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

Yevgenia L. Khodor, Joseph Rodriguez, Katharine C. Abruzzi, Chih Hang Anthony Tang, Michael T. Marr, Michael Rosbash

Research output: Contribution to journalArticlepeer-review

190 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)2502-2512
Number of pages11
JournalGenes and Development
Issue number23
StatePublished - Dec 1 2011


  • Cotranscriptional
  • Nascent sequencing
  • Pre-mRNA splicing
  • Transcriptional coupling

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology


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