "doi": "10.1101/gr.243378.118", "pmid": "31740578", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "gr.243378.118"}, {"db": "pmc", "key": "PMC6886497"}], "notes": [], "created": "2020-11-08T15:49:22.722Z", "modified": "2026-09-11T13:23:26.043Z"}, {"entity": "publication", "iuid": "27dbd96ac71a4ea7a48cb95ee9592335", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/27dbd96ac71a4ea7a48cb95ee9592335.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/27dbd96ac71a4ea7a48cb95ee9592335"}}, "title": "System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection.", "authors": [{"family": "Garcia-Moreno", "given": "Manuel", "initials": "M"}, {"family": "Noerenberg", "given": "Marko", "initials": "M"}, {"family": "Ni", "given": "Shuai", "initials": "S"}, {"family": "J\u00e4rvelin", "given": "Aino I", "initials": "AI"}, {"family": "Gonz\u00e1lez-Almela", "given": "Esther", "initials": "E"}, {"family": "Lenz", "given": "Caroline E", "initials": "CE"}, {"family": "Bach-Pages", "given": "Marcel", "initials": "M"}, {"family": "Cox", "given": "Victoria", "initials": "V"}, {"family": "Avolio", "given": "Rosario", "initials": "R"}, {"family": "Davis", "given": "Thomas", "initials": "T"}, {"family": "Hester", "given": "Svenja", "initials": "S"}, {"family": "Sohier", "given": "Thibault J M", "initials": "TJM"}, {"family": "Li", "given": "Bingnan", "initials": "B"}, {"family": "Heikel", "given": "Gregory", "initials": "G"}, {"family": "Michlewski", "given": "Gracjan", "initials": "G"}, {"family": "Sanz", "given": "Miguel A", "initials": "MA"}, {"family": "Carrasco", "given": "Luis", "initials": "L"}, {"family": "Ricci", "given": "Emiliano P", "initials": "EP"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Davis", "given": "Ilan", "initials": "I"}, {"family": "Fischer", "given": "Bernd", "initials": "B"}, {"family": "Mohammed", "given": "Shabaz", "initials": "S"}, {"family": "Castello", "given": "Alfredo", "initials": "A"}], "type": "journal article", "published": "2019-04-04", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "issn-l": "1097-2765", "volume": "74", "issue": "1", "pages": "196-211.e11"}, "abstract": "The compendium of RNA-binding proteins (RBPs) has been greatly expanded by the development of RNA-interactome capture (RIC). However, it remained unknown if the complement of RBPs changes in response to environmental perturbations and whether these rearrangements are important. To answer these questions, we developed \"comparative RIC\" and applied it to cells challenged with an RNA virus called sindbis (SINV). Over 200 RBPs display differential interaction with RNA upon SINV infection. These alterations are mainly driven by the loss of cellular mRNAs and the emergence of viral RNA. RBPs stimulated by the infection redistribute to viral replication factories and regulate the capacity of the virus to infect. For example, ablation of XRN1 causes cells to be refractory to SINV, while GEMIN5 moonlights as a regulator of SINV gene expression. In summary, RNA availability controls RBP localization and function in SINV-infected cells.", "doi": "10.1016/j.molcel.2019.01.017", "pmid": "30799147", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S1097-2765(19)30037-1"}, {"db": "pmc", "key": "PMC6458987"}], "notes": [], "created": "2020-10-09T14:04:46.802Z", "modified": "2026-09-11T13:23:26.095Z"}, {"entity": "publication", "iuid": "dd2ce89e67a9412a97fa4367a5fdc073", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dd2ce89e67a9412a97fa4367a5fdc073.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dd2ce89e67a9412a97fa4367a5fdc073"}}, "title": "Transcription-driven chromatin repression of Intragenic transcription start sites.", "authors": [{"family": "Nielsen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-2336-1146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4712573bdc943768cc289b977b74f35.json"}}, {"family": "Ard", "given": "Ryan", "initials": "R", "orcid": "0000-0002-9070-9747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b7dd13a6df4e1aa77fced747dc0f2a.json"}}, {"family": "Leng", "given": "Xueyuan", "initials": "X", "orcid": "0000-0003-1758-413X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a25df91a0dbd4cfdb2153413d594f0b6.json"}}, {"family": "Ivanov", "given": "Maxim", "initials": "M", "orcid": "0000-0001-7548-3316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/118c370e68264073b11197ae6ecdc5ab.json"}}, {"family": "Kindgren", "given": "Peter", "initials": "P", "orcid": "0000-0003-0947-2648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4859124d29c242f080ed0b695e38d57c.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Marquardt", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1709-2717", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c0e928664724466ad7e558bef348c86.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "15", "issue": "2", "pages": "e1007969"}, "abstract": "Progression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a \"positional information system\" for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The conserved FACT histone chaperone complex is required for this repression mechanism. Genome-wide Transcription Start Site (TSS) mapping reveals thousands of discrete intragenic TSS positions in fact mutants, including downstream promoters that initiate alternative transcript isoforms. We find that histone H3 lysine 4 mono-methylation (H3K4me1), an Arabidopsis RNAPII elongation signature, is enriched at FACT-repressed intragenic TSSs. Our analyses suggest that FACT is required to repress intragenic TSSs at positions that are in part characterized by elevated H3K4me1 levels. In sum, conserved and plant-specific chromatin features correlate with the co-transcriptional repression of intragenic TSSs. Our insights into TSS repression by RNAPII transcription promise to inform the regulation of alternative transcript isoforms and the characterization of gene regulation through the act of pervasive transcription across eukaryotic genomes.", "doi": "10.1371/journal.pgen.1007969", "pmid": "30707695", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-01434"}, {"db": "pmc", "key": "PMC6373976"}], "notes": [], "created": "2020-10-09T14:05:14.182Z", "modified": "2026-09-11T13:23:26.241Z"}, {"entity": "publication", "iuid": "ae2b1a33937b4349ab0bc6e99ee6c36c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae2b1a33937b4349ab0bc6e99ee6c36c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae2b1a33937b4349ab0bc6e99ee6c36c"}}, "title": "Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus.", "authors": [{"family": "Gaviraghi", "given": "Marco", "initials": "M", "orcid": "0000-0003-2791-3638", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ddcd646af6e43cb947faee968a71119.json"}}, {"family": "Vivori", "given": "Claudia", "initials": "C"}, {"family": "Pareja Sanchez", "given": "Yerma", "initials": "Y"}, {"family": "Invernizzi", "given": "Francesca", "initials": "F"}, {"family": "Cattaneo", "given": "Angela", "initials": "A"}, {"family": "Santoliquido", "given": "Benedetta Maria", "initials": "BM"}, {"family": "Frenquelli", "given": "Michela", "initials": "M"}, {"family": "Segalla", "given": "Simona", "initials": "S"}, {"family": "Bachi", "given": "Angela", "initials": "A"}, {"family": "Doglioni", "given": "Claudio", "initials": "C"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Cittaro", "given": "Davide", "initials": "D"}, {"family": "Tonon", "given": "Giovanni", "initials": "G", "orcid": "0000-0003-2973-5038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/220855f227fc4b59beaaf12a7b30af60.json"}}], "type": "journal article", "published": "2018-12-03", "journal": {"title": "EMBO J.", "issn": "1460-2075", "issn-l": "0261-4189", "volume": "37", "issue": "23", "pages": null}, "abstract": "Focal deletions occur frequently in the cancer genome. However, the putative tumor-suppressive genes residing within these regions have been difficult to pinpoint. To robustly identify these genes, we implemented a computational approach based on non-negative matrix factorization, NMF, and interrogated the TCGA dataset. This analysis revealed a metagene signature including a small subset of genes showing pervasive hemizygous deletions, reduced expression in cancer patient samples, and nucleolar function. Amid the genes belonging to this signature, we have identified PNRC1, a nuclear receptor coactivator. We found that PNRC1 interacts with the cytoplasmic DCP1\u03b1/DCP2 decapping machinery and hauls it inside the nucleolus. PNRC1-dependent nucleolar translocation of the decapping complex is associated with a decrease in the 5'-capped U3 and U8 snoRNA fractions, hampering ribosomal RNA maturation. As a result, PNRC1 ablates the enhanced proliferation triggered by established oncogenes such as RAS and MYC These observations uncover a previously undescribed mechanism of tumor suppression, whereby the cytoplasmic decapping machinery is hauled within nucleoli, tightly regulating ribosomal RNA maturation.", "doi": "10.15252/embj.201899179", "pmid": "30373810", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "embj.201899179"}, {"db": "pmc", "key": "PMC6276881"}], "notes": [], "created": "2020-10-09T14:05:44.542Z", "modified": "2026-09-11T13:23:26.266Z"}, {"entity": "publication", "iuid": "1d58e37cbaa04852b9cba0842fe202da", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d58e37cbaa04852b9cba0842fe202da.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d58e37cbaa04852b9cba0842fe202da"}}, "title": "The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock.", "authors": [{"family": "Garre", "given": "Elena", "initials": "E", "orcid": "0000-0002-3827-4977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25e0cc8c80894d33acf9c3d516901537.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "S\u00e1nchez Del Pino", "given": "Manuel", "initials": "M", "orcid": "0000-0001-9696-7600", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f44e2bb8541e4595aa1f6efb42fd0e6b.json"}}, {"family": "Alepuz", "given": "Paula", "initials": "P"}, {"family": "Sunnerhagen", "given": "Per", "initials": "P", "orcid": "0000-0002-0967-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bfbdcd30697840179ea856ec013bc527.json"}}], "type": "journal article", "published": "2018-07-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "14", "issue": "7", "pages": "e1007563"}, "abstract": "RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5' end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered.", "doi": "10.1371/journal.pgen.1007563", "pmid": "30059503", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-00309"}, {"db": "pmc", "key": "PMC6085073"}], "notes": [], "created": "2019-01-17T13:57:08.240Z", "modified": "2026-09-11T13:23:26.278Z"}, {"entity": "publication", "iuid": "9129e3fde5f24d85b21ee5393aac7fe8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9129e3fde5f24d85b21ee5393aac7fe8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9129e3fde5f24d85b21ee5393aac7fe8"}}, "title": "Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.", "authors": [{"family": "Ladds", "given": "Marcus J G W", "initials": "MJGW"}, {"family": "van Leeuwen", "given": "Ingeborg M M", "initials": "IMM"}, {"family": "Drummond", "given": "Catherine J", "initials": "CJ"}, {"family": "Chu", "given": "Su", "initials": "S"}, {"family": "Healy", "given": "Alan R", "initials": "AR"}, {"family": "Popova", "given": "Gergana", "initials": "G"}, {"family": "Pastor Fern\u00e1ndez", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Mollick", "given": "Tanzina", "initials": "T"}, {"family": "Darekar", "given": "Suhas", "initials": "S"}, {"family": "Sedimbi", "given": "Saikiran K", "initials": "SK"}, {"family": "Nekulova", "given": "Marta", "initials": "M"}, {"family": "Sachweh", "given": "Marijke C C", "initials": "MCC"}, {"family": "Campbell", "given": "Johanna", "initials": "J"}, {"family": "Higgins", "given": "Maureen", "initials": "M"}, {"family": "Tuck", "given": "Chloe", "initials": "C"}, {"family": "Popa", "given": "Mihaela", "initials": "M"}, {"family": "Safont", "given": "Mireia