{"entity": "researcher", "timestamp": "2026-08-15T13:17:26.068Z", "family": "Navarro", "given": "F", "initials": "F", "orcid": "0000-0002-4180-422X", "affiliations": ["Departamento de Biolog\u00eda Experimental-Gen\u00e9tica, Universidad de Ja\u00e9n, Ja\u00e9n, Spain", "Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Ja\u00e9n, Ja\u00e9n, Spain"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/2abed56af56f41fcb118d39f21b9a8e5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/2abed56af56f41fcb118d39f21b9a8e5"}}, "publications": [{"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": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1874-9399(23)00090-1"}], "notes": [], "created": "2023-11-23T09:13:48.750Z", "modified": "2025-04-08T06:12:37.945Z"}, {"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": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10778713"}, {"db": "pii", "key": "ijms25010507"}], "notes": [], "created": "2024-11-26T08:29:47.844Z", "modified": "2024-11-26T08:29:47.885Z"}, {"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": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8244751"}], "notes": [], "created": "2020-11-28T17:34:48.540Z", "modified": "2022-11-04T11:32:12.747Z"}]}