{"entity": "researcher", "timestamp": "2026-08-15T13:00:52.168Z", "family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "affiliations": ["Faculty of Science and Engineering, Cell Biology, \u00c5bo Akademi University, Turku, Finland.", "Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland.", "KTH Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713"}}, "publications": [{"entity": "publication", "iuid": "c01198fedcdf445cb43469abd027afdc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c01198fedcdf445cb43469abd027afdc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c01198fedcdf445cb43469abd027afdc"}}, "title": "Flipping a switch on BRD4: How to control the do-it-all.", "authors": [{"family": "van Hout", "given": "Femke A H", "initials": "FAH"}, {"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}], "type": "journal article", "published": "2024-11-21", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "84", "issue": "22", "pages": "4257-4259", "issn-l": "1097-2765"}, "abstract": "In this issue, Devaiah et al.1 identify JNK-catalyzed phosphorylation to convert bromodomain-containing protein 4 (BRD4) from a chromatin regulator to a transcription activator.", "doi": "10.1016/j.molcel.2024.10.039", "pmid": "39577398", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1097-2765(24)00879-7"}], "notes": [], "created": "2024-11-28T10:59:52.257Z", "modified": "2025-04-07T06:56:07.502Z"}, {"entity": "publication", "iuid": "0de25be8391c4b48b5027a6ce1eacf11", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0de25be8391c4b48b5027a6ce1eacf11.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0de25be8391c4b48b5027a6ce1eacf11"}}, "title": "CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses.", "authors": [{"family": "Prajapati", "given": "Bina", "initials": "B"}, {"family": "Sokolova", "given": "Maria", "initials": "M"}, {"family": "Sidorenko", "given": "Ekaterina", "initials": "E"}, {"family": "Kyriacou", "given": "Mikael", "initials": "M"}, {"family": "Kyher\u00f6inen", "given": "Salla", "initials": "S"}, {"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}, {"family": "Vartiainen", "given": "Maria K", "initials": "MK", "orcid": "0000-0002-2017-0475", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/621897c9b10541df95d8462481eaf0d9.json"}}], "type": "journal article", "published": "2024-07-01", "journal": {"title": "J. Cell. Sci.", "issn": "1477-9137", "volume": "137", "issue": "13", "issn-l": "0021-9533"}, "abstract": "Myocardin-related transcription factors (MRTFs) are coactivators of serum response factor (SRF), and thereby regulate cytoskeletal gene expression in response to actin dynamics. MRTFs have also been implicated in transcription of heat shock protein (HSP)-encoding genes in fly ovaries, but the mechanisms remain unclear. Here, we demonstrate that, in mammalian cells, MRTFs are dispensable for gene induction of HSP-encoding genes. However, the widely used small-molecule inhibitors of the MRTF-SRF transcription pathway, derived from CCG-1423, also efficiently inhibit gene transcription of HSP-encoding genes in both fly and mammalian cells in the absence of MRTFs. Quantifying RNA synthesis and RNA polymerase distribution demonstrates that CCG-1423-derived compounds have a genome-wide effect on transcription. Indeed, tracking nascent transcription at nucleotide resolution reveals that CCG-1423-derived compounds reduce RNA polymerase II elongation, and severely dampen the transcriptional response to heat shock. The effects of CCG-1423-derived compounds therefore extend beyond the MRTF-SRF pathway into nascent transcription, opening novel opportunities for their use in transcription research.", "doi": "10.1242/jcs.261790", "pmid": "38841882", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "361133"}], "notes": [], "created": "2024-11-28T11:00:16.838Z", "modified": "2024-11-28T11:00:16.883Z"}, {"entity": "publication", "iuid": "e828ce675a4841d8b424e2589dfe0caa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e828ce675a4841d8b424e2589dfe0caa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e828ce675a4841d8b424e2589dfe0caa"}}, "title": "Stress biology: Complexity and multifariousness in