I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it nomenclature Based on it, I try to figure out what is hsa-let-7a. As far as I understood, hsa refers to human but I expected a "mir" or "miR" after hsa but there is a word "let" .So my question is that hsa-let-7a is a name for a single mature miRNA or is it a name of a miRNA family(if there exists such a thing) ?
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asked Mar 22, 2015 at 15:19
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2$\begingroup$ let-7 is a miRNA family (let stands for lethal). It was one of the first to be discovered, in fact (in C elegans). let-7a is a single member of the family. It seems rare in science that established names are changed to match newer nomenclature, though I don't know if that's the case here. $\endgroup$– canadianerMar 22, 2015 at 18:22
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1$\begingroup$ Another such example: There is an miRNA in Drosophila called bantam (Just bantam) $\endgroup$– WYSIWYGMar 23, 2015 at 9:34
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2 Answers
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Some general aspects about miRNA nomenclature in addition to canadianer's answer:
mirrefers to the pre-miRNA whereasmiRrefers to the mature formmir-x-ymir-x-zfor examplemir-1-1andmir-1-2refer to different precursors that give rise to same mature miRNA (i.e.miR-1). These different precursors can be regulated differently.- The mature miRNA resulting from the 5' arm of the precursor hairpin has a suffix of
-5p; similarly the product from the 3' arm has the suffix of-3p. Previously, the lesser expressed/abundant (or unexpressed) of the two products was designated with an asterisk. For e.g.miR-124*. This convention is obsolete now. Any miRNA by default has the-5p/3psuffix. This is useful especially in case oflet-7because there is no uppercase notation to differentiate precursor from the mature miRNA. For example, the mature form is always denoted ashsa-let-7b-5peven though the-3pis never expressed. - A "family" consists of miRNAs with the same seed sequence (usually 2nd-9th residue). Sometimes it can be observed that one of the arms is less conserved than the other between different precursors. For example in the case of
let-7the-3p(s)do not have a conserved seed sequence, however, all-5p(s)have the same seed sequence.
And as mentioned in the other answer, the name let-7 just sticks around because of historical reasons.
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let-7 is a miRNA family (let stands for lethal) and, in fact, was one of the first to be discovered (in Caenorhabditis elegans). let-7a is but one of many members of the family, with orthologs in many species. It seems rare in biology that established names are changed to match newer nomenclature, though I can't say for sure if that is why many (but not all) of the let-7 family members don't follow the standard.
Edit: Coincidentally, I was just reading a review about miRNA and came cross this informative excerpt which should at least give some sense of legitimacy to my above speculation.
Ha M, Kim VN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Bio 15(8):509-524
The nomenclature of miRNA genes is somewhat inconsistent. The genes found in early genetic studies were named after their phenotypes (for example, lin-4, let-7 and lsy-6), whereas most miRNAs found from cloning or sequencing received numerical names (for example, the lin-4 homologues in other species are called mir-125).
Roush S, Slack FJ. 2008. The let-7 family of microRNAs. Trends Cell Biol 18(10):505-516
The lethal-7 (let-7) gene was initially discovered as an essential developmental gene in C. elegans and, later, as one of the first miRNAs (Figure 1). Soon afterwards, a simple BLAST (basic local alignment search tool) search revealed exact matches to the mature let-7 miRNA sequence in the emerging Drosophila melanogaster and human genomes. It is now known that mature let-7 is highly conserved across animal species.
The let-7 family of miRNAs is often present in multiple copies in a genome (Table 1). To distinguish between multiple isoforms, a letter is placed after let-7 to indicate a let-7 with a slightly different sequence, and a number at the end denotes that the same sequence is present in multiple genomic locations. For example, humans have ten mature let-7-family sequences (Figure 3) that are produced from 13 precursor sequences (Figure 4). Three separate precursors produce the mature let-7a sequence (let-7a-1, let-7a-2 and let-7a-3) and precursors from two different genomic locations produce the let-7f (let-7f-1 and let-7f-2) sequence. However, the size of the family can differ between organisms. Drosophila (fly) has only one let-7, whereas the zebrafish Danio rerio has 11 mature sequences in 19 loci throughout its genome…
Early characterization of let-7:
answered Mar 23, 2015 at 4:47