{"doi":"10.1101/314310","title":"Repression of divergent noncoding transcription by a sequence-specific transcription factor","abstract":"<jats:title>Summary</jats:title>\n                <jats:p>Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeller. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality towards productive transcription.</jats:p>","journal":null,"year":null,"id":589695,"datarank":0.38098236746882863,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.13956668060371358,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.13956668060371358,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":4,"citers_with_citation_signal":4,"citers_with_endowment":4,"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":1508641,"name":"Harshil Patel","orcid":null,"position":1,"is_corresponding":false},{"id":141484,"name":"Minghao Chia","orcid":null,"position":2,"is_corresponding":false},{"id":141482,"name":"Fabien Moretto","orcid":null,"position":3,"is_corresponding":false},{"id":145292,"name":"David Frith","orcid":null,"position":4,"is_corresponding":false},{"id":145294,"name":"Ambrosius P. Snijders","orcid":null,"position":5,"is_corresponding":false},{"id":684973,"name":"Folkert J. van Werven","orcid":"0000-0002-6685-2084","position":6,"is_corresponding":false},{"id":1508735,"name":"Andrew CK Wu","orcid":"0000-0002-2429-2496","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Repression of divergent noncoding transcription by a sequence-specific transcription factor","abstract":"<jats:title>Summary</jats:title>\n                <jats:p>Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeller. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality towards productive transcription.</jats:p>","is_dataset_classified":null,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"20725694","pmcid":null,"openalex_id":"https://openalex.org/W2803491474","authors":[],"funders":[{"funder_name":"Wellcome Trust","grant_id":"unidentified","title":"unidentified"}],"total_grants":1,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2020,"count":2},{"year":2022,"count":1},{"year":2024,"count":1}],"oa_status":"green","license":"CC BY","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2018/05/17/314310.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2018/05/17/314310.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/314310","host_type":"publisher"},{"url":"https://doi.org/10.1101/314310","host_type":"repository"},{"url":"https://figshare.com/articles/journal_contribution/Repression_of_divergent_noncoding_transcription_by_a_sequence-specific_transcription_factor/12952070","host_type":"repository"},{"url":"http://www.cell.com/article/S1097276518308785/pdf","host_type":""},{"url":"https://doi.org/10.1016/j.molcel.2018.10.018","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/30576656","host_type":""},{"url":"http://dx.doi.org/10.1016/j.molcel.2018.10.018","host_type":""},{"url":"https://dx.doi.org/10.1016/j.molcel.2018.10.018","host_type":""},{"url":"https://dx.doi.org/10.1101/314310","host_type":""},{"url":"http://dx.doi.org/10.1101/314310","host_type":""}],"fields_of_study":["Genomics and Chromatin Dynamics","CRISPR and Genetic Engineering","Fungal and yeast genetics research","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Promoter","Transcription factor II D","General transcription factor","Transcription coregulator","Biology","TAF2","Transcription factor","E-box","Sp3 transcription factor","Transcription (linguistics)","Response element","Upstream activating sequence","Genetics","Transcription factor II B","RNA polymerase II","Pioneer factor","Transcription factor II A","Gene","Gene expression","Ribosomal Proteins","Binding Sites","RNA, Untranslated","Saccharomyces cerevisiae Proteins","Transcription, Genetic","Telomere-Binding Proteins","RNA, Fungal","Saccharomyces cerevisiae","Chromatin Assembly and Disassembly","Article","Shelterin Complex","Gene Expression Regulation, Fungal","Protein Interaction Domains and Motifs","Promoter Regions, Genetic","Protein Binding","Transcription Factors"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-24T04:07:17.257159Z","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":[]}