{"doi":"10.1073/pnas.1309384110","title":"Species-specific factors mediate extensive heterogeneity of mRNA 3′ ends in yeasts","abstract":"<jats:p>\n                    Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3′ ends. Here we show that polyadenylated 3′ termini in three yeast species (\n                    <jats:italic>Saccharomyces cerevisiae</jats:italic>\n                    ,\n                    <jats:italic>Kluyveromyces lactis</jats:italic>\n                    , and\n                    <jats:italic>Debaryomyces hansenii</jats:italic>\n                    ) are remarkably heterogeneous. Instead of a few discrete 3′ ends, the average yeast gene has an “end zone,” a &gt;200 bp window with &gt;60 distinct poly(A) sites, the most used of which represents only 20% of the mRNA molecules. The pattern of polyadenylation within this zone varies across species, with\n                    <jats:italic>D. hansenii</jats:italic>\n                    possessing a higher focus on a single dominant point closer to the ORF terminus. Some polyadenylation occurs within mRNA coding regions with a strong bias toward the promoter. The polyadenylation pattern is determined by a highly degenerate sequence over a broad region and by a local sequence that relies on A residues after the cleavage point. Many dominant poly(A) sites are predicted to adopt a common secondary structure that may be recognized by the cleavage/polyadenylation machinery. We suggest that the end zone reflects a region permissive for polyadenylation, within which cleavage occurs preferentially at the A-rich sequence. In\n                    <jats:italic>S. cerevisiae</jats:italic>\n                    strains,\n                    <jats:italic>D. hansenii</jats:italic>\n                    genes adopt the\n                    <jats:italic>S. cerevisiae</jats:italic>\n                    polyadenylation profile, indicating that the polyadenylation pattern is mediated primarily by species-specific factors.\n                  </jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2013,"id":44241,"datarank":1.732480857162805,"base_score":4.02535169073515,"endowment":4.02535169073515,"self_citation_contribution":0.6038027536102726,"citation_network_contribution":1.1286781035525324,"self_endowment_contribution":0.6038027536102726,"citer_contribution":1.1286781035525324,"corpus_percentile":null,"corpus_rank":null,"citation_count":55,"citer_count":38,"citers_with_citation_signal":31,"citers_with_endowment":31,"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":208541,"name":"Joseph V. Geisberg","orcid":null,"position":1,"is_corresponding":false},{"id":208616,"name":"Yi Jin","orcid":null,"position":2,"is_corresponding":false},{"id":208617,"name":"Xiaochun Fan","orcid":null,"position":3,"is_corresponding":false},{"id":11009,"name":"Kevin Struhl","orcid":"0000-0002-4181-7856","position":4,"is_corresponding":false},{"id":19995,"name":"Zarmik Moqtaderi","orcid":"0000-0002-2785-7034","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":4.02535169073515,"endowment":4.02535169073515,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"23776204","pmcid":"PMC3703967","openalex_id":"https://openalex.org/W1968079984","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R37 GM030186","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"GM30186","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM030186","title":null}],"total_grants":3,"fwci":2.5435,"citation_percentile":0.89295899,"influential_citations":4,"citation_trend":[{"year":2014,"count":11},{"year":2015,"count":4},{"year":2016,"count":2},{"year":2017,"count":5},{"year":2018,"count":2},{"year":2019,"count":5},{"year":2020,"count":2},{"year":2021,"count":1},{"year":2022,"count":7},{"year":2023,"count":7},{"year":2024,"count":4},{"year":2025,"count":1},{"year":2026,"count":4}],"oa_status":"bronze","license":null,"oa_locations":[{"url":"https://www.pnas.org/content/pnas/110/27/11073.full.pdf","host_type":"journal"},{"url":"https://www.pnas.org/content/pnas/110/27/11073.full.pdf","host_type":"BRONZE"},{"url":"https://www.pnas.org/content/pnas/110/27/11073.full.pdf","host_type":"publisher"},{"url":"https://pnas.org/doi/pdf/10.1073/pnas.1309384110","host_type":"publisher"},{"url":"https://doi.org/10.1073/pnas.1309384110","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/23776204","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3703967","host_type":"repository"}],"fields_of_study":["RNA Research and Splicing","RNA and protein synthesis mechanisms","RNA modifications and cancer","Medicine","Biology","3' Untranslated Regions","Base Sequence","Debaryomyces","Evolution, Molecular","Genetic Variation","Kluyveromyces","Molecular Sequence Data","Nucleic Acid Conformation","RNA 3' End Processing","RNA 3' Polyadenylation Signals","RNA, Fungal","RNA, Messenger","Saccharomyces cerevisiae","Species Specificity","Yeasts"],"mesh_terms":["Base Sequence","Kluyveromyces","Molecular Sequence Data","Nucleic Acid Conformation","RNA, Fungal","RNA, Messenger","Saccharomyces cerevisiae","Species Specificity","Genetic Variation","Yeasts","Evolution, Molecular","3' Untranslated Regions","RNA 3' End Processing","RNA 3' Polyadenylation Signals","Debaryomyces"],"keywords":["Polyadenylation","Cleavage and polyadenylation specificity factor","Saccharomyces cerevisiae","Biology","Cleavage factor","Kluyveromyces lactis","Cleavage (geology)","Genetics","Primary transcript","Coding region","Post-transcriptional modification","Gene","Messenger RNA","Alternative splicing","RNA-binding protein","Evolution","Gene Expression","Transcription Termination","Mrna Processing","3′ End Formation"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-17T04:33:00.915127Z","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":[]}