health and disease.", "authors": [{"family": "Mayer", "given": "Matthias P", "initials": "MP"}, {"family": "Blair", "given": "Laura", "initials": "L"}, {"family": "Blatch", "given": "Gregory L", "initials": "GL"}, {"family": "Borges", "given": "Thiago J", "initials": "TJ"}, {"family": "Chadli", "given": "Ahmed", "initials": "A"}, {"family": "Chiosis", "given": "Gabriela", "initials": "G"}, {"family": "de Thonel", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0003-0405-0745", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07a4bbc138414fcc9b423a44474c94ab.json"}}, {"family": "Dinkova-Kostova", "given": "Albena", "initials": "A"}, {"family": "Ecroyd", "given": "Heath", "initials": "H"}, {"family": "Edkins", "given": "Adrienne L", "initials": "AL"}, {"family": "Eguchi", "given": "Takanori", "initials": "T"}, {"family": "Fleshner", "given": "Monika", "initials": "M"}, {"family": "Foley", "given": "Kevin P", "initials": "KP"}, {"family": "Fragkostefanakis", "given": "Sotirios", "initials": "S"}, {"family": "Gestwicki", "given": "Jason", "initials": "J"}, {"family": "Goloubinoff", "given": "Pierre", "initials": "P"}, {"family": "Heritz", "given": "Jennifer A", "initials": "JA"}, {"family": "Heske", "given": "Christine M", "initials": "CM"}, {"family": "Hibshman", "given": "Jonathan D", "initials": "JD"}, {"family": "Joutsen", "given": "Jenny", "initials": "J"}, {"family": "Li", "given": "Wei", "initials": "W", "orcid": "0000-0003-3344-1403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a26a8c8ad0c4fb2a03f541eac672081.json"}}, {"family": "Lynes", "given": "Michael", "initials": "M"}, {"family": "Mendillo", "given": "Marc L", "initials": "ML"}, {"family": "Mivechi", "given": "Nahid", "initials": "N"}, {"family": "Mokoena", "given": "Fortunate", "initials": "F"}, {"family": "Okusha", "given": "Yuka", "initials": "Y"}, {"family": "Prahlad", "given": "Veena", "initials": "V"}, {"family": "Repasky", "given": "Elizabeth", "initials": "E"}, {"family": "Sannino", "given": "Sara", "initials": "S"}, {"family": "Scalia", "given": "Federica", "initials": "F"}, {"family": "Shalgi", "given": "Reut", "initials": "R"}, {"family": "Sistonen", "given": "Lea", "initials": "L", "orcid": "0000-0003-1341-2867", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aafaee6a2aca4f4783add9775d660b74.json"}}, {"family": "Sontag", "given": "Emily", "initials": "E"}, {"family": "van Oosten-Hawle", "given": "Patricija", "initials": "P"}, {"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}, {"family": "Wickramaratne", "given": "Anushka", "initials": "A"}, {"family": "Wang", "given": "Shawn Xiang Yang", "initials": "SXY"}, {"family": "Zininga", "given": "Tawanda", "initials": "T"}], "type": "congress", "published": "2024-02-00", "journal": {"title": "Cell Stress Chaperones", "issn": "1466-1268", "volume": "29", "issue": "1", "pages": "143-157", "issn-l": null}, "abstract": "Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response, unfolded protein response, and integrated stress response, that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate the expression of most genes but increase the expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in the repair of stress-induced damage to macromolecules and cellular structures. Sixty-one years after the discovery of the heat shock response by Ferruccio Ritossa, many aspects of stress biology are still enigmatic. Recent progress in the understanding of stress responses and molecular chaperones was reported at the 12th International Symposium on Heat Shock Proteins in Biology, Medicine and the Environment in the Old Town Alexandria, VA, USA from 28th to 31st of October 2023.", "doi": "10.1016/j.cstres.2024.01.006", "pmid": "38311120", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10939078"}, {"db": "pii", "key": "S1355-8145(24)00046-4"}], "notes": [], "created": "2024-11-28T11:01:05.447Z", "modified": "2025-04-08T06:14:10.081Z"}, {"entity": "publication", "iuid": "c62fa1e5013c45b3952af1abfb63a3c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c62fa1e5013c45b3952af1abfb63a3c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c62fa1e5013c45b3952af1abfb63a3c7"}}, "title": "Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release.", "authors": [{"family": "Wang", "given": "Zhijia", "initials": "Z", "orcid": "0000-0003-4260-6193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/17262be8acb2493ebab23bc6f8bf2820.json"}}, {"family": "Himanen", "given": "Samu