MLL3/MLL4 methyltransferase activities control early embryonic development and ESC differentiation in a lineage-selective manner

H3K4me1 methyltransferases MLL3 (KMT2C) and MLL4 (KMT2D) are critical for enhancer activation, cell differentiation and development. However, roles of MLL3/4 enzymatic activities and MLL3/4-mediated enhancer H3K4me1 in these processes remain unclear. Here, we report that constitutive elimination of both MLL3 and MLL4 enzymatic activities prevents initiation of gastrulation and leads to early embryonic lethality in mice. However, selective elimination of MLL3/4 enzymatic activities in embryonic, but not extraembryonic, lineages leaves gastrulation largely intact. Consistently, embryonic stem cells (ESCs) lacking MLL3/4 enzymatic activities can differentiate towards the three embryonic germ layers but show aberrant differentiation to extraembryonic endoderm and trophectoderm. The failure in extraembryonic endoderm differentiation can be attributed to markedly reduced enhancer-binding of the lineage-determining transcription factor GATA6. Furthermore, we show that MLL3/4-catalyzed H3K4me1 is largely dispensable for enhancer activation during ESC differentiation. Together, our findings suggest a lineage-selective, but enhancer activation-independent, role of MLL3/4 methyltransferase activities in early embryonic development and ESC differentiation. Overall design: Expression profiling by RNA-Seq in ESCs (D0), at D4/D10 of EB differentiation and at D8/D16 of neural differentiation, and ChIP-Seq profiling of MLL4 as well as active enhancer marks H3K4me1 and H3K27ac in ESCs (D0), at D4 of EB differentiation and at D8 of neural differentiation, profiling of chromatin accessibility by ATAC-Seq in ESCs (D0) and at D4 of EB differentiation