Chromatin structure influences transcription, but its role in subsequent RNA 
processing is unclear. Here we present analyses of high-throughput data that 
imply a relationship between nucleosome positioning and exon definition. First, 
we have found stable nucleosome occupancy within human and Caenorhabditis 
elegans exons that is stronger in exons with weak splice sites. Conversely, we 
have found that pseudoexons--intronic sequences that are not included in mRNAs 
but are flanked by strong splice sites--show nucleosome depletion. Second, the 
ratio between nucleosome occupancy within and upstream from the exons correlates 
with exon-inclusion levels. Third, nucleosomes are positioned central to exons 
rather than proximal to splice sites. These exonic nucleosomal patterns are also 
observed in non-expressed genes, suggesting that nucleosome marking of exons 
exists in the absence of transcription. Our analysis provides a framework that 
contributes to the understanding of splicing on the basis of chromatin 
architecture.