High Density Nucleosome Occupancy Map of Human Chromosome 9p21-22 Reveals Steady-State and Virus-Induced Chromatin Organization of the Type I Interferon Gene Cluster. Homo sapiens

Genome-wide investigations have dramatically increased our understanding of nucleosome positioning and the role of chromatin in gene regulation, yet some genomic regions have been poorly represented in human nucleosome maps. Here, a new high-density nucleosome mapping strategy was used to generate locus-wide maps of human chromosome 9p21-22, which contains the type I interferon (IFN) gene cluster that includes 16 IFNA genes and the single IFNΒ1, IFNE, and IFNW1 genes. The nucleosome organization of this biomedically important locus was determined at steady state and during a time course of Sendai virus infection, a potent inducer of IFN gene expression. These maps visualize the region’s chromatin architecture and reveal features of nucleosome-mediated gene regulation that are attributable to all IFN promoters. Moreover, computational analysis illustrates that nucleosomes in this locus exhibit preferences for particular dinucleotide and oligomer DNA sequence motifs in vivo, which are similar to those reported for lower eukaryotes.