The characterisation of piRNA-related 19mers in the mouse

Harald M Oey,Neil A Youngson,Emma Whitelaw

doi:10.1186/1471-2164-12-315

Abstract

BackgroundPiwi interacting RNA, or piRNA, is a class of small RNA almost exclusively expressed in the germline where they serve essential roles in retrotransposon silencing. There are two types, primary and secondary piRNA, and the latter is a product of enzymatic cleavage of retrotransposons' transcripts directed by the former. Recently, a new class of 19nt long RNA was discovered that is specific to testis and appears to be linked to secondary piRNA biogenesis.ResultsWe locate clusters of the testis-specific 19mers, which we call piRNA-related 19mers (pr19RNA), and characterise the transcripts from which they are derived. Most pr19RNA clusters were associated with retrotransposons and unannotated antisense transcripts overlapping piRNA clusters. At these loci the abundance of 19mers was found to be greater than that of secondary piRNAs.ConclusionWe find that pr19RNAs are distinguished from other RNA populations by their length and flanking sequence, allowing their identification without requiring overlapping piRNAs. Using such sequence features allows identification of the source transcripts, and we suggest that these likely represent the substrates of primary piRNA-guided RNA cleavage events. While pr19RNAs appear not to bind directly to Miwi or Mili, their abundance relative to secondary piRNAs, in combination with their precise length, suggests they may be more than by-products of secondary piRNA biogenesis.

Highlights

Piwi interacting RNA, or Piwi-interacting small RNAs (piRNAs), is a class of small RNA almost exclusively expressed in the germline where they serve essential roles in retrotransposon silencing
Small RNAs derived from intracisternal A particles (IAPs) in testis It is known that p-piRNAs target retrotransposons such as IAPs and long interspersed nuclear elements (LINEs) and facilitate cleavage and repression of these genomic parasites in the testes [9,11]
We noticed a abundant group of precisely 19 nt long RNAs (Figure 1A). Both the 19mers and the piRNAs were found to map in similar numbers to the sense and the antisense strands of the IAP repeats, a distribution that has been shown previously for the piRNAs and that may be explained by widespread sense and antisense transcription of these elements [11,26]

Summary

Introduction

Piwi interacting RNA, or piRNA, is a class of small RNA almost exclusively expressed in the germline where they serve essential roles in retrotransposon silencing. There are two types, primary and secondary piRNA, and the latter is a product of enzymatic cleavage of retrotransposons’ transcripts directed by the former. Piwi-interacting small RNAs (piRNAs) are almost exclusively expressed in the germline where they serve essential roles in retrotransposon silencing [1,2,3,4,5]. The p-piRNAs are identified by their length, spanning ~24-30 ribonucleotides (nt) and the presence of a 5’ U They are mostly derived from long non-coding RNAs transcribed from distinct genomic loci known as piRNA clusters [5,7].

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