Extended Data Fig. 1

Transient disruption of PRC2 triggers permanent activation of a large subset of repressed target genes in differentiated somatic cells. a, Proportions of non-responsive and responsive genes among the indicated totals of H3K27me3-positive genes, in NPCs, ESCs and iMEF line B after treatment with PRC2 inhibitors and washout, and in iMEF lines A and B after genetic deletion of Ezh2 followed by rescue. H3K27me3 profiles in ESCs were determined from a published data set²⁶. NPC, mouse neural progenitor cells. ESC, mouse embryonic stem cells. iMEF, immortalized mouse embryonic fibroblasts. b, Metaplots of average ATAC-seq density over the interval TSS -/ + 3 kb for the full sets of H3K27me3-positive and transcriptionally responsive PRC2 targets in NPC (ref. ³⁶) and iMEF A (this study). NPC H3K27me3-positive and responsive: n = 5169 and n = 412 genes respectively; iMEF A H3K27me3-positive and responsive: n = 8344 and n = 326 genes respectively. p-values refer to two-sided Mann–Whitney tests comparing read counts for H3K27me3-positive and responsive genes over the interval. c, Western blot of nuclear extracts from the indicated conditions (n = 2 biologically independent samples). PRC2i, PRC2 inhibition with 2 µM UNC1999 and 4 µM A-395. d, MA plots comparing RNA-seq levels of H3K27me3-positive genes in ESCs cultured with PRC2 inhibitors, or after washout of the inhibitors, to mock-treated cells. CPM, counts per million. FC, fold change. Significantly differentially expressed genes (Benjamini-Hochberg-adjusted p < 0.05 for two-sided likelihood ratio test on negative binomial generalized linear model) are indicated in red. e, Western blot of nuclear extracts from the indicated conditions. Representative example of n = 2 independent samples. f, Heatmap of RNA-seq levels (log2 fold change versus the mean of the two mock replicates) in the indicated conditions for the full sets of reversible and irreversible PRC2 targets in iMEF B. g, Left, heatmap of RNA-seq levels (log2 fold change versus the mean of the two wild-type replicates) in the indicated conditions for the full sets of reversible and irreversible PRC2 targets in iMEF A. Right, metaplots of average H3K27me3 ChIP-seq density over the interval TSS – 3 kb to TES + 3 kb for the full sets of reversible and irreversible PRC2 targets in iMEF A in the indicated conditions. TSS, transcription start site. TES, transcription end site. h, As in g but in iMEF B.

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