Recent ChIP experiments indicate that spliceosome assembly and splicing can 
occur cotranscriptionally in S. cerevisiae. However, only a few genes have been 
examined, and all have long second exons. To extend these studies, we analyzed 
intron-containing genes with different second exon lengths by using ChIP as well 
as whole-genome tiling arrays (ChIP-CHIP). The data indicate that U1 snRNP 
recruitment is independent of exon length. Recursive splicing constructs, which 
uncouple U1 recruitment from transcription, suggest that cotranscriptional U1 
recruitment contributes to optimal splicing efficiency. In contrast, U2 snRNP 
recruitment, as well as cotranscriptional splicing, is deficient on short second 
exon genes. We estimate that > or =90% of endogenous yeast splicing is 
posttranscriptional, consistent with an analysis of posttranscriptional 
snRNP-associated pre-mRNA.