{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kapral TH"],"funding":["Austrian Science Fund FWF","University of Vienna","National Natural Science Foundation of China","VolkswagenStiftung LIFE","National Key Research and Development Plan of China","Beijing Advanced Innovation Center for Structural Biology","Bio-Computing Platform of China National Center for Protein Sciences Beijing"],"pagination":["9984-9999"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9508846"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["50(17)"],"pubmed_abstract":["Autogenous interactions between mRNAs and the proteins they encode are implicated in cellular feedback-loop regulation, but their extent and mechanistic foundation are unclear. It was recently hypothesized that such interactions may be common, reflecting the role of intrinsic nucleobase-amino acid affinities in shaping the genetic code's structure. Here we analyze a comprehensive set of CLIP-seq experiments involving multiple protocols and report on widespread autogenous interactions across different organisms. Specifically, 230 of 341 (67%) studied RNA-binding proteins (RBPs) interact with their own mRNAs, with a heavy enrichment among high-confidence hits and a preference for coding sequence binding. We account for different confounding variables, including physical (overexpression and p"],"journal":["Nucleic acids research"],"pubmed_title":["Widespread autogenous mRNA-protein interactions detected by CLIP-seq."],"pmcid":["PMC9508846"],"funding_grant_id":["31522030","P 30550","2016YFA0500803","31771461","98187","P 30680-B21"],"pubmed_authors":["Lu ZJ","Kapral TH","Zhao W","Zagrovic B","Farnhammer F"],"additional_accession":[]},"is_claimable":false,"name":"Widespread autogenous mRNA-protein interactions detected by CLIP-seq.","description":"Autogenous interactions between mRNAs and the proteins they encode are implicated in cellular feedback-loop regulation, but their extent and mechanistic foundation are unclear. It was recently hypothesized that such interactions may be common, reflecting the role of intrinsic nucleobase-amino acid affinities in shaping the genetic code's structure. Here we analyze a comprehensive set of CLIP-seq experiments involving multiple protocols and report on widespread autogenous interactions across different organisms. Specifically, 230 of 341 (67%) studied RNA-binding proteins (RBPs) interact with their own mRNAs, with a heavy enrichment among high-confidence hits and a preference for coding sequence binding. We account for different confounding variables, including physical (overexpression and p","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Sep","modification":"2025-04-18T20:57:36.365Z","creation":"2025-04-07T08:55:41.4Z"},"accession":"S-EPMC9508846","cross_references":{"pubmed":["36107779"],"doi":["10.1093/nar/gkac756"]}}