I’m trying to detect RNA modification of low abundant species in mammalian cells. I am wondering whether there are any protocols/kits for a high sensitivity and high throughput detection of RNA modifications, i.e. 2'O-ribose methylation and pseudouridylation. More specifically, I’m wondering whether there have been any qRT/RT-PCR methods to detect them in recent years.
Concerning the 2'O methylation, have a look to this paper that came out recently on NAR "RTL-P: a sensitive approach for detecting sites of 2′-O-methylation in RNA molecules"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488209/
Thank you very much for your helpful advice :-) It seems this is what I am looking for indeed! Do you (or anyone who is reading this post) think it will work also for pseudouridylation? They didn't discuss about it in the manuscript.
I am not sure that it can work for pseudouridylation, since the modification does not occur on the ribose, but on the base. The principle on which the RTL-P is based seem to work only on modification on the sugar.
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