Abstract
Cotranscriptional splicing, in which mRNA is spliced as it is being transcribed, is thought to be necessary for proper gene regulation of many genes in eukaryotic cells. While studies have shown that splicing takes place cotranscriptionally in yeast, in higher eukaryotes, where genes contain multiple introns with widespread alternative splicing, the question of whether cotranscriptional splicing is a general phenomenon remains. Khodor et al. investigated what fractions of genes are cotranscriptionally spliced and what fraction of splicing occurs cotranscriptionally in
Drosophila
. The results demonstrate that the majority of introns show cotranscriptional splicing, although this process is intron-specific.
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.