V", "initials": "SV", "orcid": "0000-0001-6927-9570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20bf49a0bd5443389978c873eea2fa0f.json"}}, {"family": "Haikala", "given": "Heidi M", "initials": "HM", "orcid": "0000-0002-8465-8568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59d7803a047048e0bb5cba52449a7b5d.json"}}, {"family": "Friedel", "given": "Caroline C", "initials": "CC", "orcid": "0000-0003-3569-4877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c605718115a440095d54f1599067989.json"}}, {"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}, {"family": "Barbori\u010d", "given": "Matja\u017e", "initials": "M", "orcid": "0000-0002-9715-2291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07252a70009b44f0b146b10395f9ce13.json"}}], "type": "journal article", "published": "2023-11-10", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "20", "pages": "10970-10991", "issn-l": "0305-1048"}, "abstract": "P-TEFb and CDK12 facilitate transcriptional elongation by RNA polymerase II. Given the prominence of both kinases in cancer, gaining a better understanding of their interplay could inform the design of novel anti-cancer strategies. While down-regulation of DNA repair genes in CDK12-targeted cancer cells is being explored therapeutically, little is known about mechanisms and significance of transcriptional induction upon inhibition of CDK12. We show that selective targeting of CDK12 in colon cancer-derived cells activates P-TEFb via its release from the inhibitory 7SK snRNP. In turn, P-TEFb stimulates Pol II pause release at thousands of genes, most of which become newly dependent on P-TEFb. Amongst the induced genes are those stimulated by hallmark pathways in cancer, including p53 and NF-\u03baB. Consequently, CDK12-inhibited cancer cells exhibit hypersensitivity to inhibitors of P-TEFb. While blocking P-TEFb triggers their apoptosis in a p53-dependent manner, it impedes cell proliferation irrespective of p53 by preventing induction of genes downstream of the DNA damage-induced NF-\u03baB signaling. In summary, stimulation of Pol II pause release at the signal-responsive genes underlies the functional dependence of CDK12-inhibited cancer cells on P-TEFb. Our study establishes the mechanistic underpinning for combinatorial targeting of CDK12 with either P-TEFb or the induced oncogenic pathways in cancer.", "doi": "10.1093/nar/gkad792", "pmid": "37811895", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10639066"}, {"db": "pii", "key": "7301302"}], "notes": [], "created": "2023-12-03T19:25:35.262Z", "modified": "2023-12-03T19:25:35.447Z"}, {"entity": "publication", "iuid": "39baaebf92ae4f5bbc420f0e6ababd12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/39baaebf92ae4f5bbc420f0e6ababd12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/39baaebf92ae4f5bbc420f0e6ababd12"}}, "title": "PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.", "authors": [{"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}, {"family": "Versluis", "given": "Philip", "initials": "P"}, {"family": "Himanen", "given": "Samu V", "initials": "SV"}, {"family": "Lis", "given": "John T", "initials": "JT", "orcid": "0000-0003-1201-9406", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/335178e3d37d4102a2fea5a7c75fdb3b.json"}}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "7039", "issn-l": "2041-1723"}, "abstract": "RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we develop Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq), which double-selects nascent RNAs and transcription complexes, and track phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncover precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide (+1 nt), through early (+18 to +30 nt) and late (+31 to +60 nt) promoter-proximal pause, and into productive elongation. Pol II CTD is predominantly unphosphorylated from initiation until the early pause-region, whereas