Differentially Methylated Regions in Human Rhombic Lip Compartments Are Enriched in Putative Active Enhancers, Human...

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.