piRNAs and their promoters

Question

[int11ap1]

Dear all,

I have the coordinates of piRNAs. I would like to set an upstream range for taking their promoters. However, I do not know what range to choose and I do not find any paper talking about it.

Normally you would select 2000bp upstream any gene for getting the promoter. But I do not know if I have to choose 2000bp or less for piRNAs. Do you know any idea about it?

Thanks

Answer 1

[Ryan Dale]

The review by Luteijn and Ketting 2014 implies that the origin of the primary piRNA precursor is unclear and may depend on species. Each piRNA may have come from a larger precursor transcript, in which case you'd need to know where that precursor's TSS is.

But even for genes, which usually have a clear TSS, there's no standard "promoter region" definition. I frequently see +/- 500 bp, 1kb, 2kb, 5kb, or 1kb, 2kb, or 5kb upstream. I've even seen 10kb upstream as a promoter definition though that seems a bit too far.

It all depends on what you're trying to do and what you're trying to ask. piRNAs generally occur in clusters, so maybe you want cluster boundaries plus-or-minus some distance. Try different distances, run your full analysis on each one, and see if the results are substantially different among the different distances.

If you get different answers for different distances, it might tell you something interesting about the biology.