Epigenome Group

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.

• Projects
• Recent publications:

1. N. Haddad, D. Jost and C. Vaillant. Perspectives: using polymer modeling to understand the formation and function of nuclear compartments. Chromosome Res (2017). doi:10.1007/s10577-016-9548-2. Article
2. D. Jost, C. Vaillant and P. Meister. Coupling 1D modifications and 3D nuclear organization: data, models and function. Curr. Opin. Cell Biol. 44, 20-27 (2017).Article
3. M.B. Zerihun, C. Vaillant and D. Jost, Effect of replication on epigenetic memory and consequences on gene transcription. Phys. Biol. 12 (2015) 026007:Article
4. D. Jost, Bifurcation in epigenetics : implications in development, proliferation, and diseases. Phys Rev E Stat Nonlin Soft Matter Phys 89(1), 010701, Jan (2014):ArticleSupp.
5. D. Jost, P. Carrivain, G. Cavalli & C. Vaillant. Modeling epigenome folding : formation and dynamics of topologically associated chromatin domains. Nucleic Acids Res. 42, 9553-9561 (2014).PMID: ArticleSupp.
6. R. Sharma, D. Jost, J. Kind, G. Gómez-Saldivar, B. van Steensel, P. Askjaer, C. Vaillant & P. Meister. Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans. Genes Dev. 28, 2591-2596 (2014) PMID:25452271:Article