Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.

Uwe Schwartz et al., (2018) Nucleic Acids Research; PMID: 30496478

Packaging of DNA into chromatin regulates DNA ac-cessibility and consequently all DNA-dependent pro-cesses. The nucleosome is the basic packaging unitof DNA forming arrays that are suggested, by bio-chemical studies, to fold hierarchically into orderedhigher-order structures of chromatin. This organiza-tion has been recently questioned using microscopytechniques, proposing an irregular structure. To ad-dress the principles of chromatin organization, weapplied an in situ differential MNase-seq strategy andanalyzed in silico the results of complete and par-tial digestions of human chromatin. We investigatedwhether different levels of chromatin packaging ex-ist in the cell. We assessed the accessibility of chro-matin within distinct domains of kb to Mb genomic re-gions, performed statistical analyses and computermodelling. We found no difference in MNase acces-sibility, suggesting no difference in fiber folding be-tween domains of euchromatin and heterochromatinor between other sequence and epigenomic fea-tures of chromatin. Thus, our data suggests the ab-sence of differentially organized domains of higher-order structures of chromatin. Moreover, we iden-tified only local structural changes, with individualhyper-accessible nucleosomes surrounding regula-tory elements, such as enhancers and transcriptionstart sites. The regulatory sites per se are occupiedwith structurally altered nucleosomes, exhibiting in-creased MNase sensitivity. Our findings provide bio-chemical evidence that supports an irregular modelof large-scale chromatin organization.