Finding miRNA & small RNA that are human-specific?

Question

[Adamc]

Hello,

I'm looking for suggestions on how to determine which miRNAs (and other small RNAs) are human-specific, in the context of only mouse and human. I found a relevant paper which looked at this in more species, and presents a reasonable method for determining species-specificity ("Evolution of the human-specific microRNA miR-941") based on alignment of miRNA precursors, but I was wondering if there are any other suggestions (or if a database for this already exists and I missed it).

Thanks!

[iraun]

Have you checked miRBase (http://www.mirbase.org/)? It is a database of published miRNA sequences and the corresponding annotations, maybe it is useful for your goal.

[Adamc]

Yes, definitely useful, but I think that adequately determining species-specificity is more involved than set operations on miRBase IDs between species?

[Manvendra Singh]

I think that from mirbase, those microRNAs having prefix 'hsa-mir' should be human specific

[Lorena Pantano]

Hi,

that's not totally true, although it helps. You can infer from miRbase which are specifics if the ID in the name is not in other species. Like hsa-miR-34c, it exists in other species like mmu. You can try to parse that, or you can look at the position of the precursor the sequence conservation using some tracks like the UCSC has.

probably there are other fancy ways, but these two are quite straight forward.

cheers

[Manvendra Singh]

Yes,

except 15 to 20 of them, none of annotated microRNAs are exclusively present in Human. Their homologues are found in primates, mouse and in others

I meant to say that hsa-mir are human specific microRNA, which does not mean that their homologues are not present in other species.

[Lorena Pantano]

No problem, for me human specific, are ones that are not present in other families, like their homologous. So I understand that this miRNA has appeared as a new miRNA in the evolution. sorry about any miss-understanding. Probably, I was biased from one of my projects where I was trying to find exactly that.

Cheers

[Manvendra Singh]

I would trust their study and pick the human specific microRNAs from their supplementary table; they showed that these microRNAs are exclusively in Humans and their orthologues are not found in other species. In their supplementary table you would find this info about all other microRNAs

hsa-mir-1302-10,
hsa-mir-1302-11
hsa-mir-1302-2
hsa-mir-3156-3
hsa-mir-3648
hsa-mir-3673
hsa-mir-3690
hsa-mir-4487
hsa-mir-4739
hsa-mir-5095
hsa-mir-659
hsa-mir-941-1
hsa-mir-941-3
hsa-mir-941-4

[Adamc]

It's based on an older version of miRBase, so I'd like to use the current version. I can try to re-run their pipeline, but I was wondering if there was anyone who's already done this, or some easier method.

[mikhail.shugay]

Of note, after the initial discovery of lin-4 in 1993, the process of miRNA discovery in 2000's was in part bioinformatics-driven. Short RNAs were predicted based on their conservation (http://www.sciencemag.org/content/294/5543/853), so the lists of miRNAs should be biased towards miRNAs broadly represented in different species.