Another interesting microRNA question! There is a reason why we hear so little about the star microRNAs: they are generally the strand of the microRNA precursor that gets degraded/not used/not sequenced. I have not looked excessively in mirBase but it is generally very one-sided when it comes to small RNAseq data: most precursors produce a very dominant microRNA, very few produce an equal amount of 3p and 5p microRNA. Not sure whether anyone has gone through the dataset and checked how many precursors really produce "significant" levels of both sides. I think miR-9 is an exception. I have no idea how this biochemically works but in cases where there is a "significant" second microRNA from the precursor, a look at its biological role (target genes) seems a no-brainer.

I think RNAseq data are wonderful to start to look for answers to this question. And if there is an indication that there is a substantial expression of the star form, then this may have to be included to understand how this precursor microRNA contributes to the phenotype, meaning both microRNAs derived from the precursor

mirBase itself has addressed this issue recently and phased out the star nomenclature:

"In this case miR-20b arises from the 5′ arm of the mir-20b hairpin, and miR-20b* arises from the 3′ arm. The “*” tells us that miR-20b* is considered a “minor” product. That means miR-20b* is found in the cell at lower concentration than miR-20b. It is often inferred that miR-20b* is non-functional, and you’ve probably noticed that miR* sequences in general magically disappear in most pictures of miRNA biogenesis, while the dominant arm is magically incorporated into the RISC complex.

But hang on a minute, a bunch of papers now tell us that miR* sequences can be functional (eg Yang et al. 2011), perhaps through binding different Agonaute proteins (a glut of papers in the past couple of years nicely reviewed by Czech and Hannon, 2011). And, of course, the miR* sequence from one hairpin might be expressed at orders of magnitude higher level than the dominant miR sequence from another hairpin. Perhaps the arm that makes the dominant product can change in different tissues, stages and species (G-J et al. 2011). Should we rename miR and miR* sequences every time someone produces an ever deeper sequencing dataset? To cap it all, the “*” character causes problems for database searches and the like.

We therefore intend to retire the miR/miR* nomenclature, in favour of the -5p/-3p nomenclature (the latter has been used in parallel for mature products of approximately equal expression, and will in future be applied to all sequences)"

I think, there is growing evidence that some of the minor forms from a precursor are important but overall, the low expression levels or absence of these minor forms makes them unlikely major important players. As always: it depends. The answer is in the big data of mirbase. If you have a candidate, you can check. Good luck!

I think there is some confusion here. Once the miRNAs get loaded on the RISC, they have at least two known fates, you can read about the ping-pong mechanism. The strand on the RISC is then able to bind to its complementary sequence on the mRNA, and cut it. As soon as a RNA molecule is detected that does not contain a message, it is degraded by the exosome machinery. This machinery has (can have) multiple exonucleases thus degrading the RNA. I am not trying to be very accurate but just giving a general idea.

Another interesting microRNA question! There is a reason why we hear so little about the star microRNAs: they are generally the strand of the microRNA precursor that gets degraded/not used/not sequenced. I have not looked excessively in mirBase but it is generally very one-sided when it comes to small RNAseq data: most precursors produce a very dominant microRNA, very few produce an equal amount of 3p and 5p microRNA. Not sure whether anyone has gone through the dataset and checked how many precursors really produce "significant" levels of both sides. I think miR-9 is an exception. I have no idea how this biochemically works but in cases where there is a "significant" second microRNA from the precursor, a look at its biological role (target genes) seems a no-brainer.

I think RNAseq data are wonderful to start to look for answers to this question. And if there is an indication that there is a substantial expression of the star form, then this may have to be included to understand how this precursor microRNA contributes to the phenotype, meaning both microRNAs derived from the precursor

mirBase itself has addressed this issue recently and phased out the star nomenclature:

"In this case miR-20b arises from the 5′ arm of the mir-20b hairpin, and miR-20b* arises from the 3′ arm. The “*” tells us that miR-20b* is considered a “minor” product. That means miR-20b* is found in the cell at lower concentration than miR-20b. It is often inferred that miR-20b* is non-functional, and you’ve probably noticed that miR* sequences in general magically disappear in most pictures of miRNA biogenesis, while the dominant arm is magically incorporated into the RISC complex.

But hang on a minute, a bunch of papers now tell us that miR* sequences can be functional (eg Yang et al. 2011), perhaps through binding different Agonaute proteins (a glut of papers in the past couple of years nicely reviewed by Czech and Hannon, 2011). And, of course, the miR* sequence from one hairpin might be expressed at orders of magnitude higher level than the dominant miR sequence from another hairpin. Perhaps the arm that makes the dominant product can change in different tissues, stages and species (G-J et al. 2011). Should we rename miR and miR* sequences every time someone produces an ever deeper sequencing dataset? To cap it all, the “*” character causes problems for database searches and the like.

We therefore intend to retire the miR/miR* nomenclature, in favour of the -5p/-3p nomenclature (the latter has been used in parallel for mature products of approximately equal expression, and will in future be applied to all sequences)"

I think, there is growing evidence that some of the minor forms from a precursor are important but overall, the low expression levels or absence of these minor forms makes them unlikely major important players. As always: it depends. The answer is in the big data of mirbase. If you have a candidate, you can check. Good luck!

Ah, I saw an important part of your question that I think I can dare to give an clear no answer: "Should we screen our isolated RNA samples for both miRNA strands always?"

No, I don't see evidence to follow this path. However, there may be sometimes more than just -3p and -5p. But I have trouble figuring this out from the mirBase data: "Evidence for human microRNA-offset RNAs in small RNA

sequencing data" or in short moRNAs. Same thing: should one screen for such stuff all the time? No. But keeping an open mind may help to detect such "aberrations" and make sense of the gibberish chaos of the transcriptome. As they Pasteur said: In the field of observation, chance favours only the prepared mind." The English speakers have a wonderful word for this: serendipity.

Thanks Dr Thomas for clarifying the things in detail

Dear Priyanka,

you are welcome. And thanks again for bringing up this question. 

I think there is more to it.  If you sequence specifically the small RNAs.  And I mean by actually cutting out the band of 20 - 50 bp and making a library out of it, you will be surprised by what you find.  At that length, you do get a huge amount of reads mapping uniquely to the genome.  But most interestingly, you actually see these coming from pretty much both the strands.  I think it has some functional importance.  But i am not sure what it is?

Dear Sameet,

I based my analysis on the data in miRBase. The small RNA-seq data in there show for the majority of the major microRNAs that just one strand "survives". There are exceptions and things may look differently for less conserved, I have to look in more detail!

Hi Dr. Thomas,

I should have been a bit more clear.  We studied this in fission yeast.  Unfortunately in that model not many attempts have been made to study miRNAs as implied in most mammalian studies.  But I think the general principles will still hold.