Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

Nat Commun. 2021 May 10;12(1):2439. doi: 10.1038/s41467-021-22666-3.


Chromatin compartmentalization reflects biological activity. However, inference of chromatin sub-compartments and compartment domains from chromosome conformation capture (Hi-C) experiments is limited by data resolution. As a result, these have been characterized only in a few cell types and systematic comparisons across multiple tissues and conditions are missing. Here, we present Calder, an algorithmic approach that enables the identification of multi-scale sub-compartments at variable data resolution. Calder allows to infer and compare chromatin sub-compartments and compartment domains in >100 cell lines. Our results reveal sub-compartments enriched for poised chromatin states and undergoing spatial repositioning during lineage differentiation and oncogenic transformation.

Publication types

  • Research Support, Non-U.S. Gov't