{"doi":"10.1261/rna.041129.113","title":"Rat1p maintains RNA polymerase II CTD phosphorylation balance","abstract":"<jats:p>In<jats:italic>S. cerevisiae</jats:italic>, the 5′-3′ exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understood. Here we describe a function of Rat1p in regulating phosphorylation levels of the C-terminal domain (CTD) of the largest RNAPII subunit, Rpb1p, during transcription elongation. The<jats:italic>rat1-1</jats:italic>mutant exhibits highly elevated levels of CTD phosphorylation as well as RNAPII distribution and transcription termination defects. These phenotypes are all rescued by overexpression of the CTD phosphatase Fcp1p, suggesting a functional relationship between the absence of Rat1p activity, elevated CTD phosphorylation, and transcription defects. We also demonstrate that<jats:italic>rat1-1</jats:italic>cells display increased RNAPII transcription kinetics, a feature that may contribute to the cellular phenotypes of the mutant. Consistently, the<jats:italic>rat1-1</jats:italic>allele is synthetic lethal with the<jats:italic>rpb1-E1103G</jats:italic>mutation, causing increased RNAPII speed, and is suppressed by the<jats:italic>rpb2-10</jats:italic>mutation, causing slowed transcription. Thus, Rat1p plays more complex roles in controlling transcription than previously thought.</jats:p>","journal":"RNA","year":2014,"id":598808,"datarank":0.41588830833596724,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.0,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":463096,"name":"Manfred Schmid","orcid":"0000-0003-0516-3055","position":1,"is_corresponding":false},{"id":1534657,"name":"Francisco Malagon","orcid":null,"position":2,"is_corresponding":false},{"id":1534658,"name":"Line Lindegaard Haaning","orcid":null,"position":3,"is_corresponding":false},{"id":463099,"name":"Torben Heick Jensen","orcid":"0000-0001-5127-1239","position":4,"is_corresponding":false},{"id":1534654,"name":"Silvia Jimeno-González","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Rat1p maintains RNA polymerase II CTD phosphorylation balance","abstract":"<jats:p>In<jats:italic>S. cerevisiae</jats:italic>, the 5′-3′ exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understood. Here we describe a function of Rat1p in regulating phosphorylation levels of the C-terminal domain (CTD) of the largest RNAPII subunit, Rpb1p, during transcription elongation. The<jats:italic>rat1-1</jats:italic>mutant exhibits highly elevated levels of CTD phosphorylation as well as RNAPII distribution and transcription termination defects. These phenotypes are all rescued by overexpression of the CTD phosphatase Fcp1p, suggesting a functional relationship between the absence of Rat1p activity, elevated CTD phosphorylation, and transcription defects. We also demonstrate that<jats:italic>rat1-1</jats:italic>cells display increased RNAPII transcription kinetics, a feature that may contribute to the cellular phenotypes of the mutant. Consistently, the<jats:italic>rat1-1</jats:italic>allele is synthetic lethal with the<jats:italic>rpb1-E1103G</jats:italic>mutation, causing increased RNAPII speed, and is suppressed by the<jats:italic>rpb2-10</jats:italic>mutation, causing slowed transcription. Thus, Rat1p plays more complex roles in controlling transcription than previously thought.</jats:p>","is_dataset_classified":null,"base_score":2.772588722239781,"endowment":2.772588722239781,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24501251","pmcid":"PMC3964916","openalex_id":"https://openalex.org/W2134800947","authors":[],"funders":[{"funder_name":"Fundação para a Ciência e a Tecnologia, I.P.","grant_id":"JPCOFUND/0004/2015","title":"Development of a Novel Multicellular In Vitro Model of Alzheimer’s disease-like Blood-Brain Barrier"}],"total_grants":1,"fwci":1.2564,"citation_percentile":0.79382419,"influential_citations":0,"citation_trend":[{"year":2014,"count":2},{"year":2015,"count":1},{"year":2016,"count":4},{"year":2017,"count":2},{"year":2018,"count":2},{"year":2020,"count":1},{"year":2021,"count":1},{"year":2024,"count":1},{"year":2025,"count":1}],"oa_status":"bronze","license":"CC BY NC","oa_locations":[{"url":"http://rnajournal.cshlp.org/content/20/4/551.full.pdf","host_type":"journal"},{"url":"http://rnajournal.cshlp.org/content/20/4/551.full.pdf","host_type":"publisher"},{"url":"https://syndication.highwire.org/content/doi/10.1261/rna.041129.113","host_type":"publisher"},{"url":"https://doi.org/10.1261/rna.041129.113","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24501251","host_type":"repository"},{"url":"http://hdl.handle.net/10261/123525","host_type":"repository"},{"url":"https://idus.us.es/handle//11441/82624","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3964916","host_type":"repository"},{"url":"http://rnajournal.cshlp.org/cgi/content/short/20/4/551","host_type":"repository"},{"url":"https://pure.au.dk/portal/en/publications/0afefb9e-aeef-46ca-b247-61ced7c21086","host_type":""},{"url":"https://europepmc.org/articles/PMC3964916","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3964916?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1261/rna.041129.113","host_type":""},{"url":"https://hdl.handle.net/11441/82624","host_type":""},{"url":"https://dx.doi.org/10.1261/rna.041129.113","host_type":""},{"url":"https://pure.au.dk/ws/files/81418148/Jimeno_Gonza_lez_2014.pdf","host_type":""}],"fields_of_study":["RNA Research and Splicing","RNA modifications and cancer","Cancer-related gene regulation","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Chromatin","Exoribonucleases","Phenotype","Phosphoprotein Phosphatases","Phosphorylation","Protein Kinases","RNA Polymerase II","Saccharomyces cerevisiae","Serine","Transcription, Genetic","Blotting, Western","Protein Structure, Tertiary","Saccharomyces cerevisiae Proteins","Chromatin Immunoprecipitation"],"keywords":["Biology","RNA polymerase II","CTD","Phosphorylation","Polymerase","Computational biology","Cell biology","Genetics","Oceanography","Gene","Gene expression","Promoter","Transcription Elongation","Transcription Termination","Ctd Phosphorylation","Chromatin Immunoprecipitation","Saccharomyces cerevisiae Proteins","Transcription, Genetic","Blotting, Western","Articles","Saccharomyces cerevisiae","Chromatin","Protein Structure, Tertiary","Phenotype","Exoribonucleases","Phosphoprotein Phosphatases","Serine","Protein Kinases"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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