I have a question regarding miRNA binding to mRNA. If a mRNA binds with miRNA, it will form miRNA-mRNA binding complex. What is the effect of this complex from the point of view of RNA-seq especially RNA-seq experiment to prepare the sample (if using Illumina technology)?
I don't really understand about biology but I think about the possible effect.
First possibility is the mRNA which binds to miRNA will not be able to bind with the sequencing kit because miRNA will block the binding between mRNA and the sequencing kit (I don't know the name but I think during amplification). The consequence is the expression result from RNA-seq comes from mRNA which doesn't bind to miRNA and we can not detect miRNA at all.
Second possibility is mRNA is fragmented. So, the region of mRNA which is not bound to miRNA can bind to the sequencing kit. The consequences of this is the region which miRNA binds to mRNA will have small or no reads aligned to it. I imagine the reads coverage after the alignment would be like a valley between 2 mountains. Area not bound to miRNA will have a good coverage and area bound to miRNA will have small coverage.
What is your opinion about this? Is it possible to extract information about miRNA binding from RNA-seq?