Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes [ChIP-seq]

Precise dynamic control of activating H3K4me3 and repressive H3K27me3 histone modifications at bivalent gene promoters is essential for normal development and frequently corrupted in cancer. Using whole genome CRISPR/Cas9 screens we identify specific roles for MTF2-PRC2.1 and PCGF1-PRC1.1 polycomb complexes, and MLL1/2-COMPASS-like complex components in maintaining bivalency. Contrary to expectations, loss of Menin or inhibition of the Menin-MLL1/2 interaction, induces activation of bivalent genes via loss of polycomb-mediated repression and defines distinct roles for MLL1/2 and Menin in gene regulation. Whilst Menin and MLL1/2 contribute to maintenance H3K4me3 at active genes, a separate Menin-independent function of MLL1/2 opposes polycomb mediated repression at bivalent genes. MLL1/2 are essential for basal transcription and, although dispensable for transcription factor driven activation, facilitate transcriptional consistency during dynamic changes in gene expression. This functional partitioning of COMPASS complex components reveals therapeutic opportunities to target oncogenic and immunosuppressive functions of PRC2 through pharmacological inhibition of Menin. Overall design: ChIPseq for H3K4me3, SUZ12 and MENIN in MENIN KO, or MEN inhibitor treated K562 cells. ChIPseq for MLL1 in embyonic stem cell line H9 pre-treated with DMSO, Menin inhibitor, EZH2 inhibitor or both Menin and EZH2 inhibitors ChIP-reChIP for H3K4me3 and H3K27me3 in K562 Cas9 cells.