Nucleosome dynamics render heterochromatin generally accessible in living human cells (MNase-seq in MCF7 nuclei)

The eukaryotic genome is packaged into chromatin, which resembles beads on a string. Each bead consists of a nucleosome containing ~147 bp of DNA wrapped around a histone octamer. The nucleosomal filament undergoes additional folding to create a complex genomic organisation which is thought to restrict the access of gene-regulatory transcription factors to the genome. Consequently, it is widely accepted that DNA accessibility, modulated by chromatin architecture, is pivotal in gene regulation. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric asatellite chromatin are static. A dynamic chromatin architecture implies that simple occlusion of transcription factor binding sites is unlikely to be critical in gene regulation. Overall design: MNase-seq experiment for MCF7 nuclei: Illumina paired-end data. Two biological replicate experiments.