Stable nucleosome positions in HOX clusters; human K562 and HeLa cells

The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes where nucleosome positions have not been examined beyond isolated loci and promoter regions. Towards this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of inter-nucleosome distances, specific loci contain regular nucleosomal arrays with 195bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3’ ends of genes. Through comparison of different cell lines, we find that increased gene expression correlates with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes. Keywords: human chromatin nucleosome positions, nucleosomes, ChIP-chip Samples include mononucleosome samples resulting from MNase digestion in two cell lines, pan-H3 and rabbit IgG ChIP-chip validation, MNase sequence bias on bare genomic DNA.