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

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  • Yuanlong Liu

    (University of Lausanne
    Swiss Cancer Center Leman
    Swiss Institute of Bioinformatics)

  • Luca Nanni

    (University of Lausanne
    Swiss Cancer Center Leman
    Swiss Institute of Bioinformatics
    Department of Electronics, Information, and Bioengineering, Politecnico di Milano)

  • Stephanie Sungalee

    (Swiss Cancer Center Leman
    Swiss Institute for Experimental Cancer Research (ISREC) School of Life Sciences, EPFL)

  • Marie Zufferey

    (University of Lausanne
    Swiss Cancer Center Leman
    Swiss Institute of Bioinformatics)

  • Daniele Tavernari

    (University of Lausanne
    Swiss Cancer Center Leman
    Swiss Institute of Bioinformatics)

  • Marco Mina

    (University of Lausanne
    Swiss Cancer Center Leman
    Swiss Institute of Bioinformatics)

  • Stefano Ceri

    (Department of Electronics, Information, and Bioengineering, Politecnico di Milano)

  • Elisa Oricchio

    (Swiss Cancer Center Leman
    Swiss Institute for Experimental Cancer Research (ISREC) School of Life Sciences, EPFL)

  • Giovanni Ciriello

    (University of Lausanne
    Swiss Cancer Center Leman
    Swiss Institute of Bioinformatics)

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.

Suggested Citation

  • Yuanlong Liu & Luca Nanni & Stephanie Sungalee & Marie Zufferey & Daniele Tavernari & Marco Mina & Stefano Ceri & Elisa Oricchio & Giovanni Ciriello, 2021. "Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22666-3
    DOI: 10.1038/s41467-021-22666-3
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    Cited by:

    1. Brent S. Perlman & Noah Burget & Yeqiao Zhou & Gregory W. Schwartz & Jelena Petrovic & Zora Modrusan & Robert B. Faryabi, 2024. "Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Ryuichiro Nakato & Toyonori Sakata & Jiankang Wang & Luis Augusto Eijy Nagai & Yuya Nagaoka & Gina Miku Oba & Masashige Bando & Katsuhiko Shirahige, 2023. "Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Jacques Serizay & Cyril Matthey-Doret & Amaury Bignaud & Lyam Baudry & Romain Koszul, 2024. "Orchestrating chromosome conformation capture analysis with Bioconductor," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    4. Hannah L. Harris & Huiya Gu & Moshe Olshansky & Ailun Wang & Irene Farabella & Yossi Eliaz & Achyuth Kalluchi & Akshay Krishna & Mozes Jacobs & Gesine Cauer & Melanie Pham & Suhas S. P. Rao & Olga Dud, 2023. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Yi Liao & Juntao Wang & Zhangsheng Zhu & Yuanlong Liu & Jinfeng Chen & Yongfeng Zhou & Feng Liu & Jianjun Lei & Brandon S. Gaut & Bihao Cao & J. J. Emerson & Changming Chen, 2022. "The 3D architecture of the pepper genome and its relationship to function and evolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Abhijit Chakraborty & Jeffrey G. Wang & Ferhat Ay, 2022. "dcHiC detects differential compartments across multiple Hi-C datasets," Nature Communications, Nature, vol. 13(1), pages 1-21, December.

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