Transcriptomics

Dataset Information

303

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. 87% of introns assayed manifest more than 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. FinallyFinally, S2 cells expressing the slow RpII215C4 mutant manifest substantially less intron retention than wild-type S2 cells. Examination of Total pA and Nascent RNA from 2 different cell populations and isolated fly heads.

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Yevgenia L Khodor   Katharine C Abruzzi  Michael T Marr II  Chih-Hang A Tang  Joseph Rodriguez  Michael Rosbash 

PROVIDER: E-GEOD-32950 | ArrayExpress | 2011-12-01

SECONDARY ACCESSION(S): GSE32950SRP008848PRJNA146467

REPOSITORIES: GEO, ArrayExpress, ENA

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Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila.

Khodor Yevgenia L YL   Rodriguez Joseph J   Abruzzi Katharine C KC   Tang Chih-Hang Anthony CH   Marr Michael T MT   Rosbash Michael M  

Genes & development 20111201 23


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, simila  ...[more]

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