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Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

Author

Listed:
  • O. Shukron

    (Ecole Normale Supérieure)

  • V. Piras

    (Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-sud, University Paris-Saclay)

  • D. Noordermeer

    (Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-sud, University Paris-Saclay)

  • D. Holcman

    (Ecole Normale Supérieure)

Abstract

Chromatin of mammalian nucleus folds into discrete contact enriched regions such as Topologically Associating Domains (TADs). Folding hierarchy and internal organization of TADs is highly dynamic throughout cellular differentiation, and are correlated with gene activation and silencing. To account for multiple interacting TADs, we developed a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency Hi-C encounters within and between TADs into direct loci interactions using cross-links at a given base-pair resolution. We reconstruct three TADs of the mammalian X chromosome for three stages of differentiation. We compute the radius of gyration of TADs and the encounter probability between genomic segments. We found 1) a synchronous compaction and decompaction of TADs throughout differentiation and 2) high order organization into meta-TADs resulting from weak inter-TAD interactions. Finally, the present framework allows to infer transient properties of the chromatin from steady-state statistics embedded in the Hi-C/5C data.

Suggested Citation

  • O. Shukron & V. Piras & D. Noordermeer & D. Holcman, 2019. "Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10402-x
    DOI: 10.1038/s41467-019-10402-x
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    Cited by:

    1. Li-Hsin Chang & Sourav Ghosh & Andrea Papale & Jennifer M. Luppino & Mélanie Miranda & Vincent Piras & Jéril Degrouard & Joanne Edouard & Mallory Poncelet & Nathan Lecouvreur & Sébastien Bloyer & Amél, 2023. "Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries," Nature Communications, Nature, vol. 14(1), pages 1-19, December.

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