Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes
Yuanlong Liu, Luca Nanni, Stéphanie Sungalee, Marie Zufferey, Daniele Tavernari, Marco Mina, Stefano Ceri, Elisa Oricchio, Giovanni Ciriello
Abstract
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.