DNA Methylation Analysis

DNA methylation is a chemical modification of the DNA by which methyl groups are added to the DNA molecule. In mammals, methylation is added to CpG sites. DNA methylation changes the activity of genes or regulatory elements, without changing the sequence. We offer different types of DNA methylation profiling, all based on next-generation sequencing. A description of these methods and how they compare with each other is provided below.


Whole-genome bisulfite sequencing allows for base-pair resolution quantification of DNA methylation across the whole genome. Although this method is considered the gold standard, it is also the most expensive as high-coverage sequencing is required across the whole genome. Advantages of WGBS include that it can be applied to all species and has low DNA input requirements ( >10 nanograms).

Reduce Representation Bisulfite Sequencing (RRBS) uses digestion with the restriction enzyme MspI to analyze a portion of the genome where DNA methylation occurs (i.e. promoters, CpG island, CpG shores). This approach still generates a genome-wide map of DNA methylation but the sequencing costs are substantially lower than WGBS. This approach can be used in all species and requires >100 nanograms of high-quality genomic DNA (see sample submission).

pie chart illustrating DMR distributions

Example of the distribution of Differentially Methylated Regions (DMRs) obtained with RRBS. Typical percentages in promoters, introns, and exons are shown.

TruSeq Methyl-Capture EPIC is a targeted approach from Illumina that targets ~3.3 million CpGs sites and allows high coverage over epigenetic regions of interest. This approach can only be used in human, and it requires >500ng of high quality DNA. - TruSeq Methyl-Capture EPIC - read more

This is a new method that does not use bisulfite conversion but instead uses an enzyme-based approach that minimizes damage to DNA. - Enzymatic Methyl-seq - read more