Abstract
Polycomb Repressive Complex 2 (PRC2) is crucial for the coordinated expression of genes during early embryonic development, catalyzing histone H3 lysine 27 trimethylation. Two distinct PRC2 complexes, PRC2.1 and PRC2.2, contain respectively MTF2 and JARID2 in embryonic stem cells (ESCs). In this study, we explored their roles in lineage specification and commitment, using single-cell transcriptomics and mouse embryoid bodies derived from Mtf2 and Jarid2 null ESCs. We observe that the loss of Mtf2 results in enhanced and faster differentiation towards cell fates from all germ layers, while the Jarid2 null cells are predominantly directed towards early differentiating precursors, with reduced efficiency towards mesendodermal lineages. These effects are caused by derepression of developmental regulators that are poised for activation in pluripotent cells and gain H3K4me3 at their promoters in the absence of PRC2 repression. Upon lineage commitment, the differentiation trajectories are relatively similar to those of wild-type cells. Together, our results uncover a major role for MTF2-containing PRC2.1 in balancing poised lineage-specific gene activation, whereas the contribution of JARID2-containing PRC2 is more selective in nature compared to MTF2. These data explain how PRC2 imposes thresholds for lineage choice during the exit of pluripotency.
Highlights
Mtf[2] null Jarid[2] null Eed null TimepointDay 0 Day 2 Day 4 Day 7 log2(Mutant/WT)Meso-endodermal lineage PluripotencyPrimordial Germ Cell EctodermalCxcr[4] Eomes Gata[6 ] Mixl[1] Pdgfra Sox[7] T
Embryoid bodies of Polycomb Repressive Complex 2 (PRC2) mutant embryonic stem cells (ESCs) differentiate to cell types across all germ layers
We and others have observed differences in core PRC2 recruitment between the loss of MTF2 (PRC2.1 mutant) or JARID2 (PRC2.2 mutant) in mESCs15,22,31. This potentially affects the repression of key lineage transcription factor genes, for example Otx[2], where EZH2 binding was dramatically reduced in the Mtf[2] null compared to the Jarid[2] null or wild-type cells (Fig. 1a)
Summary
Embryoid bodies of PRC2 mutant ESCs differentiate to cell types across all germ layers. This potentially affects the repression of key lineage transcription factor genes, for example Otx[2], where EZH2 binding was dramatically reduced in the Mtf[2] null compared to the Jarid[2] null or wild-type cells (Fig. 1a) We wondered how such a loss of PRC2 subunits affects the exit of pluripotency and early germ layer differentiation. Clusters 9, 10, 13, and 16, mainly Eed null cells, appear to be restricted in differentiation (Fig. 1e; bottom right region of UMAP) and do not share a similar path compared to the WT cells and other PRC2 subunit mutants in both early and late stage differentiation Compared to these cells, the transcriptomes of Mtf[2] null and Jarid[2] null ES cells exhibit smaller differences with WT ES cells, but still form genotypespecific clusters when not differentiated (clusters 3, 8, and 0 for, respectively, wild type, Mtf[2] null, and Jarid[2] null cells).
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