Extended Data Fig. 3: Loss of PRC1 drives derepression of bivalent genes.
From: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes
a, Immunoblot of K-562 Cas9, PCGF1-KO and EED-KO cells ± 10 ng ml−1 IFN-γ (40 h). b,c, Cell surface MHC-I in K-562 Cas9 cells transduced with either control or PCGF1 sgRNA. c, Mean percentage of MHC-I expression from three experiments, indicated by points. Unpaired two-tailed Student’s t-test, P = 0.0295. d, qRT-PCR for MHC-I genes in K-562 Cas9 cells transduced with control or PCGF1 sgRNA. Bars indicate mean ± s.d. of technical triplicates from a representative experiment. e, Cell surface MHC-I in EED-KO cells transduced with control or MTF2 sgRNA. Representative plot from three experiments (Supplementary Fig. 3). f, Immunoblot of K-562 Cas9 and EED-KO cells transduced with control and PCGF1 sgRNA. g,h, Cell surface MHC-I in K-562 Cas9 cells transduced with RING1A and/or RING1B sgRNA, following treatment with 10 ng ml−1 IFN-γ for 36 h. h, Bars show mean fold change in MFI from 3–5 experiments, indicated by points. Unpaired two-tailed Student’s t-test, P values are indicated. i, Immunoblot of K-562 Cas9 cells transduced with the indicated sgRNA. j, Genomic snapshots of bivalent MHC-I genes showing H3K4me3, H3K27me3 and H2AK119Ub CUT&Tag in K-562 Cas9 (control), EED-KO and PCGF1-KO cells. The H3K4me3 and H3K27me3 control tracks are the same control tracks in Fig. 6f. k, H2AK119Ub CUT&Tag in K-562 cells transduced with control or MTF2 sgRNA. Heatmaps show bivalent genes −3kb TSS/+3 kb TES. Genomic regions are ordered by H2AK119Ub read density in the control sample.