Mayoral", "initials": "MM"}, {"family": "Gelebart", "given": "Pascal", "initials": "P"}, {"family": "Fandalyuk", "given": "Zinayida", "initials": "Z"}, {"family": "Thompson", "given": "Alastair M", "initials": "AM"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Yngve", "given": "Ulrika", "initials": "U"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "D'Hollander", "given": "Agathe C A", "initials": "ACA"}, {"family": "Franco", "given": "Marcela", "initials": "M"}, {"family": "Zhao", "given": "Yan", "initials": "Y"}, {"family": "H\u00e5kansson", "given": "Maria", "initials": "M"}, {"family": "Walse", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Larsson", "given": "Karin", "initials": "K", "orcid": "0000-0002-6403-2736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa1a266a524a4ebea48e81b6e0fdaefa.json"}}, {"family": "Peat", "given": "Emma M", "initials": "EM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Lunec", "given": "John", "initials": "J"}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Carmena", "given": "Mar", "initials": "M", "orcid": "0000-0002-2352-1066", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cefa7c4f49b64e2ab8b3b18daed08034.json"}}, {"family": "Earnshaw", "given": "William C", "initials": "WC"}, {"family": "McCarthy", "given": "Anna R", "initials": "AR"}, {"family": "Westwood", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-0630-0138", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b8919c7896f483fab56ecfe5fbca639.json"}}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Bhatia", "given": "Ravi", "initials": "R"}, {"family": "McCormack", "given": "Emmet", "initials": "E"}, {"family": "La\u00edn", "given": "Sonia", "initials": "S"}], "type": "journal article", "published": "2018-05-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "9", "issue": "1", "pages": "2071"}, "abstract": "The original PDF version of this Article listed the authors as \"Marcus J.G.W. Ladds,\" where it should have read \"Marcus J. G. W. Ladds, Ingeborg M. M. van Leeuwen, Catherine J. Drummond et al.#\".Also in the PDF version, it was incorrectly stated that \"Correspondence and requests for materials should be addressed to S. L\u00edn.\", instead of the correct \"Correspondence and requests for materials should be addressed to S. La\u00edn.\"This has been corrected in the PDF version of the Article. The HTML version was correct from the time of publication.", "doi": "10.1038/s41467-018-04198-5", "pmid": "29789663", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-04198-5"}, {"db": "pmc", "key": "PMC5964109"}], "notes": [], "created": "2020-10-09T14:06:26.600Z", "modified": "2026-09-11T13:23:26.334Z"}, {"entity": "publication", "iuid": "dd99bbbf46d34e018e82500bd8e285e5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dd99bbbf46d34e018e82500bd8e285e5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dd99bbbf46d34e018e82500bd8e285e5"}}, "title": "A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.", "authors": [{"family": "Ladds", "given": "Marcus J G W", "initials": "MJGW"}, {"family": "van Leeuwen", "given": "Ingeborg M M", "initials": "IMM"}, {"family": "Drummond", "given": "Catherine J", "initials": "CJ"}, {"family": "Chu", "given": "Su", "initials": "S"}, {"family": "Healy", "given": "Alan R", "initials": "AR"}, {"family": "Popova", "given": "Gergana", "initials": "G"}, {"family": "Pastor Fern\u00e1ndez", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Mollick", "given": "Tanzina", "initials": "T"}, {"family": "Darekar", "given": "Suhas", "initials": "S"}, {"family": "Sedimbi", "given": "Saikiran K", "initials": "SK"}, {"family": "Nekulova", "given": "Marta", "initials": "M"}, {"family": "Sachweh", "given": "Marijke C C", "initials": "MCC"}, {"family": "Campbell", "given": "Johanna", "initials": "J"}, {"family": "Higgins", "given": "Maureen", "initials": "M"}, {"family": "Tuck", "given": "Chloe", "initials": "C"}, {"family": "Popa", "given": "Mihaela", "initials": "M"}, {"family": "Safont", "given": "Mireia Mayoral", "initials": "MM"}, {"family": "Gelebart", "given": "Pascal", "initials": "P"}, {"family": "Fandalyuk", "given": "Zinayida", "initials": "Z"}, {"family": "Thompson", "given": "Alastair M", "initials": "AM"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Yngve", "given": "Ulrika", "initials": "U"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "D'Hollander", "given": "Agathe C A", "initials": "ACA"}, {"family": "Franco", "given": "Marcela", "initials": "M"}, {"family": "Zhao", "given": "Yan", "initials": "Y"}, {"family": "H\u00e5kansson", "given": "Maria", "initials": "M"}, {"family": "Walse", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Larsson", "given": "Karin", "initials": "K", "orcid": "0000-0002-6403-2736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa1a266a524a4ebea48e81b6e0fdaefa.json"}}, {"family": "Peat", "given": "Emma M", "initials": "EM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Lunec", "given": "John", "initials": "J"}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Carmena", "given": "Mar", "initials": "M", "orcid": "0000-0002-2352-1066", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cefa7c4f49b64e2ab8b3b18daed08034.json"}}, {"family": "Earnshaw", "given": "William C", "initials": "WC"}, {"family": "McCarthy", "given": "Anna R", "initials": "AR"}, {"family": "Westwood", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-0630-0138", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b8919c7896f483fab56ecfe5fbca639.json"}}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Bhatia", "given": "Ravi", "initials": "R"}, {"family": "McCormack", "given": "Emmet", "initials": "E"}, {"family": "La\u00edn", "given": "Sonia", "initials": "S"}], "type": "journal article", "published": "2018-03-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "9", "issue": "1", "pages": "1107"}, "abstract": "The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidate the mechanism of action of a chiral tetrahydroindazole (HZ00), and through target deconvolution, we deduce that its active enantiomer (R)-HZ00, inhibits dihydroorotate dehydrogenase (DHODH). The chiral specificity of HZ05, a more potent analog, is revealed by the crystal structure of the (R)-HZ05/DHODH complex. Twelve other DHODH inhibitor chemotypes are detailed among the p53 activators, which identifies DHODH as a frequent target for structurally diverse compounds. We observe that HZ compounds accumulate cancer cells in S-phase, increase p53 synthesis, and synergize with an inhibitor of p53 degradation to reduce tumor growth in vivo. We, therefore, propose a strategy to promote cancer cell killing by p53 instead of its reversible cell cycle arresting effect.", "doi": "10.1038/s41467-018-03441-3", "pmid": "29549331", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03441-3"}, {"db": "pmc", "key": "PMC5856786"}], "notes": [], "created": "2018-12-03T14:45:37.634Z", "modified": "2026-09-11T13:23:26.348Z"}, {"entity": "publication", "iuid": "502327f3318743059356bc1f313337e3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/502327f3318743059356bc1f313337e3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/502327f3318743059356bc1f313337e3"}}, "title": "From transcriptional complexity to cellular phenotypes: Lessons from yeast.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "Yeast", "issn": "1097-0061", "issn-l": "0749-503X", "volume": "34", "issue": "12", "pages": "475-482"}, "abstract": "Pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves thousands of coding and non-coding RNAs. However, to date, the biological impact of transcriptome complexity is still poorly understood. Here I will review how subtle variations of the transcriptome can lead to divergent cellular phenotypes by fine-tuning both its coding potential and regulation. I will discuss strategies that can be used to link molecular variations with divergent biological outcomes. Finally, I will explore the implication of transcriptional complexity for our understanding of gene expression in the context of cell-to-cell phenotypic variability. Copyright \u00a9 2017 John Wiley & Sons, Ltd.", "doi": "10.1002/yea.3277", "pmid": "28866863", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:42:14.858Z", "modified": "2026-09-11T13:23:26.390Z"}, {"entity": "publication", "iuid": "a50f96638ff94d76be15192e8ca024f2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a50f96638ff94d76be15192e8ca024f2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a50f96638ff94d76be15192e8ca024f2"}}, "title": "Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.", "authors": [{"family": "Chabbert", "given": "Christophe D", "initials": "CD"}, {"family": "Adjalley", "given": "Sophie H", "initials": "SH"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}], "type": "journal article", "published": "2017-10-14", "journal": {"title": "Methods in molecular biology (Clifton, N.J.)", "issn": "1940-6029", "issn-l": "1064-3745", "volume": "1689", "issue": null, "pages": "177-194"}, "abstract": "Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.", "doi": "10.1007/978-1-4939-7380-4_16", "pmid": "29027175", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:13:10.999Z", "modified": "2026-09-11T13:23:26.411Z"}, {"entity": "publication", "iuid": "c250903c895747548da43dce98d193b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c250903c895747548da43dce98d193b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c250903c895747548da43dce98d193b8"}}, "title": "The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation.", "authors": [{"family": "G\u00f3mez-Herreros", "given": "Fernando", "initials": "F"}, {"family": "Margaritis", "given": "Thanasis", "initials": "T"}, {"family": "Rodr\u00edguez-Gal\u00e1n", "given": "Olga", "initials": "O"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Begley", "given": "Victoria", "initials": "V"}, {"family": "Mill\u00e1n-Zambrano", "given": "Gonzalo", "initials": "G"}, {"family": "Morillo-Huesca", "given": "Macarena", "initials": "M"}, {"family": "Mu\u00f1oz-Centeno", "given": "Mari Cruz", "initials": "MC"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE", "orcid": "0000-0002-1992-513X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac4f5d4d6cd54c1bbafeec15e97e5c49.json"}}, {"family": "de la Cruz", "given": "Jes\u00fas", "initials": "J"}, {"family": "Holstege", "given": "Frank C P", "initials": "FCP"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}], "type": "journal article", "published": "2017-09-19", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "45", "issue": "16", "pages": "9302-9318"}, "abstract": "Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis. We found that the in vivo depletion of one of these factors, Arb1, activated transcription elongation in the set of genes involved directly in ribosome assembly. Under these depletion conditions, Spt6 was physically targeted to the up-regulated genes, where it helped maintain their chromatin integrity and the synthesis of properly stable mRNAs. The mRNA profiles of a large set of ribosome biogenesis mutants confirmed the existence of a feedback regulatory network among ribosome assembly genes. The transcriptional response in this network depended on both the specific malfunction and the role of the regulated gene. In accordance with our screening, Spt6 positively contributed to the optimal operation of this global network. On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes.", "doi": "10.1093/nar/gkx529", "pmid": "28637236", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "3868324"}, {"db": "pmc", "key": "PMC5737610"}], "notes": [], "created": "2018-12-03T14:41:44.035Z", "modified": "2026-09-11T13:23:26.502Z"}, {"entity": "publication", "iuid": "91dbbb280f104d8d967e6921953af1f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/91dbbb280f104d8d967e6921953af1f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/91dbbb280f104d8d967e6921953af1f9"}}, "title": "eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Alepuz", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2017-07-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "45", "issue": "12", "pages": "7326-7338"}, "abstract": "eIF5A