Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila
- Yevgenia L. Khodor1,2,
- Joseph Rodriguez1,2,
- Katharine C. Abruzzi1,2,
- Chih-Hang Anthony Tang1,2,
- Michael T. Marr II2,3 and
- Michael Rosbash1,2,4
- 1Howard Hughes Medical Institute, National Center for Behavioral Genomics,
- 2Department of Biology,
- 3Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
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 RpII215C4 mutant show substantially less intron retention than wild-type S2 cells.
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Footnotes
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↵4 Corresponding author.
E-mail rosbash{at}brandeis.edu.
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Supplemental material is available for this article.
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Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.178962.111.
- Received September 12, 2011.
- Accepted October 13, 2011.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press