title: Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila.
abstract: To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. Eighty-seven percent of the introns assayed manifest >50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly or slowly, with ∼3% being almost completely retained in nascent pre-mRNA. Although individual introns showed slight but statistically significant differences in splicing efficiency, similar global levels of splicing were seen from both sources. Importantly, introns with low cotranscriptional splicing efficiencies are present in the same primary transcript with efficiently spliced introns, indicating that splicing is intron-specific. The analysis also indicates that cotranscriptional splicing is less efficient for first introns, longer introns, and introns annotated as alternative. Finally, S2 cells expressing the slow RpII215(C4) mutant show substantially less intron retention than wild-type S2 cells.
authors.affiliation: Howard Hughes Medical Institute, National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: Yevgenia L
authors.initials: YL
authors.lastname: Khodor
authors.forename: Joseph
authors.initials: J
authors.lastname: Rodriguez
authors.forename: Katharine C
authors.initials: KC
authors.lastname: Abruzzi
authors.forename: Chih-Hang Anthony
authors.initials: CH
authors.lastname: Tang
authors.forename: Michael T
authors.initials: MT
authors.lastname: Marr
authors.forename: Michael
authors.initials: M
authors.lastname: Rosbash
mesh_terms: D000818:Animals; D004330:Drosophila / Q000235:genetics* / Q000378:metabolism; D007438:Introns; D009154:Mutation; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger