title: Large-scale analysis of branchpoint usage across species and cell lines.
abstract: The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2-5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background. We have developed a novel method whereby raw lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data set of branchpoint sequences with quality metrics. This analysis discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight into the biogenesis of intron circles. Finally, matching branch site usage with isoform selection across the extensive panel of ENCODE RNA-seq data sets offers insight into the mechanisms by which branchpoint usage drives alternative splicing.
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Allison J
authors.initials: AJ
authors.lastname: Taggart
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Chien-Ling
authors.initials: CL
authors.lastname: Lin
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Barsha
authors.initials: B
authors.lastname: Shrestha
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Claire
authors.initials: C
authors.lastname: Heintzelman
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Seongwon
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.|Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA.|Hassenfeld Child Health Innovation Institute of Brown University, Providence, Rhode Island 02912, USA.
authors.forename: William G
authors.initials: WG
authors.lastname: Fairbrother
mesh_terms: D000465:Algorithms; D000818:Animals; D020029:Base Pairing; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D020125:Mutation, Missense; D022821:RNA Splice Sites; D012326:RNA Splicing; D000072260:RNA Splicing Factors / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D022821:RNA Splice Sites; D000072260:RNA Splicing Factors; D012333:RNA, Messenger