detection of DNA methylation is common but in case if u are not getting methylation in DNA , how significant to check RNA methylation for the same gene using bisulfite sequencing, I have no experience in that.
RNA has multitude of modifications. With the most common being m6A and mC. Both of them presenting themselves in the regulatory regions (5' and 3'UTRs). So to answer your question yes there are methods and kits for bisulphite conversion of RNA (mC) and antibody based capture methods for m6A.
The bisulphite kit is sensitive enough to prevent RNA degradation while conversion.
http://www.zymoresearch.com/epigenetics/rna-methylation/bisulfite-conversion/ez-rna-methylation-kit
But more importantly "Significance of the experiment ", It would all depend on your interest in experimenting with RNA methylation and what led you to believe that it is a viable to explore this line of thought. (which I cant answer without background information)
thank you for your valuable reply, i am looking for epigenetic modification on chromatin of Sox9 in case of mouse. this gene expressing in one tissue type and not in another tissue type. i need to explore reasons behind this switch on and off. therefore i looked at DNA methylation status of promoter of this gene. both tissue type has no methylated CpG at promoter of this gene, therefore i thought of checking RNA methylation before moving on to the HISTONE marks.
Sox9 is a developmentally relevant gene with very specific tissue type expression. Now, You need to understand that there are different levels of regulation employed starting from the base sequence to more complex modifications to achieve the desired expression patterns. Promoter methylation necessarily may not reveal the intricacy of this process. there might be intergenic or intronic differential methylation .I would say you need to explore the gene as a whole rather than just concentrating on the promoter.
Good luck.
ok, i am agree on this but i need some of the reference so that i can correlate some of these modifications,if found with expression pattern of this gene. references in which such genomic region are playing role as a regulatory element would be very important for me. but just finding some modifications are not enough to say anything about regulation , i need to look for how they are doing so? are they really playing role in regulation .
i am also worried about HYDROXY METHYLATION.i need to check these too to have clear image of modification at these genomic locations.
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