how to visualize DNA methylation regions in a given genome sequence??

Question

[kifayatvet]

Hi

I'm sorry for the basic question but I am confused which bioinformatics tool should I use to locate DNA methylation regions in a given short sequence of the genome. I would really appreciate some clarification. thanks in advance.

Answer 1

[ATpoint]

In mammalian genomes, DNA methylation typically occurs at CG-dinucleotides (CpG sites). If a CpG site (or any larger aggregation of CpGs like CpG islands or floats) are indeed methylated needs to be determined by experiment, e.g. via Sanger sequencing after bisulfite treatment (lowest thoroughput method) or NGS-based assays like Reduced representation bisulfite sequencing (RRBS) or whole-genome-bisulfite sequencing.

Answer 2

[pltbiotech_tkarthi]

CpG islands are the most preferable sites of DNA methylation. So you can predict CpG islands using EMBOSS server https://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/ or other servers and you could interpret the methylation preferable sites.

[Devon Ryan]

It's unclear how this would assist in any way with looking at DNA methylation.