Iam working with miRNAs and in our lab we detect different miRNAs threeshould in different cell lines and it seems like it is vary and these variations has nothing to do with protein expression level !! Is this logic !!
miRNA is complicated Topic but interesting too :) .... Thank you for your answer
Hi Hamed,
your question is tackles an important issue. Thanks for bringing it up. I struggle with this myself. The major problem seems that according to several studies, the target sites are in a "vastly" overrepresented compared to the active microRNA complexes. Therefore, most of the microRNAs do not target well. What I mean by this is that many genes/mRNAs will be affected but only few to an extent that will result in "tuning" of gene expression, i.e. change in the mean expression value. For most of the target sites bound there will be little effect since the miRNA will not occupy enough sites for a specific mRNA/gene. So, most of the target sites may actually function as a "buffer" against microRNA fluctuations unless the fluctuation reaches a threshold. Passing this threshold will then, depending on the cellular transcriptome/context, lead to clear changes in gene expression of the target gene and measurable phenotypic effects. That is how I interpret microRNAs. I assume, that most "real targets" (the genes that show the most robust and strongest regulation in regard to fold change) are genes that are not highly expressed (otherwise they would become buffers and soak up a lot of microRNA complex without resulting in a "major" change in gene expression). So, the targets that are discussed and studied in papers are the targets that fulfill these criteria: they change significantly (you can "see" it and have some sort of statistics to confirm its regulation), robustly (you can repeat the experiment and this gene will be always nicely effected), and they may change in many cell types. The last aspect may not be true for all of the target genes.
Is there evidence in the literature that these kind of target genes are universal or tissue specific? If you do a meta-analysis of the targets of an individual microRNA, you will see that some targets are identified in many cell types, others just in a few. I assume, there will be some cell types where the target gene is at the right level while in others it is not...
The other type of "target" is not often discussed. They are the mRNAs that soak up a lot of the microRNA because they are relatively highly expressed, can bind the microRNA-RISC in a decent fashion, but the effect of the miRNA is too weak on them to actually influence the expression of these mRNAs. Does that make sense? That is currently my view on the topic.
Perhaps the microRNA fine-tunes the expression of this second class of targets while the "real targets" are tuned, not fine-tuned. No idea how to measure whether microRNAs play a role in buffering mRNA expression. For that purpose one would have to have more information about the feedback loops etc??
Hope this helps.
Hi Tomas, I like this theory that miRNAs can bind to unspecific genes and this the reason why the effect on gene expression is sometimes not strong. It is sometimes tricky to judge miRNA function through measuring it threshold. I THINK it is only ‘masking’ phenome which means that mRNAs can mask their binding sites under stress circumstances to keep miRNAs avoided or to keep them away from binding to the effective sites ‘may be methylation, Ubi …. Etc’ can be involved. I also agree with you about the miRNAs sponges which are complexes to soak up miRNAs overexpression. Moreover, I read article recently which stated that overexpression of certain miRNAs to the level which exceed the threshold can lead to an increase in protein expression J which is really unexpected.
Finally, miRNAs are of course very well connected to the epigenome and I think we still need more efforts to really understand how they are regulated before using them in translational research.
Thank you so much for you kind reply
Hamed
Hi
Adding to above discussion. I came across that says 90 percent of mirna not become part of risc but binds to rbps.so that remains black box to add threshold concept to show effect
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