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

Yuanlong Liu, Luca Nanni, Stephanie Sungalee, Marie Zufferey, Daniele Tavernari, Marco Mina, Stefano Ceri, Elisa Oricchio and Giovanni Ciriello ()
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Yuanlong Liu: University of Lausanne
Luca Nanni: University of Lausanne
Stephanie Sungalee: Swiss Cancer Center Leman
Marie Zufferey: University of Lausanne
Daniele Tavernari: University of Lausanne
Marco Mina: University of Lausanne
Stefano Ceri: Department of Electronics, Information, and Bioengineering, Politecnico di Milano
Elisa Oricchio: Swiss Cancer Center Leman
Giovanni Ciriello: University of Lausanne

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22666-3

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DOI: 10.1038/s41467-021-22666-3

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