KMT2D temporally activates neuronal transcriptional factor genes to mediate cerebellar granule cell differentiation

Spatiotemporal gene expression is the fundamental feature of cellular differentiation, including neuron differentiation. The epigenetic mechanism underlying spatiotemporal gene regulation during in vivo neuron differentiation remains largely unknown. Granule cells (GCs) constitute the vast majority of neurons in the cerebellum, which contains most of neurons in the brain. Here, we show that <i>Atoh1-Cre</i>-mediated knockout (ACKO) of <i>Kmt2d</i> encoding the lysine methyltransferase KMT2D (MLL4) in cerebellar GC lineage inhibits the transition of GC progenitors to GCs while cell non-autonomously affecting other cerebellar cells. <i>Kmt2d</i> ACKO impaired cerebellum-associated behaviors and caused facial peculiarity, microcephaly, and reduced body size in mice. KMT2D temporally activated neuronal differentiation programs in cerebellar GCs. KMT2D-mediated activation of the key neuronal transcription factor genes <i>En2</i>, <i>Pax6</i>, and <i>Myt1l</i> via super-enhancer/enhancer programming was critical for GC differentiation. These findings reveal a unique epigenetic mechanism in which KMT2D temporally orchestrates gene expression required for cerebellar GC differentiation by programming neuronal enhancers.