Differentially Methylated Regions in Human Rhombic Lip Compartments Are Enriched in Putative Active Enhancers, Human Accelerated Regions, and Medulloblastoma Copy Number Aberrations

The cerebellar rhombic lip (RL) of the prenatal hindbrain is a progenitor niche essential for cerebellar glutamatergic neurogenesis. Humans demonstrate a structural elaboration of this niche with a rhombic lip subventricular zone (RL-SVZ). Disruption of this zone causes cerebellar malformations and tumors, yet its gene regulatory networks are poorly understood. We present a predicted gene regulatory network for the human RL inferred from epigenomic maps of the developing human cerebellum. We generated DNA methylomes from microdissected mid-gestation human RL ventricular zone (RL-VZ) and RL-SVZ (N = 9; 15-16 post-conception weeks) using low-input Enzymatic MethylSeq, and profiled histone marks of active promoters and enhancers in whole fetal cerebellum (N = 6; 14 and 18 weeks). Transition from RL-VZ to RL-SVZ is accompanied by widespread hypomethylation, including 9,855 differentially methylated regions (DMRs) enriched for binding sites of ATOH1, NEUROD1/2, and HMGA1. Of these, 88.9% are hypomethylated in RL-SVZ, enriched in active enhancers and human accelerated regions, and depleted at promoters. By integrating DMRs with bulk tissue histone maps as well as single-cell chromatin accessibility and transcriptomic maps of the mid-gestation cerebellum, we inferred over 100,000 transcription factor-enhancer-gene links. Twenty-five DMRs overlap human accelerated regions near genes implicated in intellectual disability, autism spectrum disorder, and neurological deficits. DMRs are also enriched in copy-number aberrations in medulloblastoma, with ~ 25% overlapping known aberrant regions, nominating disrupted promoters and enhancers. These data provide a framework for interpreting non-coding variation in human cerebellar development and disease.