Genetic analysis of the cardiac methylome at single nucleotide resolution in the Spontaneously Hypertensive Rat and the Brown Norway Rat

Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes, but the extent to which these vary between individuals and are regulated by germline sequence variation is poorly understood. Here, we used whole-genome bisulfite sequencing in multiple animals from an inbred model of cardiovascular disease, the spontaneously hypertensive rat (SHR), and from control Brown Norway (BN)rats, to define at single-nucleotide resolution the genetic architecture of cytosine methylation in the mammalian heart. Variability in CpG methylation was much greater between than within the SHR and BN strains and analysis of 10.6 million CpG dinucleotides identified 77,088 that were differentially methylated between the strains. CpG cytosine methylation in parental strains, F1 hybrids and recombinant inbred strains showed that inter-strain differences in CpG methylation are substantially cis-regulated, mostly in a monogenic fashion, explaining almost 60% of inter-strain variation in CpG methylation at cis-linked loci. Remarkably, we found local sequence motifs associated with increased and decreased methylation that are conserved across tissues of rats, mice and humans, suggesting a common mechanism contributing to the regulation of CpG cytosine methylation. These data will stimulate investigation of the molecular basis of locally regulated variation in CpG methylation and will provide a valuable resource for the study of the role of CpG methylation in development of cardiovascular disease phenotypes such as cardiac hypertrophy and failure.