{"doi":"10.26508/lsa.202101063","title":"Molecular and genetic dissection of recursive splicing","abstract":"Intronic ratchet points (RPs) are abundant within long introns in the Drosophila genome and consist of juxtaposed splice acceptor and splice donor (SD) sites. Although they appear to encompass zero-nucleotide exons, we recently clarified that intronic recursive splicing (RS) requires a cryptic exon at the RP (an RS-exon), which is subsequently always skipped and thus absent from mRNA. In addition, Drosophila encodes a smaller set of expressed exons bearing features of RS. Here, we investigate mechanisms that regulate the choice between RP and RS-exon SDs. First, analysis of Drosophila RP SD mutants demonstrates that SD competition suppresses inclusion of cryptic exons in endogenous contexts. Second, characterization of RS-exon reporters implicates exonic sequences as influencing choice of RS-exon usage. Using RS-exon swap and mutagenesis assays, we show exonic sequences can determine RS-exon inclusion. Finally, we provide evidence that splicing can suppress utilization of RP SDs to enable RS-exon expression. Overall, multiple factors can influence splicing of Drosophila RS-exons, which usually result in their complete suppression as zero-nucleotide RPs, but occasionally yield translated RS-exons.","journal":"Life Science Alliance","year":2022,"id":35902,"datarank":0.2980043505291912,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.05658866366407614,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.05658866366407614,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":4,"citers_with_citation_signal":3,"citers_with_endowment":3,"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":182938,"name":"Chaz Scala","orcid":null,"position":1,"is_corresponding":false},{"id":182939,"name":"Shu Kondo","orcid":null,"position":2,"is_corresponding":false},{"id":182940,"name":"Eric C Lai","orcid":"0000-0002-8432-5851","position":3,"is_corresponding":false},{"id":182937,"name":"Brian Joseph","orcid":"0000-0001-9876-0021","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"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":"34759052","pmcid":"PMC8605326","openalex_id":"https://openalex.org/W3213306876","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"R01-NS083833 and R01-GM083300","title":null},{"funder_name":"NINDS NIH HHS","grant_id":"R01 NS083833","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM083300","title":null},{"funder_name":"NCI NIH HHS","grant_id":"P30 CA008748","title":null},{"funder_name":"National Institutes of Health","grant_id":"2R01GM083300-06","title":"Non-canonical miRNA biogenesis mechanisms in Drosophila and mammals"},{"funder_name":"National Institutes of Health","grant_id":"2P30CA008748-43","title":"MOUSE GENETICS"},{"funder_name":"National Institutes of Health","grant_id":"2R01NS083833-06","title":"Mechanism and regulation of Hu family RNA binding proteins during neural alternative polyadenylation"},{"funder_name":"Memorial Sloan Kettering Core","grant_id":"","title":null}],"total_grants":8,"fwci":0.2443,"citation_percentile":0.53966325,"influential_citations":0,"citation_trend":[{"year":2023,"count":2},{"year":2024,"count":1},{"year":2025,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.life-science-alliance.org/content/lsa/5/1/e202101063.full.pdf","host_type":"journal"},{"url":"https://www.life-science-alliance.org/content/lsa/5/1/e202101063.full.pdf","host_type":"GOLD"},{"url":"https://www.life-science-alliance.org/content/lsa/5/1/e202101063.full.pdf","host_type":"publisher"},{"url":"https://syndication.highwire.org/content/doi/10.26508/lsa.202101063","host_type":"publisher"},{"url":"https://doi.org/10.26508/lsa.202101063","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/34759052","host_type":"repository"},{"url":"https://doaj.org/article/1898289f4d1840d99199ae5234d67390","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8605326","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8605326","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8605326?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.26508/lsa.202101063","host_type":""},{"url":"https://dx.doi.org/10.26508/lsa.202101063","host_type":""}],"fields_of_study":["RNA Research and Splicing","RNA modifications and cancer","RNA and protein synthesis mechanisms","Medicine","Biology","0301 basic medicine","0303 health sciences","03 medical and health sciences","Alternative Splicing","Animals","Base Sequence","Drosophila","Exons","Gene Expression Regulation","Introns","Mutagenesis","RNA Splice Sites","RNA Splicing","Regulatory Sequences, Nucleic Acid"],"mesh_terms":["Animals","Base Sequence","Drosophila","Exons","Gene Expression Regulation","Introns","Regulatory Sequences, Nucleic Acid","RNA Splicing","Mutagenesis","Alternative Splicing","RNA Splice Sites"],"keywords":["Exon","Tandem exon duplication","RNA splicing","Exon trapping","Exon shuffling","Exonic splicing enhancer","Genetics","Splice site mutation","Biology","Intron","Alternative splicing","Exon skipping","splice","RNA","Gene","Base Sequence","Exons","Regulatory Sequences, Nucleic Acid","Introns","Gene Expression Regulation","Mutagenesis","Animals","Drosophila","RNA Splice Sites","Research Articles"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Reduced inequalities"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-10T11:05:47.026068Z","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":[]}