Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells

Abstract

SummaryWhen self-renewing pluripotent cells receive a differentiation signal, ongoing cell duplication needs to be coordinated with entry into a differentiation program. Accordingly, transcriptional activation of lineage specifiers genes and cell differentiation is confined to the G1-phase of the cell cycle by unknown mechanisms. We found that Polycomb repressive complex 2 (PRC2) subunits are differentially recruited to lineage specifier gene promoters across cell cycle in mouse embryonic stem cells (mESCs). Jarid2 and the catalytic subunit Ezh2 are dramatically accumulated at target promoters during S and G2, while the transcriptionally activating subunits EPOP and EloB are enriched during G1. Importantly, fluctuations in the recruitment of PRC2 subunits promote changes in RNA synthesis and RNA polymerase II binding that are compromised in Jarid2 -/- mESCs. Overall, we show that differential recruitment of PRC2 subunits across cell cycle enables the establishment of a chromatin state that facilitates the induction of cell differentiation in G1.

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

“…While the relationship between PRC2mediated histone methylation and DNA methylation is not fully understood, DNA methylation may serve to "lock in" gene silencing with a mechanism with more robust mitotic inheritance 147 . PRC2 targets in stem cells include pluripotency/stemness genes [148][149][150] , and are enriched for bivalent H3K27me3/H3K4me3 marks 151,152 , suggesting that PRC2 results in "poising" rather than in complete silencing at those sites. In contrast, more differentiated cells reinforce gene silencing by increasing the length of H3K27me3 domains, or through complementary silencing mechanisms including DNA methylation [114][115][116] .…”

ARGONAUTE proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells

“…In order to determine whether H3K27me3 loss correlates with changes in the expression of the Ago2&1_KO DEGs, we clustered ChIP-seq levels at transcript regions using kmeans (k=4) clustering (Dataset EV2) (Ramírez et al, 2016). The first cluster (cluster_1) represents the genes most strongly enriched in H3K27me3 in WT and highly overlaps with known bivalent genes in mESCs (Asenjo et al, 2020)…”

“…For the comparison of the H3K27me3 ChIP-seq cluster_1 with known bivalent genes, the list of highconfidence bivalent "HC-Bivalent" genes from (Asenjo et al, 2020) was retrieved.…”

Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

“…Although the concept of G1 as a window for cell fate change has been around for decades ( Mummery et al., 1987 ; Pierce et al., 1984 ; Wells, 1982 ), only recently it was shown, for both human and mouse PSCs, that G1-sorted cells respond more rapidly to differentiation cues than S- or G2-sorted cells, which do not respond until the next G1 phase ( Calder et al., 2013 ; Coronado et al., 2013 ; Pauklin and Vallier, 2013 ; Sela et al., 2012 ). Studies have also reported “noisy” expression of developmental genes during G1 ( Asenjo et al., 2020 ; Singh et al., 2013 ), which could represent a temporal priming step that enables PSCs to tip the balance from self-renewal to lineage specification. This finding was independently validated using PRO-seq analysis in mouse PSCs, which revealed a weak but consistent activation of various lineage-related genes and enhancers during early and late G1 phase ( Pelham-Webb et al, 2020 ).…”

“…Studies in human PSCs have implicated signaling molecules (Smads, Cyclins), which naturally fluctuate during cell cycle, concluding that varying levels of these factors allow for differentiation to endoderm in early G1 and neuroectoderm in late G1 ( Pauklin et al., 2016 ; Pauklin and Vallier, 2013 ). Others consider that transient relaxation of repressive mechanisms during M-to-G1, such as the recently described cell-cycle-dependent fluctuations of PRC2 subunits ( Asenjo et al., 2020 ), could be sufficient to allow for gene de-repression. In agreement, promoters of transiently G1-activated genes predominantly enriched for binding of PRC2 components ( Pelham-Webb et al, 2020 ).…”