Variably methylated genes showed considerable methylation volatility for single CpG sites with methylation levels changing from completely unmethylated to completely methylated several times throughout the sequenced promoter region.
Teh and coworkers [ 183] have investigated the genotypes and DNA methylomes of 237 neonates and found some 1500 punctuate regions of the methylome highly variable across individuals, termed variably methylated regions (VMRs), against a homogeneous background.
Regression trees for individual cancer types (Additional file 1: Figure S4) were learned using the average level of methylation computed across all the probes in the cancer-specific variably methylated probe set as the response variable.
The observation that CGIs in Clusters II and III tend to exhibit highly methylome-specific patterns of DNA methylation is thus consistent with the idea that intragenic and intergenic CpG sites are highly variably methylated and exhibit tissue-specific DNA methylation.
These plots visually demonstrate the distribution of methylated and unmethylated probes, whereby a large fraction of the variably methylated sites have very low levels of methylation in controls and become aberrantly hypermethylated in tumors (Additional file 1: Figure S1A).
They have identified the locations of variable regions of DNA methylation among individuals in mouse liver and termed them variably methylated regions (VMRs).
Recently it has been shown, that variably methylated regions (VMRs) exist in the genome which are highly variable in DNA-methylation among individuals [38].
Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that correlate to DNA methylation measured in easy accessible peripheral tissues.
We develop a region discovery method tailored to Infinium 450K methylation data, for differentially methylated region (DMR) and variably methylated region (VMR) discovery.
For the variably methylated genes (AKAP12, BRMS1, KiSS-1 and TIMP3), no significant correlations between methylation-score and mRNA expression were detected.
Significance analysis and statistical dissection of variably methylated regions.
