I have two cell lines, in one the miRNA binds to its target mRNA, in the other it seems to be block. How do you determine what is blocking the miRNA from binding to the mRNA? Is it protein or RNA? What is the best way to get at the answer? Thanks! -j
This is based on luciferase assay for the binding. I have measured the specific miRNA, and it is present.
Dear Archana, do you know of any good programs where you can find out if another ncRNA is acting like a sponge?
Dear Kamil, thank you for your valuable input. i've been thinking about the Ago IP too.
This dilemma is an intriguing problem that I am hoping to figure out.
-J
Hi! There's a decent databse/algorithm (www.microrna.gr/LncBase) which provides both experimentally validated and predicted miRNA targets on lncRNAs. Not entirely sure if that's what you're looking for, but if your miRNA binds to a specific lncRNA which is more highly expressed in one of the cell lines, the lncRNA could conceivably be causing the effect you're seeing. Here's the paper describing the database:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531175/pdf/gks1246.pdf
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