Advancing Epigenetics Towards Systems Biology

Cédric Vaillant

Laboratory of Physics, CNRS-Ecole Normale Supérieure de Lyon, Lyon, France

Physics of epigenome regulation

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cedric vaillant

The general objective of our group is to build quantitative models of the epigenomic-based mechanisms of gene regulation involved in the short- and long-term cellular response. Using theoretical approaches from statistical and numerical physics and in close collaboration with experimentalists, we study the "1D" assembly of the different eu- and heterochromatin states along the genome (nucleation, spreading, compartmentalization and mitotic/meiotic inheritance), and their "3D" folding and nuclear organization. At the nucleosomal and gene scales, we are currently developing molecular models accounting for the combined action of chromatin regulators and DNA binding proteins to understand the mechanisms by which chromatin states achieve their functions. At larger scale, we use coarse-grained models to derive the structural and dynamical properties of the epigenome: (i) the regulation of epigenomic domains (ii) their folding into spatial compartments and (iii) finally the coupling between 3D organization and 1D assembly. Ultimately our goal is to provide a general framework to understand how the epigenome is regulated and how its affect gene expression: from its establishment during development and differentiation to its deregulation in diseases.

Peoples:

  • Daniel JOST (CNRS Research Associate, University of Grenoble, TIMC-IMAG, Grenoble)
  • Noëlle Haddad: PhD

Latest publications

The folding landscape of the epigenome.

27042992 - 2016-04-05
Phys Biol 2016 Apr 4;13(2):026001

Olarte-Plata JD, Haddad N, Vaillant C, Jost D

Effect of replication on epigenetic memory and consequences on gene transcription.

25884278 - 2015-04-18
Phys Biol 2015 Apr 17;12(2):026007

Zerihun MB, Vaillant C, Jost D

Intasome architecture and chromatin density modulate retroviral integration into nucleosome.

25807893 - 2015-03-27
Retrovirology 2015 Feb 7;12(1):13

Benleulmi MS, Matysiak J, Henriquez DR, Vaillant C, Lesbats P, Calmels C, Naughtin M, Leon O, Skalka AM, Ruff M, Lavigne M, Andreola ML, Parissi V

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