Hi Sharif

Excellent question and very interesting reflection.

I suffered the same critics from reviewers. Thinking in a very simplistic way, complex eukaryotic organisms are very redundant. So, they have many ways to do the same things. In consequence it should be very difficult to find a "master" miRNA which will regulate a very important gene or pathway. On the other hand, a multiple and complex effect is expected, involving many miRNAs that are working together. Of course that you can find "master" miRNAs in simple organisms, but in humans this is very difficult.

If you want to find interesting miRNAs in a particular process, I would suggest you to use a complex approach, combining information about target recognition and also about pathways. You can distinguish different categories of targeted mRNAs if you pinpoint them into biochemical pathways. More relevant miRNAs will target "receptors" instead of "effectors".

Of course this is not an easy task.. Analysis of many variables is needed. More relevant miRNAs will be the ones that regulate more targets. On the other hand, the most relevant targets will be those regulated with more miRNAs at the same time.

Take a look at this paper where we did this kind of approach.

https://www.ncbi.nlm.nih.gov/pubmed/27500760

Best of luck. Waiting for your feedback.

Paco

hi see these link 

https://www.ncbi.nlm.nih.gov › NCBI › Literature › PubMed Central (PMC)

https://www.ncbi.nlm.nih.gov › NCBI › Literature › PubMed Central (PMC)

Hi Sharif

Excellent question and very interesting reflection.

I suffered the same critics from reviewers. Thinking in a very simplistic way, complex eukaryotic organisms are very redundant. So, they have many ways to do the same things. In consequence it should be very difficult to find a "master" miRNA which will regulate a very important gene or pathway. On the other hand, a multiple and complex effect is expected, involving many miRNAs that are working together. Of course that you can find "master" miRNAs in simple organisms, but in humans this is very difficult.

If you want to find interesting miRNAs in a particular process, I would suggest you to use a complex approach, combining information about target recognition and also about pathways. You can distinguish different categories of targeted mRNAs if you pinpoint them into biochemical pathways. More relevant miRNAs will target "receptors" instead of "effectors".

Of course this is not an easy task.. Analysis of many variables is needed. More relevant miRNAs will be the ones that regulate more targets. On the other hand, the most relevant targets will be those regulated with more miRNAs at the same time.

Take a look at this paper where we did this kind of approach.

https://www.ncbi.nlm.nih.gov/pubmed/27500760

Best of luck. Waiting for your feedback.

Paco

Hi Sharif,

I doubt the reviewers are asking for you to identify the only target for a miRNA but to identify the possible targets and perhaps to then validate some of these. This confirms those miRNAs as genuine. In my experience the majority of miRNAs don't have hundreds of targets but just a few. I have used TAPIR (http://bioinformatics.psb.ugent.be/webtools/tapir/)  in conjunction with degradome data for target prediction. In quite a few cases I havn't been able to find any possible target at all.

It's usually requested that you perform validation of the miRNA/target pairing for a couple of those you have predicted. This can be done using modified 5' RACE to confirm cleavage at the predicted target site.

 It's very important that miRNA studies go beyond the bioinformatic approches. Validation of miRNA/targets place them as functional active within an organism.   

We will publish shortly (hopefully) a manuscript that can help you in this interesting, as Francisco pointed, refection with associated methodology. Cheers

Dear Francisco,

I liked your comments and I agree with you. Complex systems should NOT be seen in a simplistic manner. I agree that there might be miRNAs which exert their major effects through targeting a single gene, but considering the nature of miRNA-mediated gene regulation, I think that in many of the complex biological processes involving mRNA-miRNA interactions, there are probably more than a single miRNA as well as more than a single gene that are involved. Thank you for your helpful answer.

Dear Rodney,

Thanks for your input, for sure validation of the predicted miRNA-mRNA interactions would add to the significance of the findings and help identify the exact biological phenomena within the cells, but it seems from the miRNA-based literature that such a bias had been existing where reviewers urge authors to narrow their mechanistic analyses down to a single target. Anyhow, in my case, I did not narrow the potential miRNA targets to a single gene, instead and after some validation experiments, I provided a list of putative gene targets which might have been mediating the observed effects. Any of those putative targets might contribute to the various phenotypes that I observed when I treated the cells with my candidate miRNAs.

Dear Inmaculada,

I look forward to reading your published work, please let us know once it is published.

Best,

Sharif

Hi there

Just to make some more noise about... I have found this application, decodeRNA, which uses an integrative approach for decoding miRNA and lncRNA function. Unfortunately you just can use single miRNAs, but I think that it could help.

http://www.decoderna.org/

You can use also miRNet, which is devoted for miRNAs, and in this case you can analyze the action of multiple miRNAs over cohort of genes and pathways. This app only work with validated miRNA targets.

http://www.mirnet.ca/

Keep moving !.. Best

Paco