One of the miRNAs identified from my recent miRNA-seq experiment with a flesh fly matches a Bombyx mori miRNA on miRBase. However, a BLAST search with the pre-miRNA sequence suggests this sequence may actually be 28s rRNA. Can miRNAs come from rRNA genes? Or is it more likely that the Bombyx miR has been misidentified?
Not sure at all, but maybe these PLOS papers could help you figure something out:
Dicer associates with rDNA in chromatin, apparently, and there are many small rDNA-derived RNAs...
10.1371/journal.pone.0012175
10.1371/journal.pone.0056842
best wishes!
Hi,
miRNAs can derive from introns, exons, antisense and intergenic regions but the biogenesis pathway differs between these categories.
"Can miRNAs come from rRNA genes?"
Yes they could.
I would also check the confidence of that Bombyx mori miRNA in miRBase. In the latest miRBase release, they have added a new feature that measures the confidence of each listed miRNA sequence. If that Bombyx mori miRNA did not derive from experimental data, then it could be a false positive.
Best regards
miRBase has some issues with annotation, so check out wheter that particular miRNA you're interested in has been curated or not and if there're any papers that confirmed the action of the Bombyx mori miRNA, did they provide enough proof that this miRNA is functional?. I agree with Georgios and suggest you to look at the newest versions of miRBase to consider the confidence score as this will point you in the right direction.
In addition, I recomend to use your mirna sequence against your fleshy fly genome (if you have it) and then take the whole locus it matches to perform the blast at ncbi; this way you would be able to tell more accurately where this particular miRNA is coming from.
there are RNA fragments derived from rRNAs which were annotated as miRNAs in miRBase but later on removed in the updated version.
example of such: http://www.mirbase.org/cgi-bin/query.pl?terms=mir2911
however, the functional role of one rRNA fragment (mir2911) as ‘Virological Penicillin’ was reported in a recent paper, http://www.nature.com/cr/journal/vaop/ncurrent/full/cr2014130a.html
for a review on fragments of RNA, http://www.ncbi.nlm.nih.gov/pubmed/21741109
It might be that the problem stems from the initial miRNA identification in your RNAseq output. There are method to detect miRNAs which are developed specifically for this purpose. Which one did you use in the first place?
This aligner has a mode specific for mirnas:
http://compbio.cs.toronto.edu/shrimp/README
Also, did you include 28s rRNA in the reference when mapping your reads?. The number of reads assigned to it vs the number of read assign to your miRNA might give a better clue on which one is actually represented in your sample.
Best
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