DNA methylation is one of several epigenetic mechanisms that organisms use to control gene expression. Aberrant DNA methylation disrupts normal gene expression and has been associated with various disorders including cancer. The exact role of region-specific DNA methylation, however, is not yet fully understood.
The experimental design entails the analysis of a cerebral brain cortex region of 10-week-old male mice from two strains (C57BL/6J and DBA/2J) in a steady-state model. The study interrogates DNA methylation using whole-genome bisulfite sequencing (WGBS), transcriptome analysis using RNA-seq, and quantitative proteomics using SWATH-MS. R packages and in-house scripts are then used to explore correlations of various omics datasets.
Our preliminary analysis identified 8,907 significant DMRs (differentially methylated regions), 1,426 significant DEGs (differentially expressed genes), and 116 significant DAPs (differentially abundant proteins) between the two mice strains under study. Interestingly, 241 DEGs genes had DMRs, and 8 genes encoding significant DAPs also harbored DMRs. Our observations are in line with known phenotype differences between these two extensively studied mouse strains and are suggestive of a critical role for DNA methylation in this process.