I am doing methylated RNA immunoprecipitation and I need a gene whose methylation level is constant and known to be sure that I immunoprecipitated the methylated RNA.
I'm not working in RNA methylation but DNA methylation, so maybe my comment won't make sense...
However if you just want to get a technical validation and normalization, you could incorporate in your sample an exogenous RNA previously treated with a methylase. If it is exogenous you will only have what you incorporated and if you control the quantity you could normalize with it.
You may find the answer to your question in these 2 founding papers which were the first to describe the distribution of the RNA methylome. However, I guess that the methylation level of one given mRNA will differ from one cell type to another..
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
Thank you so much to share your experiences with me. They are important and helpful.
Excellent answer Matthias. Which alternative methods do you recommend?
Thanks
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