In this study, Ma¨tlik et al. used RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in progenitor cerebellar granule cells. Inhibition of H3K27 methyltransferases EZH1/2 perturbed glial-guided migration while accelerating neuronal maturation, and this study demonstrates that temporally regulated H3K4me3/H3K27me3 bivalency influences neurodevelopmental gene expression, lineage specification, migration, and differentiation.