is an essential protein involved in protein synthesis, cell proliferation and animal development. High eIF5A expression is observed in many tumor types and has been linked to cancer metastasis. Recent studies have shown that eIF5A facilitates the translation elongation of stretches of consecutive prolines. Activated eIF5A binds to the empty E-site of stalled ribosomes, where it is thought to interact with the peptidyl-tRNA situated at the P-site. Here, we report a genome-wide analysis of ribosome stalling in Saccharomyces cerevisiae eIF5A depleted cells using 5Pseq. We confirm that, in the absence of eIF5A, ribosomes stall at proline stretches, and extend previous studies by identifying eIF5A-dependent ribosome pauses at termination and at >200 tripeptide motifs. We show that presence of proline, glycine and charged amino acids at the peptidyl transferase center and at the beginning of the peptide exit tunnel arrest ribosomes in eIF5A-depleted cells. Lack of eIF5A also renders ribosome accumulation at the stop codons. Our data indicate specific protein functional groups under the control of eIF5A, including ER-coupled translation and GTPases in yeast and cytoskeleton organization, collagen metabolism and cell differentiation in humans. Our results support a broad mRNA-specific role of eIF5A in translation and identify the conserved motifs that affect translation elongation from yeast to humans.", "doi": "10.1093/nar/gkx479", "pmid": "28549188", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "3854954"}, {"db": "pmc", "key": "PMC5499558"}], "notes": [], "created": "2018-12-03T14:43:13.077Z", "modified": "2026-09-11T13:23:26.516Z"}, {"entity": "publication", "iuid": "870d2cc0e99142219515cc786192460c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/870d2cc0e99142219515cc786192460c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/870d2cc0e99142219515cc786192460c"}}, "title": "Long Non Coding RNA Biology", "authors": [], "type": "book", "published": "2017-00-00", "journal": {"title": "Springer", "issn": "0065-2598", "issn-l": null, "volume": "[book]", "issue": null, "pages": null}, "abstract": "ISBN 978-981-10-5203-3", "doi": "10.1007/978-981-10-5203-3", "pmid": null, "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:09:51.426Z", "modified": "2026-09-11T13:23:26.532Z"}, {"entity": "publication", "iuid": "2f2e9220341543c3b1f3a5374868971a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2f2e9220341543c3b1f3a5374868971a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2f2e9220341543c3b1f3a5374868971a"}}, "title": "A global genetic interaction network maps a wiring diagram of cellular function.", "authors": [{"family": "Costanzo", "given": "Michael", "initials": "M"}, {"family": "VanderSluis", "given": "Benjamin", "initials": "B"}, {"family": "Koch", "given": "Elizabeth N", "initials": "EN"}, {"family": "Baryshnikova", "given": "Anastasia", "initials": "A"}, {"family": "Pons", "given": "Carles", "initials": "C"}, {"family": "Tan", "given": "Guihong", "initials": "G"}, {"family": "Wang", "given": "Wen", "initials": "W"}, {"family": "Usaj", "given": "Matej", "initials": "M"}, {"family": "Hanchard", "given": "Julia", "initials": "J"}, {"family": "Lee", "given": "Susan D", "initials": "SD"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Styles", "given": "Erin B", "initials": "EB"}, {"family": "Billmann", "given": "Maximilian", "initials": "M"}, {"family": "van Leeuwen", "given": "Jolanda", "initials": "J"}, {"family": "van Dyk", "given": "Nydia", "initials": "N"}, {"family": "Lin", "given": "Zhen-Yuan", "initials": "ZY"}, {"family": "Kuzmin", "given": "Elena", "initials": "E"}, {"family": "Nelson", "given": "Justin", "initials": "J"}, {"family": "Piotrowski", "given": "Jeff S", "initials": "JS"}, {"family": "Srikumar", "given": "Tharan", "initials": "T"}, {"family": "Bahr", "given": "Sondra", "initials": "S"}, {"family": "Chen", "given": "Yiqun", "initials": "Y"}, {"family": "Deshpande", "given": "Raamesh", "initials": "R"}, {"family": "Kurat", "given": "Christoph F", "initials": "CF"}, {"family": "Li", "given": "Sheena C", "initials": "SC"}, {"family": "Li", "given": "Zhijian", "initials": "Z"}, {"family": "Usaj", "given": "Mojca Mattiazzi", "initials": "MM"}, {"family": "Okada", "given": "Hiroki", "initials": "H"}, {"family": "Pascoe", "given": "Natasha", "initials": "N"}, {"family": "San Luis", "given": "Bryan-Joseph", "initials": "BJ"}, {"family": "Sharifpoor", "given": "Sara", "initials": "S"}, {"family": "Shuteriqi", "given": "Emira", "initials": "E"}, {"family": "Simpkins", "given": "Scott W", "initials": "SW"}, {"family": "Snider", "given": "Jamie", "initials": "J"}, {"family": "Suresh", "given": "Harsha Garadi", "initials": "HG"}, {"family": "Tan", "given": "Yizhao", "initials": "Y"}, {"family": "Zhu", "given": "Hongwei", "initials": "H"}, {"family": "Malod-Dognin", "given": "Noel", "initials": "N"}, {"family": "Janjic", "given": "Vuk", "initials": "V"}, {"family": "Przulj", "given": "Natasa", "initials": "N"}, {"family": "Troyanskaya", "given": "Olga G", "initials": "OG"}, {"family": "Stagljar", "given": "Igor", "initials": "I"}, {"family": "Xia", "given": "Tian", "initials": "T"}, {"family": "Ohya", "given": "Yoshikazu", "initials": "Y"}, {"family": "Gingras", "given": "Anne-Claude", "initials": "AC"}, {"family": "Raught", "given": "Brian", "initials": "B"}, {"family": "Boutros", "given": "Michael", "initials": "M"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Moore", "given": "Claire L", "initials": "CL"}, {"family": "Rosebrock", "given": "Adam P", "initials": "AP"}, {"family": "Caudy", "given": "Amy A", "initials": "AA"}, {"family": "Myers", "given": "Chad L", "initials": "CL"}, {"family": "Andrews", "given": "Brenda", "initials": "B"}, {"family": "Boone", "given": "Charles", "initials": "C"}], "type": "journal article", "published": "2016-09-23", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "353", "issue": "6306", "pages": "aaf1420-aaf1420"}, "abstract": "We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.", "doi": "10.1126/science.aaf1420", "pmid": "27708008", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "353/6306/aaf1420"}, {"db": "pmc", "key": "PMC5661885"}, {"db": "mid", "key": "NIHMS915069"}, {"db": "Dryad", "key": "10.5061/dryad.4291s"}], "notes": [], "created": "2018-12-03T14:41:09.586Z", "modified": "2026-09-11T13:23:26.546Z"}, {"entity": "publication", "iuid": "c2ff77e524d846c997b0f80c3010a410", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c2ff77e524d846c997b0f80c3010a410.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c2ff77e524d846c997b0f80c3010a410"}}, "title": "Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.", "authors": [{"family": "Chen", "given": "Yun", "initials": "Y"}, {"family": "Pai", "given": "Athma A", "initials": "AA"}, {"family": "Herudek", "given": "Jan", "initials": "J"}, {"family": "Lubas", "given": "Michal", "initials": "M"}, {"family": "Meola", "given": "Nicola", "initials": "N"}, {"family": "J\u00e4rvelin", "given": "Aino I", "initials": "AI"}, {"family": "Andersson", "given": "Robin", "initials": "R", "orcid": "0000-0003-1516-879X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af2c9c777ea343f79ede5e0ccc973274.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Jensen", "given": "Torben Heick", "initials": "TH", "orcid": "0000-0001-5127-1239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f63375fe0a24f95b0b6bb6674d7a3b1.json"}}, {"family": "Sandelin", "given": "Albin", "initials": "A", "orcid": "0000-0002-7109-7378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9618b5e69c14c6e9df631a8abfcd77c.json"}}], "type": "journal article", "published": "2016-09-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036", "volume": "48", "issue": "9", "pages": "984-994"}, "abstract": "Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here we found that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but owing to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provide a framework with which evolution shapes transcriptomes.", "doi": "10.1038/ng.3616", "pmid": "27455346", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "ng.3616"}, {"db": "pmc", "key": "PMC5008441"}, {"db": "mid", "key": "EMS68836"}], "notes": [], "created": "2018-12-03T14:40:59.166Z", "modified": "2026-09-11T13:23:26.586Z"}, {"entity": "publication", "iuid": "a5c2555e02664af1b05911fe415c1786", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a5c2555e02664af1b05911fe415c1786.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a5c2555e02664af1b05911fe415c1786"}}, "title": "Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation.", "authors": [{"family": "Chlamydas", "given": "Sarantis", "initials": "S"}, {"family": "Holz", "given": "Herbert", "initials": "H"}, {"family": "Samata", "given": "Maria", "initials": "M"}, {"family": "Chelmicki", "given": "Tomasz", "initials": "T"}, {"family": "Georgiev", "given": "Plamen", "initials": "P"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "D\u00fcndar", "given": "Friederike", "initials": "F"}, {"family": "Dasmeh", "given": "Pouria", "initials": "P"}, {"family": "Mittler", "given": "Gerhard", "initials": "G"}, {"family": "Cadete", "given": "Filipe Tavares", "initials": "FT"}, {"family": "Ram\u00edrez", "given": "Fidel", "initials": "F"}, {"family": "Conrad", "given": "Thomas", "initials": "T"}, {"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "Raja", "given": "Sunil", "initials": "S"}, {"family": "Manke", "given": "Thomas", "initials": "T"}, {"family": "Luscombe", "given": "Nicholas M", "initials": "NM"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Akhtar", "given": "Asifa", "initials": "A"}], "type": "journal article", "published": "2016-06-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "issn-l": "1545-9985", "volume": "23", "issue": "6", "pages": "580-589"}, "abstract": "Proper gene expression requires coordinated interplay among transcriptional coactivators, transcription factors and the general transcription machinery. We report here that MSL1, a central component of the dosage compensation complex in Drosophila melanogaster and Drosophila virilis, displays evolutionarily conserved sex-independent binding to promoters. Genetic and biochemical analyses reveal a functional interaction of MSL1 with CDK7, a subunit of the Cdk-activating kinase (CAK) complex of the general transcription factor TFIIH. Importantly, MSL1 depletion leads to decreased phosphorylation of Ser5 of RNA polymerase II. In addition, we demonstrate that MSL1 is a phosphoprotein, and transgenic flies expressing MSL1 phosphomutants show mislocalization of the histone acetyltransferase MOF and histone H4 K16 acetylation, thus ultimately causing male lethality due to a failure of dosage compensation. We propose that, by virtue of its interaction with components of the general transcription machinery, MSL1 exists in different phosphorylation states, thereby modulating transcription in flies.", "doi": "10.1038/nsmb.3233", "pmid": "27183194", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "nsmb.3233"}], "notes": [], "created": "2018-12-03T14:40:35.333Z", "modified": "2026-09-11T13:23:26.595Z"}, {"entity": "publication", "iuid": "6e47b4a2e6c7458ab928443267acda76", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6e47b4a2e6c7458ab928443267acda76.