Does anyone have a ratified DNA methylation analysis protocol for a non-CpG island region?
I have a gene with differential expression in two genotypes and want to check whether the methylation status of the gene in different tissues differs between genotypes. But when I analysed the CpG content of the region, I found there was no CpG island
Sure thing, methylation analysis is especially interesting for non-CpG island regions. Most methods for analyzing methylation allow you to look for methylation differences within and without a CpG-island context. Methods could range from Bisulfite sequencing to Infinium 450K HumanMethylation chips. Which method you end up preferring depends on your organism, the gene, costs, etc. In this context bisulfite sequencing would give you methylation ratios on a base resolution whereas 450K chips would only focus on predefined regions (on the human genome).
Dear Reid,
Bisulphite dequencing is surely a method to analyze the methylation patterns in the CpG as well as non-CpG regions. The protocol holds true for all methylated C/non methylated C, whether in CpG or not.
Best,
Somnath.
Dear Mr. Reid,
I would like to recommend you this article (http://hmg.oxfordjournals.org/content/20/22/4299.long) & I hope that it will answer your question.
Regards,
yes as long as you have CpG sites. however, this doesn't mean that the methylation of this site affects the expression of the gene of interest
- Badges
- Science topic