Soutenance de Amith Zafal

A multitude of stable and heritable phenotypes arise from the same DNA sequence, owing to epigenetic regulatory mechanisms relying on the molecular cooperativity of “reader-writer” histone modifying enzymes. In this thesis, we focus on the fundamental mechanisms behindepigenome regulation and memory encoded by post-translational modifications of histone tails. Our aim is to develop general mechanistic frameworks of epigenomic regulation and memory integrating key biochemical and physical processes in order to investigate how such generic principles can be contextualized to specific biological systems.We introduce a unifiedmodeling framework, the “Painter model”, describing the mechanistic interplay between sequence-specific recruitment of chromatin regulators, chromatin-state-specific reader-writer processes and long-range spreading mechanisms. A systematic analysis of the model building blocks highlights the crucial impact of tridimensional chromatin organization and state-specific recruitment of enzymes on the stability of epigenomic domains andon gene expression. In particular, we show that enhanced 3D compaction of the genome and enzyme limitation facilitate the formation of ultra-stable, confined chromatin domains. The model also captures how chromatin state dynamics impact the intrinsic transcriptionalproperties of the region, slower kinetics leading to noisier expression. We apply our framework to analyze experimental data, from the propagation of γH2AX around DNA breaks in human cells to the maintenance of heterochromatin in fission yeast, illustrating how the painter model can be used to extract quantitative information on epigenomic molecular processes. To go beyond the effective 3D description, we study explicit 3D polymer dynamics. Specifically, to investigate the caveats of simulating genes or regions of interest which are usually much smaller compared to the full length of a chromosome. Since the physics of long, topologically-constrained polymers may significantly deviate from those of shorter chains, we theoretically investigate the extent of the minimal genomic region that one should explicitly consider around a given locus in order to effectively capture the correct dynamical and structural properties of the domain of interest. We show that this minimal size depends on the overall epigenomic context and on the entanglement properties of the long polymer. Finally, we present the ongoing work, integrating the painter model with explicit 3D polymer dynamics. We introduce a theoretical framework coupling 3D polymer dynamics and epigeneome regulation by diffusing HMEs, the “Living painter” model, that exhibits intriguing properties on the coupling between 3D genome folding and epigenetic spreading, reflecting the scope and extension of the thesis.