{"doi":"10.1038/nsmb.1913","title":"Gene-specific RNA polymerase II phosphorylation and the CTD code","abstract":null,"journal":"Nature Structural & Molecular Biology","year":2010,"id":629147,"datarank":0.8157118963384794,"base_score":5.438079308923196,"endowment":5.438079308923196,"self_citation_contribution":0.8157118963384794,"citation_network_contribution":0.0,"self_endowment_contribution":0.8157118963384794,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":229,"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":1439678,"name":"Benjamin Erickson","orcid":"0009-0000-5605-3783","position":1,"is_corresponding":false},{"id":1629239,"name":"Weifei Luo","orcid":null,"position":2,"is_corresponding":false},{"id":1629240,"name":"David Seward","orcid":null,"position":3,"is_corresponding":false},{"id":1629241,"name":"Joel H Graber","orcid":null,"position":4,"is_corresponding":false},{"id":1629242,"name":"David D Pollock","orcid":null,"position":5,"is_corresponding":false},{"id":1629243,"name":"Paul C Megee","orcid":null,"position":6,"is_corresponding":false},{"id":1629244,"name":"David L Bentley","orcid":null,"position":7,"is_corresponding":false},{"id":381030,"name":"Hyunmin Kim","orcid":"0000-0003-0835-5044","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Gene-specific RNA polymerase II phosphorylation and the CTD code","abstract":"Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to transcription and may act as a 'code' that controls mRNA synthesis and processing. To examine the code in budding yeast, we mapped genome-wide CTD Ser2, Ser5 and Ser7 phosphorylations and the CTD-associated termination factors Nrd1 and Pcf11. Phospho-CTD dynamics are not scaled to gene length and are gene-specific, with highest Ser5 and Ser7 phosphorylation at the 5' ends of well-expressed genes with nucleosome-occupied promoters. The CTD kinases Kin28 and Ctk1 markedly affect Pol II distribution in a gene-specific way. The code is therefore written differently on different genes, probably under the control of promoters. Ser7 phosphorylation is enriched on introns and at sites of Nrd1 accumulation, suggesting links to splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III-transcribed genes.","is_dataset_classified":null,"base_score":5.438079308923196,"endowment":5.438079308923196,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"20835241","pmcid":"PMC3048030","openalex_id":"https://openalex.org/W2151298550","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"3R01GM063873-06S1","title":"Elongation and termination of transcripts by RNA pol II"},{"funder_name":"NIGMS NIH HHS","grant_id":"GM58613","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM058613","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM083127","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM066213","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"GM066213","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM072706","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM063873","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R01GM066213-02","title":"Molecular Anal. of Pericentric Sister Chromatid Cohesion"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM058613-04","title":"COUPLING OF TRANSCRIPTION WITH 5 AND 3 MRNA PROCESSING"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM083127-07","title":"Modeling evolution of functional context in proteins"},{"funder_name":"Howard Hughes Medical Institute","grant_id":"","title":null},{"funder_name":"Howard Hughes Medical Institute","grant_id":"","title":null}],"total_grants":13,"fwci":12.4488,"citation_percentile":0.99284219,"influential_citations":0,"citation_trend":[{"year":2012,"count":43},{"year":2013,"count":35},{"year":2014,"count":29},{"year":2015,"count":19},{"year":2016,"count":11},{"year":2017,"count":14},{"year":2018,"count":9},{"year":2019,"count":12},{"year":2020,"count":9},{"year":2021,"count":6},{"year":2022,"count":3},{"year":2023,"count":6},{"year":2024,"count":6},{"year":2025,"count":5}],"oa_status":"green","license":"Springer TDM","oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3048030","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3048030","host_type":"repository"},{"url":"http://www.nature.com/articles/nsmb.1913.pdf","host_type":"publisher"},{"url":"http://www.nature.com/articles/nsmb.1913","host_type":"publisher"},{"url":"https://doi.org/10.1038/nsmb.1913","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/20835241","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3048030","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3048030?pdf=render","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/pmc3048030?pdf=render","host_type":""},{"url":"https://dx.doi.org/10.1038/nsmb.1913","host_type":""}],"fields_of_study":["RNA Research and Splicing","Genomics and Chromatin Dynamics","RNA and protein synthesis mechanisms","0301 basic medicine","03 medical and health sciences","0303 health sciences","Chromatin Immunoprecipitation","Cyclin-Dependent Kinases","DNA, Fungal","Genes, Fungal","Genome-Wide Association Study","Introns","Macromolecular Substances","Models, Genetic","Phosphorylation","Phosphoserine","Promoter Regions, Genetic","Protein Kinases","Protein Processing, Post-Translational","RNA Polymerase II","RNA, Fungal","RNA, Messenger","RNA-Binding Proteins","Saccharomyces cerevisiae","Saccharomyces cerevisiae Proteins","Transcription, Genetic","mRNA Cleavage and Polyadenylation Factors"],"mesh_terms":["DNA, Fungal","Genes, Fungal","Introns","Models, Genetic","Phosphorylation","Phosphoserine","Promoter Regions, Genetic","Protein Kinases","Protein Processing, Post-Translational","RNA Polymerase II","RNA, Fungal","RNA, Messenger","Saccharomyces cerevisiae","Transcription, Genetic","RNA-Binding Proteins","Cyclin-Dependent Kinases","Saccharomyces cerevisiae Proteins","mRNA Cleavage and Polyadenylation Factors","Macromolecular Substances","Chromatin Immunoprecipitation","Genome-Wide Association Study"],"keywords":["RNA polymerase II","CTD","Promoter","Transcription factor II D","Biology","Transcription (linguistics)","Molecular biology","Intron","Gene","RNA polymerase II holoenzyme","Cell biology","Genetics","Gene expression","mRNA-Cleavage-and-Polyadenylation-Factors","Chromatin Immunoprecipitation","Saccharomyces cerevisiae Proteins","Transcription, Genetic","Macromolecular Substances","Transcription-Genetic","Genes, Fungal","RNA-Polymerase-II","RNA-Binding-Proteins","610","Models-Genetic","Saccharomyces-cerevisiae","Saccharomyces cerevisiae","Macromolecular-Substances","Saccharomyces-cerevisiae-Proteins","Phosphoserine","RNA, Messenger","Phosphorylation","DNA, Fungal","Promoter Regions, Genetic","Promoter-Regions-Genetic","DNA-Fungal","Models, Genetic","RNA-Messenger","RNA-Binding Proteins","RNA, Fungal","540","Cyclin-Dependent Kinases","Introns","Cyclin-Dependent-Kinases","RNA-Fungal","Protein-Kinases","Genes-Fungal","Genome-Wide-Association-Study","Protein Kinases","Protein Processing, Post-Translational","Protein-Processing-Post-Translational","Genome-Wide Association Study"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-05T17:08:30.550155Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}