Fig 1: Displacement of Menin from distant genomic loci activates bivalent gene expression.(a) H3K4me3 ChIP-seq and H3K27me3 CUT&Tag in K-562 Cas9 cells, and Menin ChIP-seq data in Cas9, 1µM VTP50469 treated (48h) and MEN1 KO cells. Genomic snapshots of Menin-KMT2A/B target gene, JMJD1C, and bivalent MHC-I gene, HLA-B. The H3K4me3 and H3K27me3 tracks are the same control tracks in Fig. 2h. (b) Venn diagram depicting overlap in genes up-regulated (FDR p-adj <0.05 and fold-change >2) after CRISPR deletion of MEN1, PSIP1 and EED. (c) Proportion of genes that are bivalent amongst genes showing increased or decreased expression (FDR p-adj <0.05 and fold-change >2) following CRISPR deletion of MEN1, PSIP1 and EED. (d) Box-plot depicting Log2FC in gene expression in K-562 MEN1 KO cells compared to Cas9 control from 3 biological replicates. Two-sided Welch’s t-tests, p=8.2e-42. (e) Volcano plot of the top 3,000 genes (Log2FC) from RNA-seq in K-562 cells treated with DMSO or 500nM VTP50469. Selected MHC-I genes are labelled. Two-sided Wald test, p-values adjusted for multiple testing. (f & g) H3K4me3, SUZ12 ChIP-seq and H3K27me3 CUT&Tag in K-562 Cas9 control and MEN1 KO cells. (f) Genomic snapshots of MHC-I genes. The tracks in control cells are the same control tracks in Fig. 2h. (g) Box-plots, from a representative experiment, depicting changes H3K4me3 (left), H3K27me3 (middle) and SUZ12 (right) at Menin and non-Menin bound, bivalent and not-bivalent genes (Log2FC). Two-sided Welch’s t-tests, p-values indicated. (h & i) Flow cytometry in human iPSCs treated with VTP50469 and/or EPZ-011989 for 5 days or indicated times. (h) Cell surface CD9, CD13, CXCR4 and KDR. (i) Points show mean percentage of CD13, CXCR4 and KDR positive cells from 4 independent experiments. p-values calculated using unpaired two-tailed t-tests comparing each sample to respective DMSO control. Significant changes are indicated. (j) Genomic snapshots of bivalent genes CD13 (ANPEP) and CXCR4 showing H3K4me3 and H3K27me3 ChIP-seq data in human embryonic cell line H9 (GEO:GSE96336, GEO:GSE96353) and human induced pluripotent stem cell line iPS-20b (GEO:GSM772844, GEO:GSM772847) 84. (d & g) Whiskers represent minimum and maximum, the box represents the interquartile range, and the centre line represents the median.