DNA methylation confers a cerebellum-specific identity in non-human primates.

Selective regulation of gene expression across distinct brain regions is crucial for establishing and maintaining subdivision identities. DNA methylation, a key regulator of gene transcription, modulates transcriptional activity through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While DNA methylation is hypothesized to play an essential role in shaping brain identity by influencing gene expression patterns, its direct contribution, especially in primates, remains largely unexplored. This study examined DNA methylation landscapes and transcriptional profiles across four brain regions, including the cortex, cerebellum, striatum, and hippocampus, using samples from 12 rhesus monkeys. The cerebellum exhibited distinct epigenetic and transcriptional signatures, with differentially methylated regions (DMRs) significantly enriched in metabolic pathways. Notably, genes harboring clustered differentially hydroxymethylated regions (DhMRs) overlapped with those implicated in schizophrenia. Moreover, 5mC located 1 kb upstream of the ATG start codon was correlated with gene expression and exhibited region-specific associations with 5hmC. These findings provide insights into the coordinated regulation of cerebellum-specific 5mC and 5hmC highlighting their potential roles in defining cerebellar identity and contributing to neuropsychiatric diseases.