I'm working on selecting mouse miRNAs to analyze and stumbling upon one confusing issue, some of the papers do not specify which arm they analyzed and they just state something like " miR-34a was upregulated". Then in the same sentence the other miRNA mentioned with its arm specified, for example: miR-335-5p. This leads to these questions:
1. Does that mean that both arms of miR-34a were analyzed and change in the overall miR-34a stem-loop was quantified?
2. Answers to previous similar questions mention about one arm being more stable: how to tell which arm is more stable if in miRBase both mature sequences are given? Do we need to look into the literature for each miRNA to find out which arm is more stable?
Appreciate any tips on this.
Thank you!
Good observation! Some papers really don't specify the arm for one miR while specifying it in another. Theoretically this could mean that both have the same action or that one of them is unstable so doesn't count, practically you need a proof or a reference.
For you first question : Knowing the sequence of the primers used for quantification could help you determine which arm is quantified.
For the second question, looking in the literature is one way, another way is using target prediction tool that relies on seed sequences. It will give you a much shorter more specific (because the evidence is sequence- based) target gene list.
https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=MIR:MIRDB
Based on this, the 2 arms of the miR of question have different targets. You may like to check this:
https://www.gsea-msigdb.org/gsea/msigdb/cards/MIR34A_3P.html
https://www.gsea-msigdb.org/gsea/msigdb/cards/MIR34A_5P.html
Hope this is helpful.
Good observation! Some papers really don't specify the arm for one miR while specifying it in another. Theoretically this could mean that both have the same action or that one of them is unstable so doesn't count, practically you need a proof or a reference.
For you first question : Knowing the sequence of the primers used for quantification could help you determine which arm is quantified.
For the second question, looking in the literature is one way, another way is using target prediction tool that relies on seed sequences. It will give you a much shorter more specific (because the evidence is sequence- based) target gene list.
https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=MIR:MIRDB
Based on this, the 2 arms of the miR of question have different targets. You may like to check this:
https://www.gsea-msigdb.org/gsea/msigdb/cards/MIR34A_3P.html
https://www.gsea-msigdb.org/gsea/msigdb/cards/MIR34A_5P.html
Hope this is helpful.
hi Maksat Babayev
During the synthesis process, the precursor miRNA stem-loop structure gets is cleaved by the RNase III enzyme Dicer, to produce miRNA-5p and miRNA-3p. The 5p strand is present in the forward (5'-3') position while the 3p strand (which will be almost complementary to the 5p strand) is located in the reverse position. You will get information for structures on the miRBase website.
Now, which strand will be functional, either both or only one strand is effective to do functional that majorly depends on two things one is their stability, another is able to enter the RISC complex to then bind to its target gene. In general, the more stable strand will be functional, and the less stable strand will be degraded. In some cases, even both strands could be functional.
Next, to do function, miRNA has to actually bind with mRNA of interest which will be complementary to the binding site on 3'UTR of your mRNA sequence. There also, either one or both may bind and inhibit transcription. Here, you need to find the validated and predicted targets using target prediction tools (ex. tragetScan).
You can consider both strand sequences one by one and test both strand sequences to pair with the gene of your study and develop some ideas. Generally, each strand has a specific set of targets that bind to the 6-8mers of mRNA which plays a key role in pathological and physiological conditions. If any miRNA targeting any gene, definitely that gene will have a different function in the heart and cancer. So, here target will define the function of that miRNA.
Hope this will be helpful.
Regards
Saurabh
This strongly depends on your target mRNA (direction and sequence).
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