Mirtron Predicted Targets In Humans

Question

[Paul]

Hi,

I'm wondering if anyone knows if there exists a database of human mirtrons and their predicted target genes?

I guess once you know the mirtron sequence you could use any miRNA prediction algorithm like TargetScan or PicTar, I wonder has anyone done this?

Cheers,

Paul.

Answer 1

[Steve Lianoglou]

I'm not sure if there is a list of known mirtrons in Hsapiens, but our lab collaborated on this paper:

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans

We've got some code up online for the SVM used to predict these mirtrons along with a tutorial on how you might use it (unfortunately MATLAB is required for this one, I think):

http://cbio.mskcc.org/leslielab/mirtrons/

I didn't work on this project, so I unfortunately can't provide much more information than that.

[Paul]

Hey Steve thanks for the reply. It turns out that there is a small list of "official" human mirtron genes in the supplementary information of this paper: http://www.sciencedirect.com/science/article/pii/S1097276507006697 although at 2007 it's a bit dated I'd think and it's a very small list at that!

Answer 2

[Martombo]

an update on the topic: http://genome.cshlp.org/content/22/9/1634.long

they used 500 publicly available small RNA seq datasets to identify 240 high confidence mirtrons and 241 lower confidence ones in the human genome http://ericlailab.com/mammalian_mirtrons/hg19/index.html

anyway they didn't study the predicted targets of these mirtrons

Answer 3

[Pierre Lindenbaum]

To find the microRNA in the Introns, I would extract the intronic regions from the UCSC knownGene table. See Exon Coordinates Of Hg19 Genome Download for extracting the exons ( it should be sightly the same thing for the introns ).

Then, I would find the intersection of those introns with the table wgRna ( snoRNA and miRNA annotations )

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz

[Paul]

I think what you are suggesting would return miRNAs which are coded in introns, as far as I know this is different from a mirtron though, which are specifically debranched introns which have length and hairpin structure of a pre-miRNA and are subsequently incorporated into the miRNA biogenesis at the step after Drosha cleavage.

[Pierre Lindenbaum]

OK, I didn't know what is a mirton until today :-P