pri-miR transcript - where does transcription start? (Sep/01/2009 )
I have a question: its accepted that mature miRs are generated, first by the cleaving pri-miRs into pre-miRs and then into mature miR's.
But, when you look at the miR loci, say in Ensembl or UCSC, the sequence/transcript they give you is really only the pre-miR! What do you do when you are interested in the pri-miR; when you are interested in where the actual transcription begins and ends? Any suggestions?
for most miR's it's the mature ~22nt mir that has been cloned, and not the precursor, so this is why only the two strands and the loop can be annotated. If you're really interested in the complete pri-miR, I think you should do 5' and 3' RACE. If your miR is located in an intron, than the complete intron is your pri-miR but for intergenic miRs, I would look for conserved upstream sequences that could be promoter elements and assume it starts around this place, but the only true way is to clone the pri-miRs by RACE I think.