Epigenetics Dynamics & Cellular Differenciation



A central epigenetic mechanism is the lysine methylation/demethylation of histones, as well as specific non-histone proteins. Lysine methylation on histones is central in imposing stable and heritable gene expression programs, being associated with both active and inactive domains of chromatin, depending on the residue that is targeted. Methylation of histone H3 on lysine 9 (H3K9) and lysine 27 (H3K27) being hallmarks of repressed chromatin. The enzymes controlling “histone” lysine methylation are called lysine methyltransferases (KMTs) and lysine demethylases (KDMs) and some can also modify non-histone substrates. They are highly specific for the targeted residue in the histone tail and, so far, around 50 KMTs and 30 KDMs have been described. We are particularly interested in KMTs specific for H3K9 and H3K27.


Our group seeks to define the biochemical and molecular mechanisms that govern the normal silencing of genes during cell fate changes. We are interested in the role of lysine methylation, especially histone methylation of H3K9 and H3K27, as well as methylation of non-histone proteins, in the regulation of muscle and embryonic stem cells (ESCs) differentiation: how the different H3K9 and H3K27 methylation levels (mono, di and tri), associated to specific nuclear compartments, are established in the cell, and how the H3K9 and H3K27 KMTs (co)-regulate the cell fate changes. We try to dissect the composition, mechanisms, the kinetic of action of these KMTs and the crosstalk between these two major epigenetic mechanisms. Unravelling the molecular mechanisms by which stem cells undergo cell fate decisions, especially differentiation, is one of the fundamental goals of modern medicine. The ability to modify a cell state is a fundamental issue that hold great promises for regenerative medicine. Thus, the expected results will improve our knowledge on the mechanisms governing chromatin modifications during cellular reprogramming, used as a tool in cellular therapy.

Experimental approaches : we combine gain- and loss-of-function, genomic (ChIP-seq, RNA-seq) and proteomic (TAP-tag/Mass spec) approaches to study KMTs at the molecular and cellular levels. We mainly use mouse ES cells and myogenic differentiation models (in vitro, ex vivo and in vivo in collaboration).


– Global identification of the genomic targets of the H3K9 KMTs and their targeting mechanisms

To study the cooperation between the different KMTs, we try to identify common genomic targets, with a special interest to genes that regulates the proliferation/differentiation balance. To this end, we are performing ChIP-Seq targeting the KMTs in both proliferating and differentiating cells. We also perform transcriptomic assays (RNA-seq, microarray) in loss- or gain-of-function conditions. We finally ask how the studied KMTs are recruited to their target genes.

– Role of post-translational modifications of H3K9 KMTs

We are studying KMTs trans-methylation events and their functional meanings. Thus, we will check if interaction between KMTs is dependent on their methylation on lysines and on their methyl-lysine binding motifs.

– Epigenetic regulation of muscle stem cells: cooperation between Polycomb group/H3K27 methylation and H3K9 methylation pathways

We try to dissect the composition, mechanisms, targets and kinetics of action of H3K9 KMTs and their link with the PcG/H3K27 methylation machinery during the proliferation-to-differentiation transition. We study how these epigenetic pathways act together to silence genes, those permanently silenced upon cell cycle exit of differentiating cells. We will also identify the factor(s) through which these machineries are co-recruited to common genomic targets.

– The case of the KMT SETDB1

We have recently uncovered that SETDB1 plays an essential role in the regulation of adult muscle satellite cells (MuSCs). Interestingly, SETDB1 has a nuclear and cytoplasmic localization, which is modulated during muscle differentiation by the canonical Wnt signaling. Our working hypothesis is that canonical Wnt signaling is required in adult MuSCs for establishing/maintaining their identity via the control of the epigenome by SETDB1 and counteracting KDMs. Thus, we investigate the mechanisms driving SETDB1 shuttling during muscle terminal differentiation and the outcome at the epigenomic level, and try to characterize SETDB1 non-histone substrates during muscle terminal differentiation.