{"doi":"10.3390/ijms21186553","title":"Splicing Enhancers at Intron–Exon Borders Participate in Acceptor Splice Sites Recognition","abstract":"<jats:p>Acceptor splice site recognition (3′ splice site: 3′ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3′ss, of which U2AF35 has a dual function: (i) It binds to the intron–exon border of some 3′ss and (ii) mediates enhancer-binding splicing activators’ interactions with the spliceosome. Alternative mechanisms for 3′ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3′ss recognition where the intron–exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3′ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3′ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons’ inclusion. Most probably, both factors stochastically bind the 3′ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3′ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants’ effects on splicing.</jats:p>","journal":"International Journal of Molecular Sciences","year":2020,"id":32648,"datarank":0.5669046101322628,"base_score":2.5649493574615367,"endowment":2.5649493574615367,"self_citation_contribution":0.38474240361923057,"citation_network_contribution":0.18216220651303217,"self_endowment_contribution":0.38474240361923057,"citer_contribution":0.18216220651303217,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":11,"citers_with_citation_signal":8,"citers_with_endowment":8,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":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":172403,"name":"Přemysl Souček","orcid":"0000-0002-9985-2531","position":1,"is_corresponding":false},{"id":172404,"name":"Pavla Hujová","orcid":"0000-0002-9692-8967","position":2,"is_corresponding":false},{"id":172405,"name":"Tomáš Freiberger","orcid":"0000-0001-6532-7053","position":3,"is_corresponding":false},{"id":172406,"name":"Lucie Grodecká","orcid":"0000-0002-4979-0352","position":4,"is_corresponding":false},{"id":172402,"name":"Tatiana Kováčová","orcid":"0000-0001-6946-0417","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":2.5649493574615367,"endowment":2.5649493574615367,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"32911621","pmcid":"PMC7554774","openalex_id":"https://openalex.org/W3084320038","authors":[],"funders":[{"funder_name":"Ministerstvo Zdravotnictví Ceské Republiky","grant_id":"NU20-02-00261","title":null},{"funder_name":"Centre for Cardiovascular Surgery and Transplantation","grant_id":"201904","title":null},{"funder_name":"Ministerstvo Školství, Mládeže a Tělovýchovy","grant_id":"MUNI/A/1099/2019","title":null}],"total_grants":3,"fwci":0.4168,"citation_percentile":0.60483302,"influential_citations":0,"citation_trend":[{"year":2021,"count":2},{"year":2022,"count":3},{"year":2024,"count":4},{"year":2025,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/1422-0067/21/18/6553/pdf?version=1599546865","host_type":"journal"},{"url":"https://www.mdpi.com/1422-0067/21/18/6553/pdf?version=1599546865","host_type":"GOLD"},{"url":"https://www.mdpi.com/1422-0067/21/18/6553/pdf?version=1599546865","host_type":"publisher"},{"url":"https://www.mdpi.com/1422-0067/21/18/6553/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/ijms21186553","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/32911621","host_type":"repository"},{"url":"https://doaj.org/article/bd0c19d704fb4bf09e85bc034451f05c","host_type":"repository"},{"url":"https://dx.doi.org/10.3390/ijms21186553","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7554774","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC7554774","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC7554774?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["RNA Research and Splicing","RNA modifications and cancer","RNA and protein synthesis mechanisms","Medicine","Chemistry","Biology","Alternative Splicing","Base Sequence","Exons","HeLa Cells","Humans","Introns","RNA Splice Sites","RNA Splicing","RNA Splicing Factors","RNA-Binding Proteins","Regulatory Sequences, Nucleic Acid","Serine-Arginine Splicing Factors","Spliceosomes","Splicing Factor U2AF"],"mesh_terms":["Serine-Arginine Splicing Factors","RNA Splicing Factors","Splicing Factor U2AF","Base Sequence","Exons","HeLa Cells","Humans","Introns","Regulatory Sequences, Nucleic Acid","RNA Splicing","RNA-Binding Proteins","Spliceosomes","Alternative Splicing","RNA Splice Sites","Hela Cells"],"keywords":["Minigene","RNA splicing","Exon","Intron","Exonic splicing enhancer","Small nuclear ribonucleoprotein","snRNP","Biology","Spliceosome","Splicing factor","Ribonucleoprotein","Genetics","Exon skipping","Splice site mutation","RNA-binding protein","Enhancer","RNA","Gene","Transcription factor","Pre-mrna Splicing","Srsf1","Splicing Enhancer","U2af35","Acceptor Splice Site Recognition"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T13:54:21.851957Z","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":[]}