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6e47b4a2e6c7458ab928443267acda76"}}, "title": "The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.", "authors": [{"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "Delgado-Ramos", "given": "Lidia", "initials": "L"}, {"family": "Ayala", "given": "Guillermo", "initials": "G"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Medina", "given": "Daniel A", "initials": "DA"}, {"family": "Carrasco", "given": "Fany", "initials": "F"}, {"family": "Gonz\u00e1lez", "given": "Ram\u00f3n", "initials": "R"}, {"family": "Andr\u00e9s-Le\u00f3n", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-0621-9914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d43e1d9225714332a03219086de777ac.json"}}, {"family": "Steinmetz", "given": "Lars", "initials": "L"}, {"family": "Warringer", "given": "Jonas", "initials": "J"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE", "orcid": "0000-0002-1992-513X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac4f5d4d6cd54c1bbafeec15e97e5c49.json"}}], "type": "journal article", "published": "2016-05-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "44", "issue": "8", "pages": "3643-3658"}, "abstract": "We analyzed 80 different genomic experiments, and found a positive correlation between both RNA polymerase II transcription and mRNA degradation with growth rates in yeast. Thus, in spite of the marked variation in mRNA turnover, the total mRNA concentration remained approximately constant. Some genes, however, regulated their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. We also detected these regulations within the heterogeneity of a wild-type cell population growing in optimal conditions. The transcriptomic analysis of sorted microcolonies confirmed that the growth rate dictates alternative expression programs by modulating transcription and mRNA decay.The regulation of overall mRNA turnover keeps a constant ratio between mRNA decay and the dilution of [mRNA] caused by cellular growth. This regulation minimizes the indiscriminate transmission of mRNAs from mother to daughter cells, and favors the response capacity of the latter to physiological signals and environmental changes. We also conclude that, by uncoupling mRNA synthesis from decay, cells control the mRNA abundance of those gene regulons that characterize fast and slow growth.", "doi": "10.1093/nar/gkv1512", "pmid": "26717982", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "gkv1512"}, {"db": "pmc", "key": "PMC4856968"}], "notes": [], "created": "2018-12-03T14:40:28.325Z", "modified": "2026-09-11T13:23:26.616Z"}, {"entity": "publication", "iuid": "456de87d27bb48c2894ba007842c75f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/456de87d27bb48c2894ba007842c75f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/456de87d27bb48c2894ba007842c75f5"}}, "title": "Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast.", "authors": [{"family": "Garrido-Godino", "given": "A I", "initials": "AI"}, {"family": "Garc\u00eda-L\u00f3pez", "given": "M C", "initials": "MC"}, {"family": "Garc\u00eda-Mart\u00ednez", "given": "J", "initials": "J"}, {"family": "Pelechano", "given": "V", "initials": "V"}, {"family": "Medina", "given": "D A", "initials": "DA"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "J E", "initials": "JE"}, {"family": "Navarro", "given": "F", "initials": "F"}], "type": "journal article", "published": "2016-05-00", "journal": {"title": "Biochim. Biophys. Acta", "issn": "0006-3002", "issn-l": null, "volume": "1859", "issue": "5", "pages": "731-743"}, "abstract": "The RPB1 mutants in the foot region of RNA polymerase II affect the assembly of the complex by altering the correct association of both the Rpb6 and the Rpb4/7 dimer. Assembly defects alter both transcriptional activity as well as the amount of enzyme associated with genes. Here, we show that the global transcriptional analysis of foot mutants reveals the activation of an environmental stress response (ESR), which occurs at a permissive temperature under optimal growth conditions. Our data indicate that the ESR that occurs in foot mutants depends mostly on a global post-transcriptional regulation mechanism which, in turn, depends on Rpb4-mRNA imprinting. Under optimal growth conditions, we propose that Rpb4 serves as a key to globally modulate mRNA stability as well as to coordinate transcription and decay. Overall, our results imply that post-transcriptional regulation plays a major role in controlling the ESR at both the transcription and mRNA decay levels.", "doi": "10.1016/j.bbagrm.2016.03.008", "pmid": "27001033", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S1874-9399(16)30053-0"}], "notes": [], "created": "2018-12-03T14:40:18.152Z", "modified": "2026-09-11T13:23:26.627Z"}, {"entity": "publication", "iuid": "c198c68fd385487cb99356ad7e92942d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c198c68fd385487cb99356ad7e92942d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c198c68fd385487cb99356ad7e92942d"}}, "title": "Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum.", "authors": [{"family": "Adjalley", "given": "Sophie H", "initials": "SH"}, {"family": "Chabbert", "given": "Christophe D", "initials": "CD"}, {"family": "Klaus", "given": "Bernd", "initials": "B"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal article", "published": "2016-03-15", "journal": {"title": "Cell Reports", "issn": "2211-1247", "issn-l": null, "volume": "14", "issue": "10", "pages": "2463-2475"}, "abstract": "A comprehensive map of transcription start sites (TSSs) across the highly AT-rich genome of P. falciparum would aid progress toward deciphering the molecular mechanisms that underlie the timely regulation of gene expression in this malaria parasite. Using high-throughput sequencing technologies, we generated a comprehensive atlas of transcription initiation events at single-nucleotide resolution during the parasite intra-erythrocytic developmental cycle. This detailed analysis of TSS usage enabled us to define architectural features of plasmodial promoters. We demonstrate that TSS selection and strength are constrained by local nucleotide composition. Furthermore, we provide evidence for coordinate and stage-specific TSS usage from distinct sites within the same transcription unit, thereby producing transcript isoforms, a subset of which are developmentally regulated. This work offers a framework for further investigations into the interactions between genomic sequences and regulatory factors governing the complex transcriptional program of this major human pathogen.", "doi": "10.1016/j.celrep.2016.02.025", "pmid": "26947071", "labels": {"Affiliated researcher": null, "SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "S2211-1247(16)30128-0"}, {"db": "pmc", "key": "PMC4806524"}, {"db": "mid", "key": "NIHMS759864"}], "notes": [], "created": "2018-12-03T14:39:54.306Z", "modified": "2026-09-11T13:23:26.755Z"}, {"entity": "publication", "iuid": "7e2e9e47afcb4fdf86e7fe0aeac57b28", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7e2e9e47afcb4fdf86e7fe0aeac57b28.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7e2e9e47afcb4fdf86e7fe0aeac57b28"}}, "title": "Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal article", "published": "2016-02-00", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "issn-l": null, "volume": "11", "issue": "2", "pages": "359-376"}, "abstract": "Co-translational mRNA degradation is a widespread process in which 5'-3' exonucleolytic degradation follows the last translating ribosome, thus producing an in vivo ribosomal footprint that delimits the 5' position of the mRNA molecule within the ribosome. To study this degradation process and ribosome dynamics, we developed 5PSeq, which is a method that profiles the genome-wide abundance of mRNA degradation intermediates by virtue of their 5'-phosphorylated (5'P) ends. The approach involves targeted ligation of an oligonucleotide to the 5'P end of mRNA degradation intermediates, followed by depletion of rRNA molecules, reverse transcription of 5'P mRNAs and Illumina high-throughput sequencing. 5PSeq can identify translational pauses at rare codons that are often masked when using alternative methods. This approach can be applied to previously extracted RNA samples, and it is straightforward and does not require polyribosome purification or in vitro RNA footprinting. The protocol we describe here can be applied to Saccharomyces cerevisiae and potentially to other eukaryotic organisms. Three days are required to generate 5PSeq libraries.", "doi": "10.1038/nprot.2016.026", "pmid": "26820793", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "nprot.2016.026"}, {"db": "pmc", "key": "PMC4732566"}, {"db": "mid", "key": "NIHMS733392"}], "notes": [], "created": "2018-12-03T14:39:37.162Z", "modified": "2026-09-11T13:23:27.071Z"}, {"entity": "publication", "iuid": "fb12e2c53d674f598cfaa0f09aac8718", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb12e2c53d674f598cfaa0f09aac8718.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb12e2c53d674f598cfaa0f09aac8718"}}, "title": "Biotin-Genomic Run-On (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast.", "authors": [{"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Miguel", "given": "Ana", "initials": "A"}, {"family": "Serna", "given": "Eva", "initials": "E"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal article", "published": "2015-10-21", "journal": {"title": "Methods in molecular biology (Clifton, N.J.)", "issn": "1940-6029", "volume": "1361", "issue": null, "pages": "125-139", "issn-l": "1064-3745"}, "abstract": "Transcription is a highly complex biological process, with extensive layers of regulation, some of which remain to be fully unveiled and understood. To be able to discern the particular contributions of the several transcription steps it is crucial to understand RNA polymerase dynamics and regulation throughout the transcription cycle. Here we describe a new nonradioactive run-on based method that maps elongating RNA polymerases along the genome. In contrast with alternative methodologies for the measurement of nascent transcription, the BioGRO method is designed to minimize technical noise that arises from two of the most common sources that affect this type of strategies: contamination with mature RNA and amplification-based technical biasing. The method is strand-specific, compatible with commercial microarrays, and has been successfully applied to both yeasts Saccharomyces cerevisiae and Candida albicans. BioGRO profiling provides powerful insights not only into the biogenesis and regulation of canonical gene transcription but also into the noncoding and antisense transcriptomes.", "doi": "10.1007/978-1-4939-3079-1_8", "pmid": "26483020", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:15:01.106Z", "modified": "2026-09-11T13:23:27.218Z"}, {"entity": "publication", "iuid": "550235968f4a477a8f440ec128e3605b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/550235968f4a477a8f440ec128e3605b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/550235968f4a477a8f440ec128e3605b"}}, "title": "Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill.", "authors": [{"family": "Wilkening", "given": "Stefan", "initials": "S"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal article", "published": "2015-10-16", "journal": {"title": "Methods in molecular biology (Clifton, N.J.)", "issn": "1940-6029", "volume": "1358", "issue": null, "pages": "295-302", "issn-l": "1064-3745"}, "abstract": "Due to the increasing appreciation of the impact of alternative polyadenylation on cellular biology, our straightforward, scalable method is of interest to any researcher studying eukaryotic transcription. In addition to high quality gene expression measurements, it precisely maps poly(A) sites and thereby permits the distinction between differential 3'UTR isoforms. As sequencing through long homopolymer stretches is not possible on the Illumina platform, we developed a method that fills up the poly(A) stretch with dTTPs before the sequencing reaction starts.", "doi": "10.1007/978-1-4939-3067-8_18", "pmid": "26463391", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:15:50.800Z", "modified": "2026-09-11T13:23:27.226Z"}, {"entity": "publication", "iuid": "4f0332e19ddc4d2f9e52b2abc9757562", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f0332e19ddc4d2f9e52b2abc9757562.