I know one miRNA regarding my study. On the other hand I think this miRNA is blocked by the another miRNA which I don't know when the conditions changed. İs there any method to identify the new miRNA that I suppose is involved in the miRNA-miRNA interaction?
Briefly, I know one but I don't know the other one. So as far as we know, this interaction occurs in the cytoplasm. I think there might be a method like precipitation to miRNA-miRNA interaction.
I hope that there is.
Sounds like an Ago2-pull down followed by seq might work for you. You'd see which miRNAs and mRNAs are incorporated into Ago2, and can even identify the binding sites: (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078052/). You could perform the pull-down in both conditions and see if there's a depletion of your miRNA of interest correlated with an increase in any other miRNA sequence.
Hi Ediz
Your idea is interesting, however not very plausible. Unless you have a natural blocking of your miRNA in the pre-mature form, bound to the "star" miRNA... I do not know it you will be able to identify the miRNA-miRNA binding with such a technique like @Robert described.
I sincerely will bet in something bigger, which is really blocking your miRNA. Did you think about the possibility of having some bigger RNAs like ceRNAs, acting as sponges of your miRNA?.
Good luck. Cheers
Paco
Whoops - my apologies, I misread your question as miRNA-mRNA interactions, not miRNA-miRNA interactions. I thought you were suggesting there was an unknown miRNA competing for the known miRNA's binding site on the mRNA. However, I agree with Francisco, given a better read of your question, I don't think an Ago2 PD would work for you're question. Thanks for the catch.
That's interesting, though - you hypothesize there is another complimentary miRNA acting as an endogenous inhibitor? I suppose you could try a biotin-labelled microRNA mimic pull down, and see if you pull down any miRNAs with it. You wouldn't be looking at the endogenously expressed miRNA and the assay would take some optimization, but it's been done previously to look for miRNA-mRNA interactions, so you might be able to adapt it. If you sequenced, you would also see if there are endogenous sponges as Francisco suggests.
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