Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq]

The DNA modifications, 5-methylcytosine (5mc) and 5-hydroxymethylcytosine (5hmc), represent powerful epigenetic regulators of temporal and spatial gene expression across unique brain cell types in health and disease. Yet, how the cooperation of these genome-wide, epigenetic marks vary across different neural cell populations serve to determine unique transcriptional signatures and alternative splicing has not been evaluated. Here we applied Nanopore sequencing of native DNA to obtain a complete, genome wide, single-base resolution atlas of 5mc and 5hmc modifications in neurons, astrocytes and microglia in the mouse cortex (over 40 million CpG sites quantified, 99% genome coverage). Cell-type specific RNA sequencing was performed in tandem to evaluate the transcript expression of all coding genes. In each cell type evaluated integrating the DNA methylation status with coding gene expression revealed 5hmc positively correlated with gene expression. We identified that 5hmC was enriched in astrocytes and demonstrated 100% positive correlation with previously described and novel astrocyte specific cell markers. As reported, 5mC methylation in promoters negatively correlated with gene expression across cell types and this modification was highest in microglia. Our analysis also identified several novel transcription factors which cooperate with 5mC and 5hmC methylation to regulate exon inclusion across all cell populations. Finally, we provide this quantitative, genome-wide, base resolution DNA methylation data as an interactive, online resource (NAM-ME, Neuronal, Astrocyte, Microglia Methylome) to serve as a benchmark dataset for those interested in the methylome landscape in pre-clinical murine models in health and disease.