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f0332e19ddc4d2f9e52b2abc9757562"}}, "title": "The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production", "authors": [{"family": "Schmid", "given": "Manfred", "initials": "M"}, {"family": "Olszewski", "given": "Pawel", "initials": "P"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Gupta", "given": "Ishaan", "initials": "I"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Jensen", "given": "Torben Heick", "initials": "TH"}], "type": "journal-article", "published": "2015-07-00", "journal": {"volume": "12", "issn": "2211-1247", "issue": "1", "pages": "128-139", "title": "Cell Reports", "issn-l": null}, "abstract": "Polyadenylation of mRNA is a key step in eukaryotic gene expression. However, despite the major impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S. cerevisiae PABP Nab2p leads to a global loss of cellular mRNA, but not of RNA lacking poly(A) tails. Disappearance of mRNA is a nuclear event, but not due to decreased transcription. Instead, the absence of Nab2p results in robust nuclear mRNA decay by the ribonucleolytic RNA exosome in a polyadenylation-dependent process. We conclude that Nab2p is required to protect early mRNA and therefore constitutes a crucial nuclear mRNA biogenesis factor.", "doi": "10.1016/j.celrep.2015.06.008", "pmid": "26119729", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:37:22.440Z", "modified": "2026-09-11T13:23:27.272Z"}, {"entity": "publication", "iuid": "81811a6433864dc1b2c6cf2136b2fe6b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/81811a6433864dc1b2c6cf2136b2fe6b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/81811a6433864dc1b2c6cf2136b2fe6b"}}, "title": "Single-cell polyadenylation site mapping reveals 3' isoform choice variability.", "authors": [{"family": "Velten", "given": "Lars", "initials": "L"}, {"family": "Anders", "given": "Simon", "initials": "S"}, {"family": "Pekowska", "given": "Aleksandra", "initials": "A"}, {"family": "J\u00e4rvelin", "given": "Aino I", "initials": "AI"}, {"family": "Huber", "given": "Wolfgang", "initials": "W"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal article", "published": "2015-06-03", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "11", "issue": "6", "pages": "812", "issn-l": "1744-4292"}, "abstract": "Cell-to-cell variability in gene expression is important for many processes in biology, including embryonic development and stem cell homeostasis. While heterogeneity of gene expression levels has been extensively studied, less attention has been paid to mRNA polyadenylation isoform choice. 3' untranslated regions regulate mRNA fate, and their choice is tightly controlled during development, but how 3' isoform usage varies within genetically and developmentally homogeneous cell populations has not been explored. Here, we perform genome-wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single-cell transcriptomic method, BATSeq. By applying BATBayes, a statistical framework for analyzing single-cell isoform data, we find that while the developmental state of the cell globally determines isoform usage, single cells from the same state differ in the choice of isoforms. Notably this variation exceeds random selection with equal preference in all cells, a finding that was confirmed by RNA FISH data. Variability in 3' isoform choice has potential implications on functional cell-to-cell heterogeneity as well as utility in resolving cell populations. ", "doi": "10.15252/msb.20156198", "pmid": "26040288", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC4501847"}, {"db": "GEO", "key": "GSE60768"}], "notes": [], "created": "2018-12-03T14:56:09.847Z", "modified": "2026-09-11T13:23:27.296Z"}, {"entity": "publication", "iuid": "1a79c12f297c45db99de7ddc3224ce3f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a79c12f297c45db99de7ddc3224ce3f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a79c12f297c45db99de7ddc3224ce3f"}}, "title": "Widespread Co-translational RNA Decay Reveals Ribosome Dynamics", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal-article", "published": "2015-06-00", "journal": {"volume": "161", "issn": "0092-8674", "issue": "6", "pages": "1400-1412", "title": "Cell", "issn-l": null}, "abstract": "It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5'-3' transcript degradation follows the last translating ribosome, producing an in vivo ribosomal footprint. By sequencing the ends of 5' phosphorylated mRNA degradation intermediates, we obtain a genome-wide drug-free measurement of ribosome dynamics. We identify general translation termination pauses in both normal and stress conditions. In addition, we describe novel codon-specific ribosomal pausing sites in response to oxidative stress that are dependent on the RNase Rny1. Our approach is simple and straightforward and does not require the use of translational inhibitors or in vitro RNA footprinting that can alter ribosome protection patterns.", "doi": "10.1016/j.cell.2015.05.008", "pmid": "26046441", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:37:05.277Z", "modified": "2026-09-11T13:23:27.318Z"}, {"entity": "publication", "iuid": "ce5a838038ec48b58954aff734fff577", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce5a838038ec48b58954aff734fff577.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce5a838038ec48b58954aff734fff577"}}, "title": "Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle", "authors": [{"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Gupta", "given": "Ishaan", "initials": "I"}, {"family": "de\u00a0Miguel-Jim\u00e9nez", "given": "Lola", "initials": "L"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal-article", "published": "2015-01-30", "journal": {"volume": "43", "issn": "1362-4962", "issue": "2", "pages": "787-802", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution following a new biotin-based genomic run-on (BioGRO) technique. Compared with conventional profiling with chromatin immunoprecipitation, the analysis of the BioGRO profiles in Saccharomyces cerevisiae shows that RNA polymerase II has unique activity profiles at both gene ends, which are highly dependent on positioned nucleosomes. This is the first demonstration of the in vivo influence of positioned nucleosomes on transcription elongation. The particular features at the 5' end and around the polyadenylation site indicate that this polymerase undergoes extensive specific-activity regulation in the initial and final transcription elongation phases. The genes encoding for ribosomal proteins show distinctive features at both ends. BioGRO also provides the first nascentome analysis for RNA polymerase III, which indicates that transcription of tRNA genes is poorly regulated at the individual copy level. The present study provides a novel perspective of the transcription cycle that incorporates inactivation/reactivation as an important aspect of RNA polymerase dynamics.", "doi": "10.1093/nar/gku1349", "pmid": "25550430", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:36:30.989Z", "modified": "2026-09-11T13:23:27.356Z"}, {"entity": "publication", "iuid": "230108a68abe429a9534d2d4c7417ec9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/230108a68abe429a9534d2d4c7417ec9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/230108a68abe429a9534d2d4c7417ec9"}}, "title": "A high-throughput ChIP-Seq for large-scale chromatin studies.", "authors": [{"family": "Chabbert", "given": "Christophe D", "initials": "CD"}, {"family": "Adjalley", "given": "Sophie H", "initials": "SH"}, {"family": "Klaus", "given": "Bernd", "initials": "B"}, {"family": "Fritsch", "given": "Emilie S", "initials": "ES"}, {"family": "Gupta", "given": "Ishaan", "initials": "I"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal article", "published": "2015-01-12", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "11", "issue": "1", "pages": "777", "issn-l": "1744-4292"}, "abstract": "We present a modified approach of chromatin immuno-precipitation followed by sequencing (ChIP-Seq), which relies on the direct ligation of molecular barcodes to chromatin fragments, thereby permitting experimental scale-up. With Bar-ChIP now enabling the concurrent profiling of multiple DNA-protein interactions, we report the simultaneous generation of 90 ChIP-Seq datasets without any robotic instrumentation. We demonstrate that application of Bar-ChIP to a panel of Saccharomyces cerevisiae chromatin-associated mutants provides a rapid and accurate genome-wide overview of their chromatin status. Additionally, we validate the utility of this technology to derive novel biological insights by identifying a role for the Rpd3S complex in maintaining H3K14 hypo-acetylation in gene bodies. We also report an association between the presence of intragenic H3K4 tri-methylation and the emergence of cryptic transcription in a Set2 mutant. Finally, we uncover a crosstalk between H3K14 acetylation and H3K4 methylation in this mutant. These results show that Bar-ChIP enables biological discovery through rapid chromatin profiling at single-nucleosome resolution for various conditions and protein modifications at once. ", "doi": "10.15252/msb.20145776", "pmid": "25583149", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC4332152"}], "notes": [], "created": "2018-12-03T14:53:46.909Z", "modified": "2026-09-11T13:23:27.368Z"}, {"entity": "publication", "iuid": "e48bfefa7096472c9c00b8a22e99e9dc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e48bfefa7096472c9c00b8a22e99e9dc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e48bfefa7096472c9c00b8a22e99e9dc"}}, "title": "Genome-wide identification of transcript start and end sites by transcript isoform sequencing", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "Jakob", "given": "Petra", "initials": "P"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal-article", "published": "2014-07-00", "journal": {"volume": "9", "issn": "1754-2189", "issue": "7", "pages": "1740-1759", "title": "Nat Protoc", "issn-l": "1750-2799"}, "abstract": "Hundreds of transcript isoforms with varying boundaries and alternative regulatory signals are transcribed from the genome, even in a genetically homogeneous population of cells. To study this transcriptional heterogeneity, we developed transcript isoform sequencing (TIF-seq), a method that allows the genome-wide profiling of full-length transcript isoforms defined by their exact 5' and 3' boundaries. TIF-seq entails the generation of full-length cDNA libraries, followed by their circularization and the sequencing of the junction fragments spanning the 5' and 3' transcript ends. By determining the respective co-occurrence of start and end sites of individual transcript molecules, TIF-seq can distinguish variations that conventional approaches for mapping single ends cannot, such as short abortive transcripts, bicistronic messages and overlapping transcripts that differ in lengths. The TIF-seq protocol we describe here can be applied to any eukaryotic organism (e.g., yeast, human), and it requires 6-10 d for generating TIF-seq libraries, 10 d for sequencing and 2-3 d for analysis.", "doi": "10.1038/nprot.2014.121", "pmid": "24967623", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:34:37.539Z", "modified": "2026-09-11T13:23:27.383Z"}, {"entity": "publication", "iuid": "fd6e37b8e84c4e3bba04782cdcd07f9b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd6e37b8e84c4e3bba04782cdcd07f9b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd6e37b8e84c4e3bba04782cdcd07f9b"}}, "title": "Association of condensin with chromosomes depends on DNA binding by its HEAT-repeat subunits", "authors": [{"family": "Piazza", "given": "Ilaria", "initials": "I"}, {"family": "Rutkowska", "given": "Anna", "initials": "A"}, {"family": "Ori", "given": "Alessandro", "initials": "A"}, {"family": "Walczak", "given": "Marta", "initials": "M"}, {"family": "Metz", "given": "Jutta", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Beck", "given": "Martin", "initials": "M"}, {"family": "Haering", "given": "Christian H", "initials": "CH"}], "type": "journal-article", "published": "2014-06-00", "journal": {"volume": "21", "issn": "1545-9993", "issue": "6", "pages": "560-568", "title": "Nat Struct Mol Biol", "issn-l": "1545-9985"}, "abstract": "Condensin complexes have central roles in the three-dimensional organization of chromosomes during cell divisions, but how they interact with