Abstract
Computational analysis of mouse piRNA sequence and biogenesis
Highlights
A recent landmark discovery has identified a novel class of small RNAs in mammalian testes that is expressed during spermatogenesis [1,2,3,4,5,6]
We refer to the PIWI-interacting small RNAs from Drosophila and Zebrafish as repeat-associated small interfering RNA (rasiRNA) and the mammalian counterparts as PIWI-interacting RNA (piRNA) without discounting functional similarity
We further show that 25% of piRNA clusters are bracketed by inverted repeats of varying length, suggesting that some of the long piRNAs single-stranded precursors [1,2,3,6,13] can form a double-strand RNA intermediate from inverted repeats that may trigger piRNA biogenesis
Summary
A recent landmark discovery has identified a novel class of small RNAs in mammalian testes that is expressed during spermatogenesis [1,2,3,4,5,6]. PiRNAs are similar to repeat-associated small interfering RNA (rasiRNA), a class of small RNAs that are responsible for transposon silencing in the Drosophila germline [13,14,15,16,17,18,19,20] (and recently identified in Zebrafish [21]), suggesting analogies between rasiRNAs and mammalian piRNAs in terms of biogenesis and function. To better understand the origin of piRNAs, we compared the available three largest mouse piRNA datasets (identified at the pachytene stage of spermatogenesis) in terms of sequence similarities and cluster organization. We focus on the three largest datasets (A–C, listed in decreasing number of piRNA sequences identified in [1,2,3]) each with thousands of distinct piRNA sequences (a recent fourth comprehensive dataset of MILI-bound piRNAs identified in the pre-pachytene stage of spermatogenesis [6] is not included in this analysis).
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