H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions in the human genome

To understand how chromatin structure is organized by different histone variants, we have measured the genome-wide distribution of NCPs (nucleosome core particles) containing the histone variants H3.3 and H2A.Z. We find a special class of NCPs containing both variants, enriched at ‘nucleosome-free regions’ of active promoters, enhancers and insulator regions. We show that previous preparative methods resulted in loss of these unstable double variant NCPs. This instability should facilitate the accessibility of transcription factors to promoters and other regulatory sites in vivo. Other combinations of variants have different distributions, consistent with distinct roles for the histone variants in modulation of gene expression.