Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

Abstract

Although technically feasible, whole-genome analysis of cytosine methylation using bisulfite sequencing remains prohibitively expensive for large eukaryotic genomes. Deng et al. use 30,000 nondegenerate padlock probes to capture ∼66,000 bisulfite-converted sites in human CpG islands and compare their methylation in fibroblasts, embryonic stem cells and induced pluripotent stem cells. Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets. We report a method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution. A set of ~30,000 padlock probes was designed to assess methylation of ~66,000 CpG sites within 2,020 CpG islands on human chromosome 12, chromosome 20, and 34 selected regions. To investigate epigenetic differences associated with dedifferentiation, we compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines. Chromosome-wide methylation patterns were similar among all lines studied, but cytosine methylation was slightly more prevalent in the pluripotent cells than in the fibroblasts. Induced pluripotent stem (iPS) cells appeared to display more methylation than embryonic stem cells. We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes.