Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells

Abstract

The potential of pluripotent cells to respond to developmental cues and trigger cell differentiation is enhanced during the G1 phase of the cell cycle, but the molecular mechanisms involved are poorly understood. Variations in polycomb activity during interphase progression have been hypothesized to regulate the cell-cycle-phase-dependent transcriptional activation of differentiation genes during lineage transition in pluripotent cells. Here, we show that recruitment of Polycomb Repressive Complex 1 (PRC1) and associated molecular functions, ubiquitination of H2AK119 and three-dimensional chromatin interactions, are enhanced during S and G2 phases compared to the G1 phase. In agreement with the accumulation of PRC1 at target promoters upon G1 phase exit, cells in S and G2 phases show firmer transcriptional repression of developmental regulator genes that is drastically perturbed upon genetic ablation of the PRC1 catalytic subunit RING1B. Importantly, depletion of RING1B during retinoic acid stimulation interferes with the preference of mouse embryonic stem cells (mESCs) to induce the transcriptional activation of differentiation genes in G1 phase. We propose that incremental enrolment of polycomb repressive activity during interphase progression reduces the tendency of cells to respond to developmental cues during S and G2 phases, facilitating activation of cell differentiation in the G1 phase of the pluripotent cell cycle.

The molecular basis of cell memory in mammals: The epigenetic cycle

“…At later stages of the cell cycle when CDK2-CyclinA is no longer active, CDK1-CyclinB phosphorylates T487 and might promote disassembly of PRC2 complex during metaphase. In fitting with these observations, Polycomb repressive activity on lineage specifier genes is enhanced in G 2 phase as compared to cells in G 1 phase in mESCs ( 124 , 140 ). In the case of the DNA methylation and H3K9me3 systems, evidence linking cell cycle machinery and methylation of DNA or H3K9 is scarcer.…”

“…In the case of mammalian ESC populations, cells in G 1 are more prone to induce expression of developmental genes and effectively differentiate than cells in S and G 2 phases ( 173 – 176 ). The higher tendency of cells in G 1 to exit pluripotency depends on the combined action of several mechanisms ( 177 ), of which current studies suggest that the TF SMAD2/3 ( 175 ), TDG ( 178 ), and the chromatin proteins trithorax ( 179 ) and polycomb ( 124 , 140 ) are key regulators. The repressive activity of PRC1 and PRC2 on lineage specifier genes is partially alleviated during the G 1 phase ( 124 , 140 , 160 ).…”

“…The higher tendency of cells in G 1 to exit pluripotency depends on the combined action of several mechanisms ( 177 ), of which current studies suggest that the TF SMAD2/3 ( 175 ), TDG ( 178 ), and the chromatin proteins trithorax ( 179 ) and polycomb ( 124 , 140 ) are key regulators. The repressive activity of PRC1 and PRC2 on lineage specifier genes is partially alleviated during the G 1 phase ( 124 , 140 , 160 ). Concordantly, cells in G 1 phase accumulate higher levels of the transcriptional activating mark H3K4me3 and its methyltransferase enzyme KMT2B at the promoter of lineage specifier genes ( 179 , 180 ).…”

“…Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analyses of a set of histone PTMs in HeLa cells have shown that the genomic distribution of H3K27me3 and other histone methylation marks (i.e., H3K36me3 and H3K4me3) are similar in asynchronous and metaphase-arrested cells ( 136 ), supporting that the Polycomb system might transmit epigenetic information through stable methylation of H3K27 through mitosis. However, characterization of the activity of PRCs during interphase transition supports that polycomb domains build up in every cell cycle in mESCs ( 124 , 140 , 141 ), suggesting that the genomic distribution of H3K27me3 is perturbed during mitosis. These studies have been carried out in different systems, and therefore, they raise the possibility that the mechanisms that endorse epigenetic memory are not identical in different cell types (human cancer HeLa-S3 cells versus mouse pluripotent ESCs).…”

“…Concordantly, cells in G 1 phase accumulate higher levels of the transcriptional activating mark H3K4me3 and its methyltransferase enzyme KMT2B at the promoter of lineage specifier genes ( 179 , 180 ). This is associated to a higher level of transcriptional activation of PRC-repressed lineage specifier genes during the G 1 phase ( 124 , 160 , 181 ) and increased cell differentiation propensity ( 140 , 173 – 176 ). The preference of pluripotent cells to enter lineage transition during G 1 might also be favored by increased UTX-mediated H3K27me3 demethylation activity during S phase, facilitating the engagement of the newly G 1 -synthesized lineage specifier TFs on their target genes ( 182 ).…”