Recent studies indicate that precursor mRNA splicing occurs cotranscriptionally 
and that nucleosome positioning may influence inclusion of internal exon 
sequences. In eukaryotic genomes, most genes are subject to alternative 
splicing. Nucleosome occupancy in sequences of different types of alternative 
events was investigated by analyzing genome-wide nucleosome positioning data 
sets from human. Nucleosomes were found to be preferentially positioned within 
constitutive exons and/or constitutive portions of alternative exons, which was 
not associated with gene expression or states of cells but was based on sequence 
and positively related with the sequence conservation of splicing sites. In 
addition, the nucleosome distribution in an alternative acceptor exon was 
different from that in an alternative donor exon. Nucleosome occupancy around 
constitutive transcription start sites also showed stronger +1 nucleosome 
enrichment and weaker nucleosome occupancy in nucleosome free regions. These 
results provided a new approach for better appreciation of the connection 
between chromatin structure and gene expression regulation.