c.ATG offers several methods to detect methylation patterns in samples of diverse origins. Particularly popular topics among our customers are the analysis of developmental and disease-related changes in DNA methylation in humans and laboratory animals using NGS technology.
DNA methylation is a major means to regulate gene expression. Differentiated cells have specific methylation patterns characteristic to the particular cell type. Methylation patterns change strongly during development, with stem cells and precursor cells having profiles distinct from each other and from fully differentiated cell types. Cancer cells often harbor massive epigenetic changes and show striking differences to non-cancerous or benign cells in their DNA methylation patterns. Many other diseases and even environmental stresses are associated with altered methylation patterns, as well.
There are a variety of methods for monitoring the methylation status of the genome, but they can generally be placed into one of two categories – they either rely on bisulfite conversion or they employ a form of methylated DNA enrichment or pulldown.
Bisulfite treatment of DNA converts all unmethylated cytosines to uracil (which is read as thymine) while 5′-methyl-cytosine is left unchanged. Currently the most complete picture of the methylome is generated via whole genome bisulfite sequencing (WGBS). However, this is the most expensive method at around 1.5X the cost of standard whole genome sequencing (WGS).
Several alternative methods to WGBS have been developed to reduce the cost and to increase the sample throughput. These focus on sequencing only a portion of the genome. One such example is “reduced representation bisulfite sequencing” (RRBS), which uses restriction enzymes and size selection to reduce the overall complexity of the genome while enriching for CpG islands (regions of high CpG density, which are preferentially methylated and often reside in the vicinity of promoters). This form of enrichment is not completely uniform, thereby slightly biasing results.