Nucleosome organization in sequences of alternative events in human genome

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.