Dramatic Increase in Cell-subset Specific Methylation Accompanies Mammalian Brain Development [hairpin BS-Seq]

Purpose: This study aims to identify cell-subset specific methylated (CSM) loci in mammalian brain methylomes and to uncover epigenetic regulatory networks associated with brain development. Methods: To generate methylation data from DNA double strands simultaneously, genome-scale hairpin bisulfite sequencing technique was used for the assessment of the levels of asymmetric DNA methylation in the human frontal cortical gray and white matters Results and conclusion: CSM loci increase dramatically during early stages of brain development. They are overrepresented in cis-regulatory elements such as active enhancers and promoters, and are enriched for GWAS variants associated with neurological-disorder-related diseases/traits. Co-methylated CSM clustering analysis indicated that the CSMs hypo-methylated in neurons are enriched for EGR1 binding sites.Our results show the functional relevance of CSM loci identified and provide insights into epigenetic complexity of mammalian brains. We first explored asymmetric DNA methylation in human fetal and adolescent brain tissues using genome-scale hairpin bisulfite sequencing technique. Based on the finding that brain methylomes are with exceeding high methylation fidelity, we developed an analytical procedure to identify CSM loci and applied it to human and mouse brain methylomes throughout the life span. We further explored the functional relevance of CSM loci via integrative “omics” analysis with ChIP-Seq data for histone modifications, transcription factor (TF) bindings and GWAS disease/trait associated variants.