DNA Methylation: The Human Body’s Genetic Stoplight

DNA Methylation: The Human Body’s Genetic Stoplight

New sequencing and array-based solutions accelerate biomarker discovery in epigenetics

DNA Methylation: The Human Body’s Genetic Stoplight
October 5, 2016

While the genome and gene expression have been a major focus of disease research for decades, more recently, researchers have begun to look at how environmental factors such as diet, exercise, or pollution levels interact with the genome to mediate disease progression.1 DNA methylation is of one of the main ways cells translate environmental cues into genetic responses. Similar to a stoplight, DNA methylation regulates the fast moving, dynamic flow of gene expression by influencing where and when genes are turned on or off. Abnormal DNA methylation and its impact on gene expression have been shown to play a role in many disease processes, including cancer, neurological disorders, diabetes, and obesity.2,3

To support epigenetics research Illumina is growing its portfolio of products for studying DNA methylation. The newest product is the TruSeq Methyl Capture EPIC Library Prep Kit—a kit for the preparation of targeted bisulfite libraries compatible with Illumina next-generation sequencing (NGS). Leveraging content from the popular Infinium MethylationEPIC BeadChip, which contains double the content of the HumanMethylation450 BeadChip, the TruSeq Methyl Capture prep kit contains a panel of 3.3 million CpG sites. These include emerging epigenetic regions of interest identified by ENCODE, FANTOM5, theEpigenomics RoadMap Consortium, and customer-based requests.

Whole-genome bisulfite sequencing (WGBS) is also available for genome-wide mapping of methylation patterns with the deepest coverage and for any genomes. However, it is still cost-prohibitive for studies with large sample numbers. With the TruSeq Methyl Capture EPIC Library Prep Kit, researchers can obtain nucleotide level resolution of every CpG site in their region of interest at 1/7th the cost of WGBS.4

The Illumina Methylation Portfolio allows researchers to move seamlessly between microarray and NGS technologies. The cost-effective MethylationEPIC BeadChip is ideal for large-scale studies and screening, and sequencing-based solutions allow researchers to dive deeper into specific regions of interest for more discovery based studies.

Epigenetic information is also highly complementary to ongoing genomics studies and allows researchers to weave together transcriptional, epigenetic, and genetic data into a powerful, integrated genomic analysis.

References:

1.       Vijayakumar NT, Judy MV. Autism spectrum disorders: Integration of the genome, transcriptome and the environment. J Neurol Sci. 2016;364:167‑76. http://www.ncbi.nlm.nih.gov/pubmed/27084239

2.       Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol. 2010;28:1057-68. http://www.ncbi.nlm.nih.gov/pubmed/20944598

3.       Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011;12:529-41. http://www.ncbi.nlm.nih.gov/pubmed/21747404

4.       Masser DR, Stanford DR, Freeman WM. Targeted DNA methylation analysis by next-generation sequencing. J Vis Exp. 2015;(96). http://www.ncbi.nlm.nih.gov/pubmed/25741966