Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes [CUT&TAG]

Precise control of activating H3K4me3 and repressive H3K27me3 histone modifications at bivalent promoters is essential for normal development and is frequently corrupted in cancer. By coupling a cell surface readout of bivalent MHC class I gene expression with whole genome CRISPR/Cas9 screens, we identify specific roles for MTF2-PRC2.1, PCGF1-PRC1.1 and Menin- KMT2A/B complexes in maintaining bivalency. Unexpectedly, genetic loss or pharmacological inhibition of Menin phenocopies the effects of polycomb disruption, resulting in derepression of bivalent genes in both cancer cells and pluripotent stem cells. Whilst Menin and KMT2A/B contribute to H3K4me3 at active genes, a separate Menin-independent function of KMT2A/B maintains H3K4me3 and opposes polycomb-mediated repression at bivalent genes. Release of KMT2A from active genes following Menin targeting alters the balance of polycomb and KMT2A at bivalent genes, facilitating gene activation. This functional partitioning of Menin-KMT2A/B complex components reveals novel therapeutic opportunities that can be leveraged through inhibition of Menin. Overall design: CUT&TAG for H3K4me3, H3K27me3 and H2AK119 in K562 Cas9 expressing, MEN1 KO, EED KO and PCGF1 KO cells. CUT&TAG for: 1) H3K4me3, H3K27me3 and H2AK119 in K562 Control sgRNA, MTF2 sgRNA and AEBP2 sgRNA cells; 2) H3K4me3 in K562 Cas9 expressing and KMT2A/B KO cells pre-treated with EZH2i +/- interferon gamma. CUT&RUN for MLL1 in K562 Cas9 expressing and MEN1 KO cells.