serine-2- and serine-5-phosphorylations are preferentially deposited in the later pause-region. Upon pause-release, serine-7-phosphorylation rapidly increases and dominates over the region where Pol II assembles elongation factors and accelerates to its full elongational speed. Interestingly, tracking CTD modifications upon heat-induced transcriptional reprogramming demonstrates that Pol II with phosphorylated CTD remains paused on thousands of heat-repressed genes. These results uncover dynamic Pol II regulation at rate-limiting steps of transcription and provide a nucleotide-resolution technique for tracking composition of engaged transcription complexes.", "doi": "10.1038/s41467-023-42715-3", "pmid": "37923726", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10624850"}, {"db": "pii", "key": "10.1038/s41467-023-42715-3"}], "notes": [], "created": "2023-12-03T19:23:57.862Z", "modified": "2023-12-03T19:23:57.921Z"}, {"entity": "publication", "iuid": "da5bb1e8f3ce455aa73f337380aafda5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/da5bb1e8f3ce455aa73f337380aafda5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/da5bb1e8f3ce455aa73f337380aafda5"}}, "title": "CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder.", "authors": [{"family": "de Thonel", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0003-0405-0745", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07a4bbc138414fcc9b423a44474c94ab.json"}}, {"family": "Ahlskog", "given": "Johanna K", "initials": "JK"}, {"family": "Daupin", "given": "Kevin", "initials": "K", "orcid": "0000-0003-3303-2319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1354bb9b65aa43f6911f457be0f2ab18.json"}}, {"family": "Dubreuil", "given": "V\u00e9ronique", "initials": "V"}, {"family": "Berthelet", "given": "J\u00e9r\u00e9my", "initials": "J"}, {"family": "Chaput", "given": "Carole", "initials": "C", "orcid": "0000-0003-4493-000X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e92e93dfaa46471ea26caef26537dc91.json"}}, {"family": "Pires", "given": "Geoffrey", "initials": "G"}, {"family": "Leonetti", "given": "Camille", "initials": "C"}, {"family": "Abane", "given": "Ryma", "initials": "R"}, {"family": "Barris", "given": "Llu\u00eds Cord\u00f3n", "initials": "LC"}, {"family": "Leray", "given": "Isabelle", "initials": "I"}, {"family": "Aalto", "given": "Anna L", "initials": "AL", "orcid": "0000-0001-5503-6447", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f15b3b1268a94fd68149b2c8263a6278.json"}}, {"family": "Naceri", "given": "Sarah", "initials": "S"}, {"family": "Cordonnier", "given": "Marine", "initials": "M"}, {"family": "Benasolo", "given": "Car\u00e8ne", "initials": "C"}, {"family": "Sanial", "given": "Matthieu", "initials": "M", "orcid": "0000-0002-0301-4710", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae90775801d6472c8ce761020762b73f.json"}}, {"family": "Duchateau", "given": "Agathe", "initials": "A"}, {"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}, {"family": "Puustinen", "given": "Mikael C", "initials": "MC"}, {"family": "Miozzo", "given": "Federico", "initials": "F", "orcid": "0000-0003-0818-9525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d27415e4312e4388bffd8d2b4c6709d1.json"}}, {"family": "Fergelot", "given": "Patricia", "initials": "P"}, {"family": "Lebigot", "given": "\u00c9lise", "initials": "\u00c9", "orcid": "0000-0003-0419-8547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/11947ffcdf7149f7b7046c1201db5094.json"}}, {"family": "Verloes", "given": "Alain", "initials": "A"}, {"family": "Gressens", "given": "Pierre", "initials": "P", "orcid": "0000-0002-0909-4221", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a57e0e7e8f2345548e3eb25bc6d50e5b.json"}}, {"family": "Lacombe", "given": "Didier", "initials": "D"}, {"family": "Gobbo", "given": "Jessica", "initials": "J"}, {"family": "Garrido", "given": "Carmen", "initials": "C"}, {"family": "Westerheide", "given": "Sandy