Nomenclature of microRNAs

Mature microRNAs

The full name of mature microRNAs is usually written like this (no bold needed):

hsa-miR-202-3p

• hsa = Homo sapien species abbreviation
• Warning! Microsoft autocorrects "hsa" to "has"
• If you see the "has" prefix in a publication, it's likely a typo
• Add "hsa" to your spellcheck dictionary
• miR = abbreviation for microRNA used when naming the RNA sequence
• MIR, all capitals, is used for gene names only, not the RNA transcript
• Not to be confused with "piR", which refers to a different class of RNAs called PIWI-binding RNAs or "piRNAs". These do not bind the same proteins as miRNAs.
• 202 = code for the precursor microRNA which can be processed into two mature microRNAs (3p or 5p)
• 3p = indicates that the mature miRNA (21-24 nt) comes from the 3-prime end of the hairpin structure

There is another mature miRNA named hsa-miR-202-5p which has a different sequence and targets different genes, but comes from the same precursor miRNA.

The precursor miRNA does not have either -3p or -5p suffixes. It is simply called:

• hsa-miR-202 (proper name of precursor)
• hsa-microRNA-202 (not used)
• miR-202 (ok if the species is known from other context)

In rare cases, if a precursor miRNA is only processed into one known mature sequence (either -3p or -5p), then the mature name might be the same as the precursor name. In miRNA-seq lists, if everything else has -3p or -5p suffixes except a handful, then that's why. 
 

Asterisk convention - old way of naming mature miRNAs

In older papers, you may see microRNAs described with or without an asterisk (no bold needed):

• hsa-miR-202
• hsa-miR-202*

That's an older and less useful convention. It has fallen out of fashion. The un-asterisked name was supposed to be the "predominant" and functional form. The asterisked one was the alternative "minor" product.

Nowadays, you should use -3p or -5p suffixes for clarity since we know that the "minor" products can also be functional. Also, there are environmental and tissue-specific differences in miRNA expression, so "predominant" and "minor" are not useful naming conventions anymore.

You can use miRbase.org to find current names. Example: hsa-miR-202* is now called hsa-miR-202-5p. Beware, the asterisk doesn't always refer to the -5p miRNA. It varies!

Historical exceptions to regular miRNA names

The first miRNA was discovered in the nematode C. elegans and called lin-4.

In humans, the first miRNAs discovered was let-7.

Neither uses the "miR" prefix, but they are both still microRNAs. Also, let-7 was later expanded into a huge family of miRNAs, so it's common to see subdivisions with letters and additional hyphenation. Examples:

• hsa-let-7a-5p
• hsa-let-7a-2-3p
• hsa-let-7b-3p
• hsa-let-7i-5p

Not microRNAs

The prefix piR- refers to PIWI-interacting RNAs (also called "piwi-RNAs" pronounced "pea-wee RNAs", or "piRNAs" pronounced "pie-RNAs"). This is another class of noncoding small RNAs that can be picked up in small RNA-sequencing. These are not microRNAs. They bind different protein complexes and regulate genes in different ways than miRNAs.

Read more:

• Ozata et al., "PIWI-interacting RNAs: small RNAs with big functions", Nature Reviews Genetics, 20, 89-109 (2019)