I am quite new in the miRNA field and are therefore lacking a lot of background.
At the moment I am analyzing the results form a miRNA microarray which is why I have some questions. The first one that came out is how can it be that the minor form of a miRNA is up- or downregulated in my array but the major form is not? As both derive from the same transcript, shouldn't then both forms behave in the same way? Do somebody know any expample at the literature were a minor miR exhibits a function that the major miR do not have? I would be grateful for any comments.
Although the major and minor miRNA originate from the same precursor transcript, in many cases miRNA minor (also referred to as miRNA* or miRNA star) is preferentially degraded as compared to miRNA major (or miRNA).
Preferential association of miRNA (as compared to miRNA*) to certain proteins during the maturation process may be responsible for this, however one cannot rule out other operating mechanisms also. This may be basis of your observations of miRNA array analysis.. and yes, there are reports where minorRNA is also reported to be functionally important.
Although the major and minor miRNA originate from the same precursor transcript, in many cases miRNA minor (also referred to as miRNA* or miRNA star) is preferentially degraded as compared to miRNA major (or miRNA).
Preferential association of miRNA (as compared to miRNA*) to certain proteins during the maturation process may be responsible for this, however one cannot rule out other operating mechanisms also. This may be basis of your observations of miRNA array analysis.. and yes, there are reports where minorRNA is also reported to be functionally important.
Ajay's right, some miRNA* are functionally and when that's the case they are loaded on the RISC complex and thus protected from degradation. Some reports suggested that evolutionary conserved star sequences during development are expressed in much higher conc. than their major counterparts. Here there's a nice paper on star miRNA sequences http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011387.
The citation is very interesting. I have been also looking for a similar clarification. I could not understand simply why the star miR are upregulated in most arrays.
Thanks
@Emanuel
Hi...
Thanks a lot for providing different papers on differential regulation and effects of miRNA and miRNA* sequences...usually people try to follow a well establised trend/hypothesis....and proving something unconventional is initially very difficult....people are not ready to believe ....when miRNAs or other small RNAs were found to be functionally important..they were a new (but not new in the system)..phenomena....and physiologically important....
miRNA* were supposed to degraded...but over the time they are also found to have some functional signifcance....
in future ...people are likley to discover ..many more functions/roles associated wit miRNAds
bye
Hi Maria,
yes minor miRs may have a function, but before you go down that road take a good look at your array data.
It is often that minors are expressed at very low levels and even slight change in expression signal is picked up as statistically significant. You may not be able to see that directly if you are looking at log-transformed, normalized data.
Consider this example:
major miR expression in sample A, 10 000 and in sample B, 14 000 = fold change 1.4 probably not significant if you have low "replicate" number
minor miR expression in sample A, 2 and in sample B, 10 = fold change 5, it looks very much, but are these expression levels and fold change biologically relevant?
Dear all, thank you very much for your interesting replies. Vlady Vladimirov and Emanuel Devers, VERY interesting articles, I will read them carefully. Elena, it is very interesting your point also, but I think that in my case the expression of the miRs* is quite high as we have stablish a expression threshold under which a miRNA is not considered in further statistical analysis. Anyway, the array was done by a microarray service who just gave us the final analysis. How I could check if the threshold is set up correctly? Anybody knows a program tool to analyze raw microarray data (.gpr files)?. (A "microarray stats for dummies" guide will be also more than welcome) . Besides, we have validated our miRs* by qPCR and it seems that the down or up regulation is for real, although by qPCR is not significative. This is another issue that I can not understand. Almost no miRNA from the array selected for validation resulted significative by qPCR. Does this maybe caused on the type of statistical analysis? We are having a hard time in trying to "match" microarray data with qPCR data, we really do not know if they "validate" or not? What "validation" means in technical / statistical terms? I am soooooooo lost with ths project!! My lab has no experience at all neither in microarrays nor miRNAs and I am completely alone with this. Thank you again. :)
Emanuel, thank you very much! I will have a look to the program. Indeed the array is not commercial but we can obtain the chip information. MEV is the microarray viewer program right?.
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