microRNAs in RNA-seq?

[Jeannine]

Hi,

I'm sure my question is a really common one, and although I could find a few different opinions on this topic I would like to ask it anyway, just to get a definite answer.
Is it possible to identify differentially expressed microRNAs in a normal RNA-seq experiment (i.e.not small RNA-seq)?
We're considering to do a miRNA microarray but will definitely do a RNA-seq in the near future, i.e.were wondering if we don't have to do the microarray at all.

Thanks,
Jeannine

[Deli Çoban]

Hi,

You can use the RNA-Seq libraries for identifiyig differentially expressed full pre-miRNA or partly degraded pre-miRNAs which generally include mature miRNAs. First of all, you blast the all desired pre-miRNAs against the RNA -Seq libraries (for good result, not map the contig sequences, directly mapping to unigen sequences).Then, you sort out the outputs for getting the pre-miRNAs and check the expression level of obtained sequences.

[HilmarBerger]

Hi,

I am not sure if anybody has shown that the expression of pre-miRNAs is a good substitute estimate for mature miRNAs, at least this article indicates the contrary: http://nar.oxfordjournals.org/lookup...ll&uritype=cgi .
In any case, with "normal" RNA-seq you will definitely not see any mature miRNAs that require specific shortRNA prorocols to capture and sequence the short sequences.

Cheers, Hilmar

[Melissa]

Deli is right. Just wanna add that very few pri-miRNAs will be detected in the transcriptome (my rough guess based on experience is probably 10% of the total miRNA families). Why not do a small RNA-seq instead of miRNA microarray?

[NicoBxl]

and pre-miRNA are not poly-A (pri-miR are) so you've to do ribo depletion libs.
and like Melissa said: try small RNA-seq instead

[plefebvre]

you definitively would not see miRNA in your RNA-seq data

[vkartha]

Could any one point me to the best annotation file to count over annotated mature miRNA sequences? I am currently using the gff file off of mirbase (is this reliable?).