BACKGROUND: The packaging of DNA into chromatin regulates transcription from 
initiation through 3' end processing. One aspect of transcription in which 
chromatin plays a poorly understood role is the co-transcriptional splicing of 
pre-mRNA.
RESULTS: Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks 
introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this 
organism reveals that this modification is enriched in coding regions and that 
its levels peak at the transcribed regions of two characteristic subgroups of 
genes. First, long genes are more likely to have higher levels of H2BK123ub1, 
correlating with the postulated role of this modification in preventing cryptic 
transcription initiation in ORFs. Second, genes that are highly transcribed also 
have high levels of H2BK123ub1, including the ribosomal protein genes, which 
comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a 
feature of introns in the yeast genome, and the disruption of this modification 
alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), 
which functionally correlates with alternative RNA splicing in humans. In 
addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in 
combination with an htb-K123R mutation, leads to synthetic lethality.
CONCLUSION: These data suggest that H2BK123ub1 facilitates cross talk between 
chromatin and pre-mRNA splicing by modulating the distribution of intronic and 
exonic histone modifications.