Characterizing methylation designs
DNA methylation users was basically measured entirely blood samples out of 100 not related person people because of the Illumina HumanMethylation450 BeadChips in the solitary-CpG-site quality having 482,421 CpG sites . single-CpG-website methylation levels is actually quantified because of the ?, the brand new ratio regarding probes for this CpG web site that will be methylated, that’s computed because methylated probe intensity split by sum of both methylated and you may unmethylated probe intensities; for this reason, ? ranges out-of no (the fresh new CpG website try unmethylated) to a single (the CpG website try completely methylated). After these types of research was in fact filtered and preprocessed (discover Materials and techniques), 394,354 CpG sites stayed over the twenty two autosomal chromosomes.
First, we examined the distribution of DNA methylation levels, ?, at CpG sites on autosomal chromosomes across all 100 individuals. The majority of CpG sites were either hypermethylated or hypomethylated (levels of methylation that are consistently higher or lower than 0.5, respectively), with 48.2% of sites with ?>0.7 and 40.4% of sites with ?<0.3 (Additional file 1: Figure S1A). Using a cutoff of 0.5, across the methylation profiles and individuals, 54.8% of these CpG sites have a methylated status (??0.5). Across the individuals, we observed distinct patterns of DNA methylation levels in different genomic regions (Additional file 1: Figure S1B). Using CGIs labeled in the UCSC genome browser , we defined CGI shores as regions 0 to 2 kb away from CGIs in both directions and CGI shelves as regions 2 to 4 kb away from CGIs in both directions . We found that CpG sites in CGIs were hypomethylated (81.2% of sites with ?<0.3) and sites in non-CGIs were hypermethylated (73.2% of sites with ?>0.7), while CpG sites in CGI shore regions had variable methylation levels following a U-shape distribution (39.0% of sites with ?>0.7 and 46.2% of sites with ?<0.3), and CpG sites in CGI shelf regions were hypermethylated (78.2% of sites with ?>0.7). These distinct patterns reflect highly context-specific DNA methylation levels genome-wide.