Nucleosome distribution near the 3' ends of genes in the human genome.

By systematic analysis of high-throughput sequencing datasets from the human genome, we found that protein-coding genes have a specific chromatin structure near transcription termination sites relative to non-coding genes, one related to polyadenylation. Nucleosome was depleted near the site of cleavage/polyadenylation (polyA site) regardless of its relative position in the gene. DNA sequence plays an improtant role in nucleosome distribution, and conservative sequence elements and the protein binding to them are major determinants in causing nucleosome depletion near polyA sites. Furthermore, nucleosome occupancy was regulated by gene transcription and RNA polymerase II (RNAPII) occupancy. Our results reveal influences on nucleosome occupancy near polyadenylation sites and constitute evidence indicating that nucleosome distribution regulates 3' end processing of protein-coding genes.