chromatin to promote chromosome segregation is largely unknown. Previous work has suggested that condensin, in addition to encircling chromatin fibers topologically within the ring-shaped structure formed by its SMC and kleisin subunits, contacts DNA directly. Here we describe the discovery of a binding domain for double-stranded DNA formed by the two HEAT-repeat subunits of the Saccharomyces cerevisiae condensin complex. From detailed mapping data of the interfaces between the HEAT-repeat and kleisin subunits, we generated condensin complexes that lack one of the HEAT-repeat subunits and consequently fail to associate with chromosomes in yeast and human cells. The finding that DNA binding by condensin's HEAT-repeat subunits stimulates the SMC ATPase activity suggests a multistep mechanism for the loading of condensin onto chromosomes.", "doi": "10.1038/nsmb.2831", "pmid": "24837193", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:34:23.906Z", "modified": "2026-09-11T13:23:27.422Z"}, {"entity": "publication", "iuid": "3b65b44d7a7b407493d2a55bd95538de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3b65b44d7a7b407493d2a55bd95538de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3b65b44d7a7b407493d2a55bd95538de"}}, "title": "Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions", "authors": [{"family": "Gupta", "given": "I", "initials": "I"}, {"family": "Clauder-Munster", "given": "S", "initials": "S"}, {"family": "Klaus", "given": "B", "initials": "B"}, {"family": "Jarvelin", "given": "A I", "initials": "AI"}, {"family": "Aiyar", "given": "R S", "initials": "RS"}, {"family": "Benes", "given": "V", "initials": "V"}, {"family": "Wilkening", "given": "S", "initials": "S"}, {"family": "Huber", "given": "W", "initials": "W"}, {"family": "Pelechano", "given": "V", "initials": "V"}, {"family": "Steinmetz", "given": "L M", "initials": "LM"}], "type": "journal-article", "published": "2014-03-20", "journal": {"volume": "10", "issn": "1744-4292", "issue": "2", "pages": "719-719", "title": "Mol Syst Biol", "issn-l": "1744-4292"}, "abstract": "Recent research has uncovered extensive variability in the boundaries of transcript isoforms, yet the functional consequences of this variation remain largely unexplored. Here, we systematically discriminate between the molecular phenotypes of overlapping coding and non-coding transcriptional events from each genic locus using a novel genome-wide, nucleotide-resolution technique to quantify the half-lives of 3' transcript isoforms in yeast. Our results reveal widespread differences in stability among isoforms for hundreds of genes in a single condition, and that variation of even a single nucleotide in the 3' untranslated region (UTR) can affect transcript stability. While previous instances of negative associations between 3' UTR length and transcript stability have been reported, here, we find that shorter isoforms are not necessarily more stable. We demonstrate the role of RNA-protein interactions in conditioning isoform-specific stability, showing that PUF3 binds and destabilizes specific polyadenylation isoforms. Our findings indicate that although the functional elements of a gene are encoded in DNA sequence, the selective incorporation of these elements into RNA through transcript boundary variation allows a single gene to have diverse functional consequences.", "doi": "10.1002/msb.135068", "pmid": "24569168", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:33:38.982Z", "modified": "2026-09-11T13:23:27.447Z"}, {"entity": "publication", "iuid": "0dccbfc2f02843e0bb8fb326487fe49a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0dccbfc2f02843e0bb8fb326487fe49a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0dccbfc2f02843e0bb8fb326487fe49a"}}, "title": "Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae", "authors": [{"family": "Magraner-Pardo", "given": "Lorena", "initials": "L"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Coloma", "given": "Mar\u00eda", "initials": "M"}, {"family": "Tordera", "given": "Vicente", "initials": "V"}], "type": "journal-article", "published": "2014-00-00", "journal": {"volume": "15", "issn": "1471-2164", "issue": "1", "pages": "247", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Specific histone modifications play important roles in chromatin functions; i.e., activation or repression of gene transcription. This participation must occur as a dynamic process. Nevertheless, most of the histone modification maps reported to date provide only static pictures that link certain modifications with active or silenced states. This study, however, focuses on the global histone modification variation that occurs in response to the transcriptional reprogramming produced by a physiological perturbation in yeast.\n\nWe did a genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after saline stress. The most striking change was rapid acetylation loss in lysines 9 and 14 of H3 and in lysine 8 of H4, associated with gene repression. The genes activated by saline stress increased the acetylation levels at these same sites, but this acetylation process was quantitatively minor if compared to that of the deacetylation of repressed genes. The changes in the tri-methylation of lysines 4, 36 and 79 of H3 and the di-methylation of lysine 79 of H3 were slighter than those of acetylation. Furthermore, we produced new genome-wide maps for seven histone modifications, and we analyzed, for the first time in S. cerevisiae, the genome-wide profile of acetylation of lysine 8 of H4.\n\nThis research reveals that the short-term changes observed in the post-stress methylation of histones are much more moderate than those of acetylation, and that the dynamics of the acetylation state of histones during activation or repression of transcription is a much quicker process than methylation.", "doi": "10.1186/1471-2164-15-247", "pmid": "24678875", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:34:13.622Z", "modified": "2026-09-11T13:23:27.455Z"}, {"entity": "publication", "iuid": "e47281a158114dcf8d0afb25a6a59237", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e47281a158114dcf8d0afb25a6a59237.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e47281a158114dcf8d0afb25a6a59237"}}, "title": "Gene regulation by antisense transcription", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal-article", "published": "2013-12-00", "journal": {"volume": "14", "issn": "1471-0056", "issue": "12", "pages": "880-893", "title": "Nat Rev Genet", "issn-l": "1471-0056"}, "abstract": "Antisense transcription, which was initially considered by many as transcriptional noise, is increasingly being recognized as an important regulator of gene expression. It is widespread among all kingdoms of life and has been shown to influence - either through the act of transcription or through the non-coding RNA that is produced - almost all stages of gene expression, from transcription and translation to RNA degradation. Antisense transcription can function as a fast evolving regulatory switch and a modular scaffold for protein complexes, and it can 'rewire' regulatory networks. The genomic arrangement of antisense RNAs opposite sense genes indicates that they might be part of self-regulatory circuits that allow genes to regulate their own expression. ", "doi": "10.1038/nrg3594", "pmid": "24217315", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:32:50.857Z", "modified": "2026-09-11T13:23:27.504Z"}, {"entity": "publication", "iuid": "428414a9e4b04d4a8b1d0157cd5041c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/428414a9e4b04d4a8b1d0157cd5041c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/428414a9e4b04d4a8b1d0157cd5041c7"}}, "title": "Polyadenylation site\u2013induced decay of upstream transcripts enforces promoter directionality", "authors": [{"family": "Ntini", "given": "Evgenia", "initials": "E"}, {"family": "J\u00e4rvelin", "given": "Aino I", "initials": "AI"}, {"family": "Bornholdt", "given": "Jette", "initials": "J"}, {"family": "Chen", "given": "Yun", "initials": "Y"}, {"family": "Boyd", "given": "Mette", "initials": "M"}, {"family": "J\u00f8rgensen", "given": "Mette", "initials": "M"}, {"family": "Andersson", "given": "Robin", "initials": "R"}, {"family": "Hoof", "given": "Ilka", "initials": "I"}, {"family": "Schein", "given": "Aleks", "initials": "A"}, {"family": "Andersen", "given": "Peter R", "initials": "PR"}, {"family": "Andersen", "given": "Pia K", "initials": "PK"}, {"family": "Preker", "given": "Pascal", "initials": "P"}, {"family": "Valen", "given": "Eivind", "initials": "E"}, {"family": "Zhao", "given": "Xiaobei", "initials": "X"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Sandelin", "given": "Albin", "initials": "A"}, {"family": "Jensen", "given": "Torben Heick", "initials": "TH"}], "type": "journal-article", "published": "2013-08-00", "journal": {"volume": "20", "issn": "1545-9993", "issue": "8", "pages": "923-928", "title": "Nat Struct Mol Biol", "issn-l": "1545-9985"}, "abstract": "Active human promoters produce promoter-upstream transcripts (PROMPTs). Why these RNAs are coupled to decay, whereas their neighboring promoter-downstream mRNAs are not, is unknown. Here high-throughput sequencing demonstrates that PROMPTs generally initiate in the antisense direction closely upstream of the transcription start sites (TSSs) of their associated genes. PROMPT TSSs share features with mRNA-producing TSSs, including stalled RNA polymerase II (RNAPII) and the production of small TSS-associated RNAs. Notably, motif analyses around PROMPT 3' ends reveal polyadenylation (pA)-like signals. Mutagenesis studies demonstrate that PROMPT pA signals are functional but linked to RNA degradation. Moreover, pA signals are under-represented in promoter-downstream versus promoter-upstream regions, thus allowing for more efficient RNAPII progress in the sense direction from gene promoters. We conclude that asymmetric sequence distribution around human gene promoters serves to provide a directional RNA output from an otherwise bidirectional transcription process.", "doi": "10.1038/nsmb.2640", "pmid": "23851456", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:32:16.624Z", "modified": "2026-09-11T13:23:27.518Z"}, {"entity": "publication", "iuid": "c399454cb5944602814748a74c277a44", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c399454cb5944602814748a74c277a44.