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Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells

Kapil Newar 1 Amith Zafal Abdulla 2 Hossein Salari 2 Eric Fanchon 1 Daniel Jost 2 
1 TIMC-BCM - Biologie Computationnelle et Modélisation
TIMC - Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525
Abstract : The Polycomb system via the methylation of the lysine 27 of histone H3 (H3K27) plays cen- tral roles in the silencing of many lineage-specific genes during development. Recent exper- imental evidence suggested that the recruitment of histone modifying enzymes like the Polycomb repressive complex 2 (PRC2) at specific sites and their spreading capacities from these sites are key to the establishment and maintenance of a proper epigenomic landscape around Polycomb-target genes. Here, to test whether such mechanisms, as a minimal set of qualitative rules, are quantitatively compatible with data, we developed a mathematical model that can predict the locus-specific distributions of H3K27 modifications based on pre- vious biochemical knowledge. Within the biological context of mouse embryonic stem cells, our model showed quantitative agreement with experimental profiles of H3K27 acetylation and methylation around Polycomb-target genes in wild-type and mutants. In particular, we demonstrated the key role of the reader-writer module of PRC2 and of the competition between the binding of activating and repressing enzymes in shaping the H3K27 landscape around transcriptional start sites. The predicted dynamics of establishment and mainte- nance of the repressive trimethylated H3K27 state suggest a slow accumulation, in perfect agreement with experiments. Our approach represents a first step towards a quantitative description of PcG regulation in various cellular contexts and provides a generic framework to better characterize epigenetic regulation in normal or disease situations.
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https://hal.archives-ouvertes.fr/hal-03431877
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Soumis le : mardi 16 novembre 2021 - 23:39:07
Dernière modification le : mardi 18 octobre 2022 - 04:29:34
Archivage à long terme le : : jeudi 17 février 2022 - 21:34:26

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Kapil Newar, Amith Zafal Abdulla, Hossein Salari, Eric Fanchon, Daniel Jost. Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells. PLoS Computational Biology, 2022, 18, ⟨10.1371/journal.pcbi.1010450⟩. ⟨hal-03431877⟩

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