miRNA gene UTRs? - (Nov/18/2009 )
Are there any Drosophila miRNA genes for which 5' and 3' UTRs are known? Or any ESTs of pri-miRNAs that might indicate putative UTRs? We are looking to potentially add endogenous UTRs to our miRNAs to help them stay in the nucleus longer so that they will be more efficiently processed by Drosha, but most websites (e.g. miRbase, flybase) only have transcription info on the actual mature miRNA. Thanks.
I'm not sure I understand your question - miRNAs are not translated, so why would they have a UTR? I suppose you could add a UTR from another gene, but I don't think that this will alter it's stability since Drosha is unlikely to recognize any UTR sequence and pre-miRNA molecules are only transported to the cytoplasm upon completion of Drosha processing.
miRNA man on Nov 19 2009, 12:16 PM said:
Is it known for sure that pre-miRNAs are transported to the cytoplasm only after Drosha processing? I am not sure that that has been clearly established. We are just thinking that adding UTR-like regions to our short miRNA sequences might help them stay in the nucleus longer for sufficient Drosha processing to occur. Endogenous pri-miRNAs are quite long (e.g. 10 kb for bantam in Drosophila), so artificially expressing short transcripts might affect the rate at which they are exported from the nucleus...
Well there are some rare cases of miRNAs being contained in either non-coding or coding exonic regions of a host gene. In this case it is certainly possible (probable?) that the miR-containing mRNA transcript is transported to the cytoplasm without any Drosha processing. (see review by Kim et al 2009, Nat Rev Mol Cell Biol).
As far as export of non-exonic miRNAs, it was shown by a couple of groups that this occurs after processing in an Exportin-5 -dependent mechanism, but you might be right that they didn't discuss the possibility of non-processed pri-miRNA transcript being exported. All of the above ignores the possibility of a Drosha-independent miRNA (mirtron) but I gather that this is not what you're interested in?