ArticleNature communications2019
Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism ofbioRxiv : the preprint server for biology · 2026Article
- Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.Nature communications · 2023Article
- A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungusVirus evolution · 2023Article
- Chromatin as self-returning walks: From population to single cell and back.Biophysical reports · 2022Review
- Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.Genome research · 2022Article
- 4D nucleome modeling.Current opinion in genetics & development · 2021Review
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Authors and funding
4 authors.
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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.
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