{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["44(8)"],"submitter":["Tan J"],"pubmed_abstract":["Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences."],"journal":["Nucleic acids research"],"pagination":["3908-21"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC4856993"],"repository":["biostudies-literature"],"pubmed_title":["Noncanonical registers and base pairs in human 5' splice-site selection."],"pmcid":["PMC4856993"],"pubmed_authors":["Tan J","Chen G","Roca X","Zhong Z","Luo S","Ho JX"],"additional_accession":[]},"is_claimable":false,"name":"Noncanonical registers and base pairs in human 5' splice-site selection.","description":"Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences.","dates":{"release":"2016-01-01T00:00:00Z","publication":"2016 May","modification":"2024-11-15T18:34:26.899Z","creation":"2019-03-27T02:13:05Z"},"accession":"S-EPMC4856993","cross_references":{"pubmed":["26969736"],"doi":["10.1093/nar/gkw163"]}}