Chromatin epigenomic domain folding: size matters

Bertrand R. Caré; Pierre-Emmanuel Emeriau; Ruggero Cortini; Jean-Marc Victor; Bertrand R. Caré; Pierre-Emmanuel Emeriau; Ruggero Cortini; Jean-Marc Victor

doi:10.3934/biophy.2015.4.517

AIMS Biophysics

2015, Volume 2, Issue 4: 517-530. doi: 10.3934/biophy.2015.4.517

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Chromatin epigenomic domain folding: size matters

1.
Sorbonne Universités UPMC Univ. Paris 06 UMR 7600 LPTMC F-75005 Paris France;
2.
CNRS UMR 7600 LPTMC F-75005 Paris France;
3.
CNRS GDR 3536

Received: 09 August 2015 Accepted: 05 September 2015 Published: 20 September 2015

In eukaryotes, chromatin is coated with epigenetic marks which induce differential gene expression profiles and eventually lead to different cellular phenotypes. One of the challenges of contemporary cell biology is to relate the wealth of epigenomic data with the observed physical properties of chromatin. In this study, we present a polymer physics framework that takes into account the sizes of epigenomic domains. We build a model of chromatin as a block copolymer made of domains with various sizes. This model produces a rich set of conformations which is well explained by finite-size scaling analysis of the coil-globule transition of epigenomic domains. Our results suggest that size-dependent folding of epigenomic domains may be a crucial physical mechanism able to provide chromatin with tissue-specific folding states, these being associated with differential gene expression.
- epigenetics,
- chromatin,
- coil-globule transition,
- polymer physics,
- finite-size effects,
- langevin dynamics
Citation: Bertrand R. Caré, Pierre-Emmanuel Emeriau, Ruggero Cortini, Jean-Marc Victor. Chromatin epigenomic domain folding: size matters[J]. AIMS Biophysics, 2015, 2(4): 517-530. doi: 10.3934/biophy.2015.4.517

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Abstract

In eukaryotes, chromatin is coated with epigenetic marks which induce differential gene expression profiles and eventually lead to different cellular phenotypes. One of the challenges of contemporary cell biology is to relate the wealth of epigenomic data with the observed physical properties of chromatin. In this study, we present a polymer physics framework that takes into account the sizes of epigenomic domains. We build a model of chromatin as a block copolymer made of domains with various sizes. This model produces a rich set of conformations which is well explained by finite-size scaling analysis of the coil-globule transition of epigenomic domains. Our results suggest that size-dependent folding of epigenomic domains may be a crucial physical mechanism able to provide chromatin with tissue-specific folding states, these being associated with differential gene expression.

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