D", "initials": "SD"}, {"family": "David", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3594-0353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e94140d0e074c9d986c6982572e6e76.json"}}, {"family": "Petitjean", "given": "Michel", "initials": "M", "orcid": "0000-0002-1745-5402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0390569852ee4418a31e12e1a298585f.json"}}, {"family": "Taboureau", "given": "Olivier", "initials": "O"}, {"family": "Rodrigues-Lima", "given": "Fernando", "initials": "F"}, {"family": "Passemard", "given": "Sandrine", "initials": "S"}, {"family": "Sab\u00e9ran-Djoneidi", "given": "D\u00e9lara", "initials": "D", "orcid": "0000-0002-2757-6419", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7497cc68bb884df8b6af4ce0f506dff2.json"}}, {"family": "Nguyen", "given": "Laurent", "initials": "L"}, {"family": "Lancaster", "given": "Madeline", "initials": "M", "orcid": "0000-0003-2324-8853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/517deea851cc4d57839b21688037b477.json"}}, {"family": "Sistonen", "given": "Lea", "initials": "L", "orcid": "0000-0003-1341-2867", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aafaee6a2aca4f4783add9775d660b74.json"}}, {"family": "Mezger", "given": "Val\u00e9rie", "initials": "V", "orcid": "0000-0003-1623-6213", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/404dcbf8cb4f42229b59804c743168ce.json"}}], "type": "journal article", "published": "2022-11-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "7002", "issn-l": "2041-1723"}, "abstract": "Patients carrying autosomal dominant mutations in the histone/lysine acetyl transferases CBP or EP300 develop a neurodevelopmental disorder: Rubinstein-Taybi syndrome (RSTS). The biological pathways underlying these neurodevelopmental defects remain elusive. Here, we unravel the contribution of a stress-responsive pathway to RSTS. We characterize the structural and functional interaction between CBP/EP300 and heat-shock factor 2 (HSF2), a tuner of brain cortical development and major player in prenatal stress responses in the neocortex: CBP/EP300 acetylates HSF2, leading to the stabilization of the HSF2 protein. Consequently, RSTS patient-derived primary cells show decreased levels of HSF2 and HSF2-dependent alteration in their repertoire of molecular chaperones and stress response. Moreover, we unravel a CBP/EP300-HSF2-N-cadherin cascade that is also active in neurodevelopmental contexts, and show that its deregulation disturbs neuroepithelial integrity in 2D and 3D organoid models of cerebral development, generated from RSTS patient-derived iPSC cells, providing a molecular reading key for this complex pathology.", "doi": "10.1038/s41467-022-34476-2", "pmid": "36385105", "labels": {"SciLifeLab Fellow": null, "Anniina Vihervaara": null}, "xrefs": [{"db": "pmc", "key": "PMC9668993"}, {"db": "pii", "key": "10.1038/s41467-022-34476-2"}], "notes": [], "created": "2022-12-01T12:21:04.038Z", "modified": "2022-12-01T12:21:04.513Z"}, {"entity": "publication", "iuid": "5f3497d661e341fb87e2d58c8444b25b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5f3497d661e341fb87e2d58c8444b25b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5f3497d661e341fb87e2d58c8444b25b"}}, "title": "Nascent RNA analyses: tracking transcription and its regulation.", "authors": [{"family": "Wissink", "given": "Erin M", "initials": "EM", "orcid": "0000-0003-1054-4899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/970cfdfb193b476f8ddcdc63424f627c.json"}}, {"family": "Vihervaara", "given": "Anniina", "initials": "A", "orcid": "0000-0001-6256-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18141880ac7c4db3a6bc41f43ec03713.json"}}, {"family": "Tippens", "given": "Nathaniel D", "initials": "ND"}, {"family": "Lis", "given": "John T", "initials": "JT", "orcid": "0000-0003-1201-9406", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/335178e3d37d4102a2fea5a7c75fdb3b.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Nat. Rev. Genet.", "issn": "1471-0064", "volume": "20", "issue": "12", "pages": "705-723", "issn-l": "1471-0056"}, "abstract": "The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.", "doi": "10.1038/s41576-019-0159-6", "pmid": "31399713", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1048955"}, {"db": "pmc", "key": "PMC6858503"}, {"db": "pii", "key": "10.1038/s41576-019-0159-6"}], "notes": [], "created": "2023-12-03T19:27:49.045Z", "modified": "2023-12-03T19:27:49.101Z"}]}