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c399454cb5944602814748a74c277a44"}}, "title": "Extensive transcriptional heterogeneity revealed by isoform profiling", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal-article", "published": "2013-04-24", "journal": {"volume": "497", "issn": "0028-0836", "issue": "7447", "pages": "127-131", "title": "Nature", "issn-l": null}, "abstract": "Transcript function is determined by sequence elements arranged on an individual RNA molecule. Variation in transcripts can affect messenger RNA stability, localization and translation, or produce truncated proteins that differ in localization or function. Given the existence of overlapping, variable transcript isoforms, determining the functional impact of the transcriptome requires identification of full-length transcripts, rather than just the genomic regions that are transcribed. Here, by jointly determining both transcript ends for millions of RNA molecules, we reveal an extensive layer of isoform diversity previously hidden among overlapping RNA molecules. Variation in transcript boundaries seems to be the rule rather than the exception, even within a single population of yeast cells. Over 26 major transcript isoforms per protein-coding gene were expressed in yeast. Hundreds of short coding RNAs and truncated versions of proteins are concomitantly encoded by alternative transcript isoforms, increasing protein diversity. In addition, approximately 70% of genes express alternative isoforms that vary in post-transcriptional regulatory elements, and tandem genes frequently produce overlapping or even bicistronic transcripts. This extensive transcript diversity is generated by a relatively simple eukaryotic genome with limited splicing, and within a genetically homogeneous population of cells. Our findings have implications for genome compaction, evolution and phenotypic diversity between single cells. These data also indicate that isoform diversity as well as RNA abundance should be considered when assessing the functional repertoire of genomes.", "doi": "10.1038/nature12121", "pmid": "23615609", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:31:45.615Z", "modified": "2026-09-11T13:23:27.529Z"}, {"entity": "publication", "iuid": "e6a6545f29bf4e08ac6c9c6224cbf4c9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e6a6545f29bf4e08ac6c9c6224cbf4c9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e6a6545f29bf4e08ac6c9c6224cbf4c9"}}, "title": "An efficient method for genome-wide polyadenylation site mapping and RNA quantification", "authors": [{"family": "Wilkening", "given": "Stefan", "initials": "S"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "J\u00e4rvelin", "given": "Aino I", "initials": "AI"}, {"family": "Tekkedil", "given": "Manu M", "initials": "MM"}, {"family": "Anders", "given": "Simon", "initials": "S"}, {"family": "Benes", "given": "Vladimir", "initials": "V"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal-article", "published": "2013-03-01", "journal": {"volume": "41", "issn": "1362-4962", "issue": "5", "pages": "e65-e65", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The use of alternative poly(A) sites is common and affects the post-transcriptional fate of mRNA, including its stability, subcellular localization and translation. Here, we present a method to identify poly(A) sites in a genome-wide and strand-specific manner. This method, termed 3'T-fill, initially fills in the poly(A) stretch with unlabeled dTTPs, allowing sequencing to start directly after the poly(A) tail into the 3'-untranslated regions (UTR). Our comparative analysis demonstrates that it outperforms existing protocols in quality and throughput and accurately quantifies RNA levels as only one read is produced from each transcript. We use this method to characterize the diversity of polyadenylation in Saccharomyces cerevisiae, showing that alternative RNA molecules are present even in a genetically identical cell population. Finally, we observe that overlap of convergent 3'-UTRs is frequent but sharply limited by coding regions, suggesting factors that restrict compression of the yeast genome.", "doi": "10.1093/nar/gks1249", "pmid": "23295673", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:31:38.750Z", "modified": "2026-09-11T13:23:27.537Z"}, {"entity": "publication", "iuid": "b0ac3042e4bb4588a702a420e67f8090", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0ac3042e4bb4588a702a420e67f8090.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0ac3042e4bb4588a702a420e67f8090"}}, "title": "Genome-wide polyadenylation site mapping.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Wilkening", "given": "Stefan", "initials": "S"}, {"family": "J\u00e4rvelin", "given": "Aino Inkeri", "initials": "AI"}, {"family": "Tekkedil", "given": "Manu M", "initials": "MM"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal article", "published": "2012-08-30", "journal": {"title": "Meth. Enzymol.", "issn": "1557-7988", "volume": "513", "issue": null, "pages": "271-296", "issn-l": "0076-6879"}, "abstract": "Alternative polyadenylation site usage gives rise to variation in 3' ends of transcripts in diverse organisms ranging from yeast to human. Accurate mapping of polyadenylation sites of transcripts is of major biological importance, since the length of the 3'UTR can have a strong influence on transcript stability, localization, and translation. However, reads generated using total mRNA sequencing mostly lack the very 3' end of transcripts. Here, we present a method that allows simultaneous analysis of alternative 3' ends and transcriptome dynamics at high throughput. By using transcripts produced in vitro, the high precision of end mapping during the protocol can be controlled. This method is illustrated here for budding yeast. However, this method can be applied to any natural or artificially polyadenylated RNA.", "doi": "10.1016/B978-0-12-391938-0.00012-4", "pmid": "22929774", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "B978-0-12-391938-0.00012-4"}], "notes": [], "created": "2018-12-04T10:23:35.000Z", "modified": "2026-09-11T13:23:27.548Z"}, {"entity": "publication", "iuid": "3fd844aac07d461e9b9648ec14b4ab22", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3fd844aac07d461e9b9648ec14b4ab22.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3fd844aac07d461e9b9648ec14b4ab22"}}, "title": "Rrp6p Controls mRNA Poly(A) Tail Length and Its Decoration with Poly(A) Binding Proteins", "authors": [{"family": "Schmid", "given": "Manfred", "initials": "M"}, {"family": "Poulsen", "given": "Mathias Bach", "initials": "MB"}, {"family": "Olszewski", "given": "Pawel", "initials": "P"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Saguez", "given": "Cyril", "initials": "C"}, {"family": "Gupta", "given": "Ishaan", "initials": "I"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Moore", "given": "Claire", "initials": "C"}, {"family": "Jensen", "given": "Torben Heick", "initials": "TH"}], "type": "journal-article", "published": "2012-07-00", "journal": {"volume": "47", "issn": "1097-2765", "issue": "2", "pages": "267-280", "title": "Molecular Cell", "issn-l": "1097-2765"}, "abstract": "Poly(A) (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability, and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the noncanonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover, as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level.", "doi": "10.1016/j.molcel.2012.05.005", "pmid": "22683267", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:29:04.967Z", "modified": "2026-09-11T13:23:27.561Z"}, {"entity": "publication", "iuid": "d5c30c3157694ab68ae9f26c19c7dd3e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d5c30c3157694ab68ae9f26c19c7dd3e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d5c30c3157694ab68ae9f26c19c7dd3e"}}, "title": "The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast.", "authors": [{"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "Ayala", "given": "Guillermo", "initials": "G"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}, {"family": "Herrero", "given": "Enrique", "initials": "E"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal article", "published": "2012-03-30", "journal": {"title": "Transcription", "issn": "2154-1272", "volume": "3", "issue": "1", "pages": "39-44", "issn-l": null}, "abstract": "It has been recently stated that stress-responding genes in yeast are enriched in cryptic transcripts and that this is the cause of the differences observed between mRNA amount and RNA polymerase occupancy profiles. Other studies have shown that such differences are mainly due to modulation of mRNA stabilities. Here we analyze the relationship between the presence of cryptic transcripts in genes and their stress response profiles. Despite some of the stress-responding gene groups being indeed enriched in specific classes of cryptic transcripts, we found no statistically significant evidence that cryptic transcription is responsible for the differences observed between mRNA and transcription rate profiles.", "doi": "10.4161/trns.3.1.19416", "pmid": "22456320", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "19416"}, {"db": "pmc", "key": "PMC3361511"}], "notes": [], "created": "2020-10-09T14:25:42.956Z", "modified": "2026-09-11T13:23:27.575Z"}, {"entity": "publication", "iuid": "9041958dad3d4782a0dcd80a5ec9ba34", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9041958dad3d4782a0dcd80a5ec9ba34.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9041958dad3d4782a0dcd80a5ec9ba34"}}, "title": "The Conserved Foot Domain of RNA Pol II Associates with Proteins Involved in Transcriptional Initiation and/or Early Elongation", "authors": [{"family": "Garc\u00eda-L\u00f3pez", "given": "M Carmen", "initials": "MC"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Mir\u00f3n-Garc\u00eda", "given": "M Carmen", "initials": "MC"}, {"family": "Garrido-Godino", "given": "Ana I", "initials": "AI"}, {"family": "Garc\u00eda", "given": "Alicia", "initials": "A"}, {"family": "Calvo", "given": "Olga", "initials": "O"}, {"family": "Werner", "given": "Michel", "initials": "M"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Navarro", "given": "Francisco", "initials": "F"}], "type": "journal-article", "published": "2011-12-00", "journal": {"volume": "189", "issn": "0016-6731", "issue": "4", "pages": "1235-1248", "title": "Genetics", "issn-l": null}, "abstract": "RNA polymerase (pol) II establishes many protein-protein interactions with transcriptional regulators to coordinate different steps of transcription. Although some of these interactions have been well described, little is known about the existence of RNA pol II regions involved in contact with transcriptional regulators. We hypothesize that conserved regions on the surface of RNA pol II contact transcriptional regulators. We identified such an RNA pol II conserved region that includes the majority of the \"foot\" domain and identified interactions of this region with Mvp1, a protein required for sorting proteins to the vacuole, and Spo14, a phospholipase D. Deletion of MVP1 and SPO14 affects the transcription of their target genes and increases phosphorylation of Ser5 in the carboxy-terminal domain (CTD). Genetic, phenotypic, and functional analyses point to a role for these proteins in transcriptional initiation and/or early elongation, consistent with their genetic interactions with CEG1, a guanylyltransferase subunit of the Saccharomyces cerevisiae capping enzyme.", "doi": "10.1534/genetics.111.133215", "pmid": "21954159", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:27:04.860Z", "modified": "2026-09-11T13:23:27.628Z"}, {"entity": "publication", "iuid": "5a6f7f48bede40a088aed65c1a7f3a9b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5a6f7f48bede40a088aed65c1a7f3a9b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5a6f7f48bede40a088aed65c1a7f3a9b"}}, "title": "A genomic view of mRNA turnover in yeast", "authors": [{"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}], "type": "journal-article", "published": "2011-08-00", "journal": {"volume": "334", "issn": "1631-0691", "issue": "8-9", "pages": "647-654", "title": "Comptes Rendus Biologies", "issn-l": null}, "abstract": "The steady-state mRNA level is the result of two opposing processes: transcription and degradation; both of which can provide important points to regulate gene expression. In the model organism yeast Saccharomyces cerevisiae, it is now possible to determine, at the genomic level, the transcription and degradation rates, as well as the mRNA amount, using DNA chip or parallel sequencing technologies. In this way, the contribution of both rates to individual and global gene expressions can be analysed. Here we review the techniques used for the genomic evaluation of the transcription and degradation rates developed for this yeast, and we discuss the integration of the data obtained to fully analyse the expression strategies used by yeast and other eukaryotic cells.", "doi": "10.1016/j.crvi.2011.05.013", "pmid": "21819946", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:27:46.113Z", "modified": "2026-09-11T13:23:27.635Z"}, {"entity": "publication", "iuid": "5ef01dcbb21e463a80e3f60b6f0c0216", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ef01dcbb21e463a80e3f60b6f0c0216.