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

PLoS Comput Biol. 2022 Sep 2;18(9):e1010450. doi: 10.1371/journal.pcbi.1010450. eCollection 2022 Sep.

Abstract

The Polycomb system via the methylation of the lysine 27 of histone H3 (H3K27) plays central roles in the silencing of many lineage-specific genes during development. Recent experimental 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 previous 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 maintenance 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.

MeSH terms

  • Animals
  • Drosophila Proteins* / metabolism
  • Epigenesis, Genetic / genetics
  • Histones* / chemistry
  • Lysine
  • Mice
  • Mouse Embryonic Stem Cells / metabolism
  • Polycomb Repressive Complex 2 / genetics
  • Polycomb Repressive Complex 2 / metabolism
  • Polycomb-Group Proteins / genetics
  • Polycomb-Group Proteins / metabolism

Substances

  • Drosophila Proteins
  • Histones
  • Polycomb-Group Proteins
  • Polycomb Repressive Complex 2
  • Lysine

Grants and funding

The research leading to these results was supported by the University Grenoble-Alpes via the SYMER program (which is funded by the French National Research Agency under the “Investissements d’Avenir” program ANR-15-IDEX-02). DJ acknowledges additional funding from the French National Research Agency [ANR-18-CE12-0006-03, ANR-18-CE45-0022-01]. EF acknowledges funding from ITMO Cancer in the framework of the French Plan Cancer (Systems Biology program). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.