Variation in patterns of methylations of histone tails reflects and modulates 
chromatin structure and function. To provide a framework for the analysis of 
chromatin function in Caenorhabditis elegans, we generated a genome-wide map of 
histone H3 tail methylations. We find that C. elegans genes show distributions 
of histone modifications that are similar to those of other organisms, with 
H3K4me3 near transcription start sites, H3K36me3 in the body of genes and 
H3K9me3 enriched on silent genes. We also observe a novel pattern: exons are 
preferentially marked with H3K36me3 relative to introns. H3K36me3 exon marking 
is dependent on transcription and is found at lower levels in alternatively 
spliced exons, supporting a splicing-related marking mechanism. We further show 
that the difference in H3K36me3 marking between exons and introns is 
evolutionarily conserved in human and mouse. We propose that H3K36me3 exon 
marking in chromatin provides a dynamic link between transcription and splicing.