Hi

The most simple and cost effective method is to do a bisulfite conversion followed by Sanger sequencing. The other options would be pyrosequencing which give you methylation rate of a certain CpG. The next expensive approach is specific panel of sequencing by NGS methods; this is more reasonable when you have multiple sample and your region is fairly large.

Best of luck

The technique of bisulfite sequencing is considered to be the “gold standard” method in DNA methylation but you can also use AFLP and RFLP as well cause they are cheaper methods but has its drawbacks.

Hi Daniel,

You can definitely perform methylation-specific PCR on bisulfite-treated samples or use post-bisulfite-based NGS applications to study the DNA methylation status of your target gene of interest. Qiagen, Zymo Research, and EpiGentek all offer commonly used bisulfite conversion kits. If you are looking to keep your experiment cheap and were just interested in one gene, look to PCR. EpiGentek’s BisulFlash DNA Modification Kit (P-1026) has a 30 min protocol with very little (< 10%) DNA degradation specifically optimized for MS-qPCR while remaining the least expensive. In general, bisulfite conversion is very harsh and may result in greater than 90% degradation of sample DNA.

Many thanks! This is very helpful.

Hi Daniel,

The current techniques for analyzing DNA methylation can be summarized as various DNA methylation analysis techniques based on bisulfite conversion, treatment of methylation-sensitive restriction enzyme and methylated DNA enrichment strategies. And different techniques provide information on DNA methylation at different levels, spanning from single-site methylation in specific genes to genome-wide methylation content. Some qualitative, lower-resolution technologies have lower costs, such as methylation-specific PCR.

Hope it helps!

The COBRA assay might be one of the cheapest and easiest methods to detect methylation on specific CpG sites (CpG found with the promoter region and/or within the CpG island closest to promoter region of the gene).