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ef01dcbb21e463a80e3f60b6f0c0216"}}, "title": "Functional consequences of bidirectional promoters", "authors": [{"family": "Wei", "given": "Wu", "initials": "W"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "J\u00e4rvelin", "given": "Aino I", "initials": "AI"}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}], "type": "journal-article", "published": "2011-07-00", "journal": {"volume": "27", "issn": "0168-9525", "issue": "7", "pages": "267-276", "title": "Trends in Genetics", "issn-l": null}, "abstract": "Several studies have shown that promoters of protein-coding genes are origins of pervasive non-coding RNA transcription and can initiate transcription in both directions. However, only recently have researchers begun to elucidate the functional implications of this bidirectionality and non-coding RNA production. Increasing evidence indicates that non-coding transcription at promoters influences the expression of protein-coding genes, revealing a new layer of transcriptional regulation. This regulation acts at multiple levels, from modifying local chromatin to enabling regional signal spreading and more distal regulation. Moreover, the bidirectional activity of a promoter is regulated at multiple points during transcription, giving rise to diverse types of transcripts.", "doi": "10.1016/j.tig.2011.04.002", "pmid": "21601935", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:27:28.885Z", "modified": "2026-09-11T13:23:27.679Z"}, {"entity": "publication", "iuid": "59be8f2c291c4c788df599c046421df5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/59be8f2c291c4c788df599c046421df5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/59be8f2c291c4c788df599c046421df5"}}, "title": "Genomic-wide methods to evaluate transcription rates in yeast.", "authors": [{"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal article", "published": "2011-04-07", "journal": {"title": "Methods in molecular biology (Clifton, N.J.)", "issn": "1940-6029", "volume": "734", "issue": null, "pages": "25-44", "issn-l": "1064-3745"}, "abstract": "Gene transcription is a dynamic process in which the desired amount of an mRNA is obtained by the equilibrium between its transcription (TR) and degradation (DR) rates. The control mechanism at the RNA polymerase level primarily causes changes in TR. Despite their importance, TRs have been rarely measured. In the yeast Saccharomyces cerevisiae, we have implemented two techniques to evaluate TRs: run-on and chromatin immunoprecipitation of RNA polymerase II. These techniques allow the discrimination of the relative importance of TR and DR in gene regulation for the first time in a eukaryote.", "doi": "10.1007/978-1-61779-086-7_2", "pmid": "21468983", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:26:46.573Z", "modified": "2026-09-11T13:23:27.695Z"}, {"entity": "publication", "iuid": "77bece0890534055bffdd5e655d84af5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/77bece0890534055bffdd5e655d84af5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/77bece0890534055bffdd5e655d84af5"}}, "title": "A Complete Set of Nascent Transcription Rates for Yeast Genes", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal-article", "published": "2010-11-16", "journal": {"volume": "5", "issn": "1932-6203", "issue": "11", "pages": "e15442", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell.", "doi": "10.1371/journal.pone.0015442", "pmid": "21103382", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:20.719Z", "modified": "2026-09-11T13:23:27.702Z"}, {"entity": "publication", "iuid": "09d29e0e98594b0d8caef0a2d989d04a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09d29e0e98594b0d8caef0a2d989d04a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09d29e0e98594b0d8caef0a2d989d04a"}}, "title": "The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors", "authors": [{"family": "Rodr\u00edguez-Gil", "given": "Alfonso", "initials": "A"}, {"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Mu\u00f1oz-Centeno", "given": "Mar\u00eda de la Cruz", "initials": "MdlC"}, {"family": "Geli", "given": "Vincent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}], "type": "journal-article", "published": "2010-08-00", "journal": {"volume": "38", "issn": "1362-4962", "issue": "14", "pages": "4651-4664", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3'/5' RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in both cases. We detected a subset of elongation-related factors that are important for maintaining the wild-type profiles of active transcription, including DSIF, Mediator, factors related to the methylation of histone H3-lysine 4, the Bur CDK and the RNA polymerase II subunit Rpb9. We conducted a more detailed investigation of the alterations caused by rpb9Delta to find that Rpb9 contributes to the intragenic profiles of active transcription by influencing the probability of arrest of RNA polymerase II.", "doi": "10.1093/nar/gkq215", "pmid": "20385590", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:00.358Z", "modified": "2026-09-11T13:23:27.710Z"}, {"entity": "publication", "iuid": "653ceadb4bdf481a87d5a1c19f84c158", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/653ceadb4bdf481a87d5a1c19f84c158.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/653ceadb4bdf481a87d5a1c19f84c158"}}, "title": "There is a steady-state transcriptome in exponentially growing yeast cells", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal-article", "published": "2010-03-17", "journal": {"volume": "27", "issn": "0749-503X", "issue": "7", "pages": "413-422", "title": "Yeast", "issn-l": null}, "abstract": "The growth of yeast cells in batches in glucose-based media is a standard condition in most yeast laboratories. Most gene expression experiments are done by taking this condition as a reference. Presumably, cells are in a stable physiological condition that can be easily reproduced in other laboratories. With this assumption, however, it is necessary to consider that the average amount of the mRNAs per cell for most genes does not change during exponential growth. That is to say, there is a steady-state condition for the transcriptome. However, this has not been rigorously demonstrated to date. In this work we take several cell samples during the exponential phase growth to perform a kinetic study using the genomic run-on (GRO) technique, which allows simultaneous measurement of the amount of mRNA and transcription rate variation at the genomic level. We show here that the steady-state condition is fulfilled for almost all the genes during most exponential growth in yeast extract-peptone-dextrose medium (YPD) and, therefore, that simultaneous measures of the transcription rates and the amounts of mRNA can be used for indirect mRNA stability calculations. With this kinetic approach, we were also able to determine the relative influence of the transcription rate and the mRNA stability changes for the mRNA variation for those genes that deviate from the steady state.", "doi": "10.1002/yea.1768", "pmid": "20301094", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:46.335Z", "modified": "2026-09-11T13:23:27.736Z"}, {"entity": "publication", "iuid": "ad57f87a0c774384b5e06be93ddc9165", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad57f87a0c774384b5e06be93ddc9165.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad57f87a0c774384b5e06be93ddc9165"}}, "title": "Regulon-specific control of transcription elongation across the yeast genome.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Jimeno-Gonz\u00e1lez", "given": "Silvia", "initials": "S"}, {"family": "Rodr\u00edguez-Gil", "given": "Alfonso", "initials": "A"}, {"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}], "type": "journal article", "published": "2009-08-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "5", "issue": "8", "pages": "e1000614", "issn-l": "1553-7390"}, "abstract": "Transcription elongation by RNA polymerase II was often considered an invariant non-regulated process. However, genome-wide studies have shown that transcriptional pausing during elongation is a frequent phenomenon in tightly-regulated metazoan genes. Using a combination of ChIP-on-chip and genomic run-on approaches, we found that the proportion of transcriptionally active RNA polymerase II (active versus total) present throughout the yeast genome is characteristic of some functional gene classes, like those related to ribosomes and mitochondria. This proportion also responds to regulatory stimuli mediated by protein kinase A and, in relation to cytosolic ribosomal-protein genes, it is mediated by the silencing domain of Rap1. We found that this inactive form of RNA polymerase II, which accumulates along the full length of ribosomal protein genes, is phosphorylated in the Ser5 residue of the CTD, but is hypophosphorylated in Ser2. Using the same experimental approach, we show that the in vivo-depletion of FACT, a chromatin-related elongation factor, also produces a regulon-specific effect on the expression of the yeast genome. This work demonstrates that the regulation of transcription elongation is a widespread, gene class-dependent phenomenon that also affects housekeeping genes.", "doi": "10.1371/journal.pgen.1000614", "pmid": "19696888", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pmc", "key": "PMC2721418"}], "notes": [], "created": "2020-10-09T14:28:27.313Z", "modified": "2026-09-11T13:23:27.769Z"}, {"entity": "publication", "iuid": "1242184ccb984faca9e226c5dd4a8939", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1242184ccb984faca9e226c5dd4a8939.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1242184ccb984faca9e226c5dd4a8939"}}, "title": "The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal article", "published": "2008-02-00", "journal": {"title": "Yeast", "issn": "0749-503X", "volume": "25", "issue": "2", "pages": "85-92", "issn-l": null}, "abstract": "Thiolutin is commonly used as a general inhibitor of transcription in yeast. It has been used to calculate mRNA decay rates by stopping the transcription and then determining the relative abundance of individual mRNAs at different times after inhibition. We report here that thiolutin is also an inhibitor of mRNA degradation, and thus its use can lead to miscalculations of mRNA half-lives. The inhibition of mRNA decay seems to affect the mRNA degradation pathway without impeding poly(A) shortening, given that the decay rate of total poly(A) amount is not reduced by thiolutin. Moreover, the thiolutin-dependent inhibition of mRNA degradation has variable effects on different functional groups of genes, suggesting that they use various degradation pathways for their mRNAs.", "doi": "10.1002/yea.1548", "pmid": "17914747", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:28:47.698Z", "modified": "2026-09-11T13:23:27.790Z"}, {"entity": "publication", "iuid": "d68fe236c52347a381b672b1209cdb30", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d68fe236c52347a381b672b1209cdb30.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d68fe236c52347a381b672b1209cdb30"}}, "title": "A genomic study of the inter-ORF distances in Saccharomyces cerevisiae.", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal article", "published": "2006-07-15", "journal": {"title": "Yeast", "issn": "0749-503X", "volume": "23", "issue": "9", "pages": "689-699", "issn-l": null}, "abstract": "The genome of eukaryotic microbes is usually quite compacted. The yeast Saccharomyces cerevisiae is one of the best-known examples. Open reading frames (ORFs) occupy about 75% of the total DNA sequence. The existence of other, non-protein coding genes and other genetic elements leaves very little space for gene promoters and terminators. We have performed an in silico study of inter-ORF distances that shows that there is a minimum distance between two adjacent ORFs that depends on the relative orientation between them. Our analyses suggest that different kinds of promoters and terminators exist with regard to their length and ability to overlap each other. The experimental testing of some putative exceptions to the minimum length model in tandemly orientated ORF pairs suggests that, in those cases, defects in promoter or terminator functionality exist that provoke transcription of polycistronic mRNAs.", "doi": "10.1002/yea.1390", "pmid": "16845687", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [], "notes": [], "created": "2020-10-09T14:29:08.530Z", "modified": "2026-09-11T13:23:27.797Z"}]}