THE IMPACT OF REPLICATION STRESS ON THE EPIGENOME OF MOUSE EMBRYONIC STEM CELLS

Epigenetic reprogramming and chromatin structure guide differentiation and define cell identity during embryogenesis. To maintain cell identity and genome integrity, epigenetic marks are faithfully inherited during DNA replication through tightly coordinated processes. Our recent work demonstrated that disruption of DNA replication, known as replication stress, can expand the cell fate of mouse embryonic stem cells (mESCs) by activating totipotency and extra-embryonic pathways. However, the underlying epigenetic mechanisms remain unclear. Preliminary data indicated that polycomb repressive complex 2 (PRC2)-targeted genes are aberrantly activated upon replication stress in mESCs. Genome-wide chromatin immunoprecipitation of suppressive and active histone marks revealed a global loss of H3K27me3 and the maintenance of H3K4me3 at gene promoters following aphidicolin-induced replication stress. Notably, the activation of a subset of bivalent developmental genes – marked by both H3K27me3 and H3K4me3 – was associated with extra-embryonic differentiation. Furthermore, 3D chromatin organization analysis revealed shifts in chromatin subcompartments from inactive to active states and from lamina-associated to H3K27me3-related inactive compartments, consistent with H3K27me3 rearrangements and a weaker nuclear lamina. These observations suggest that active H3K27 methylation may occur in gene deserts near stalled replication forks or DNA damage sites, as indicated by increased interactions between PRC2, replisome factors, and double-strand breaks. In summary, our findings propose a role for PRC2 in mediating the replication stress response by altering chromatin dynamics, which ultimately expands cell fate by lowering reprogramming barriers. These insights improve our understanding of how unresolved replication stress can disrupt cell identity and lead to aberrant differentiation or de-differentiation during embryonic development, cancer onset, and aging.