There is a saying that, “each microRNA can have hundreds of target mRNAs, and each mRNA can be targeted by hundreds of miRNAs”. If that’s true, then how the heck are we supposed to know what’s going on in that crazy transcriptome? What does it mean when a miRNA and predicted target don’t explain the phenotype of interest? Are miRNA expression array profiles really an effective way to characterize disease?

Some talented researchers at the German Cancer Research Center set out to tackle questions like those in their latest paper. Dr. Peter Lichter and team have come up with an interesting workflow to see just how functional those pesky miRNAs are on an ‘omic’ level. They used RNA- interacting protein IP followed by next-generation sequencing of co-precipitated RNAs (RIP-Seq) which allowed the researchers to see if a miRNA and target gene are interacting in the RNA Induced Silencing Complex (RISC) (in this case they chose the notorious AGO2).

Here’s what they found:

100 RISC associated mRNAs in miR-155-expressing cells, of which 67 were ‘ in silico’ predicted miR-155 target genes.

predicted miR-155 target genes. “An integrated analysis of the corresponding expression profiles indicated that these targets were either regulated by mRNA decay or by translational repression.”

However, the real interesting finding was that they “identified a recurrent disproportional enrichment of several miRNAs, including miR-155 and miRNAs of the miR-17-92 cluster, in the AGO2-associated precipitates, suggesting discrepancies in miRNA expression and activity”.

So when it comes down to it, the take home message is that miRNA expression levels may not be very indicative of their actual activity. It appears that there are many more factors to consider, and novel research in the field should take this into account when interpreting miRNA expression profiles. For those of you stuck wondering what your miRNA expression results mean, it looks like there’s a new workflow in town.

Read all the details in RNA Biology, June 2013