Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide.

ABSTRACT: BACKGROUND:Proximity ligation based techniques, like Hi-C, involve restriction digestion followed by ligation of formaldehyde cross-linked chromatin. Distinct chromatin states can impact the restriction digestion, and hence the visibility in the contact maps, of engaged loci. Yet, the extent and the potential impact of digestion bias remain obscure and under-appreciated in the literature. RESULTS:Through analysis of 45 Hi-C datasets, lamina-associated domains (LADs), inactive X-chromosome in mammals, and polytene bands in fly, we first established that the DNA in condensed chromatin had lesser accessibility to restriction endonucleases used in Hi-C as compared to that in decondensed chromatin. The observed bias was independent of known systematic biases, was not appropriately corrected by

SUBMITTER: Chandradoss KR 

PROVIDER: S-EPMC7036197 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature