Single cell methylation, RNA, and ATAC sequencing of brain tissue in inbred mouse strains

Despite the extraordinary advances in genetics over the last two decades, relating genetic variants to behavior remains a fundamental challenge in understanding human disease. Particularly in mice, progress is frustrated by the low resolution of genetic mapping, and consequently by the thousands of candidate causal variants that must be screened. As an approach to prioritizing causative variants, we examined the relationship between DNA methylation and genetic variation generating genome-wide, base-pair resolution maps of multiple cell types from the hippocampus of eight fully sequenced inbred strains of Mus musculus. We find that at CpG densities cells of less than 40 CpG/Kb, cells compensate for loss of methylated sites by recruiting additional sites to maintain methylation levels. At higher CpG densities the exact location of a methylated site becomes more important; specific sites are maintained even at the cost of reducing the number of methylated sites. This implies that the functional consequences of sequence variation, as mediated by methylation changes, depend on local CpG density. We test this hypothesis by assessing the impact of mutations on single cell transcript abundance for two inbred strains (C57BL/6J and DBA/2J). In regions of high CpG density, mutations have an effect five times larger than in regions of low density, which, from single cell ATAC-seq data, we localize to enhancers. With approximately tenfold fewer mutations in high than low density CpG regions, candidate variants affecting behavior can be prioritized based on CpG density and localization to functional annotations. Furthermore, the distribution of functional elements with respect to CpG density indicates that the increased mutational load associated with methylation may be targeted to a subset of functional elements.