Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs isolated from the mammalian germline that interact with the Piwi (P-element Induced Wimpy Testis) subfamily of proteins. The Piwi subfamily comprises Piwi, Aubergine and AGO3 in flies, MILI, MIWI and MIWI2 in mice, and HILI, HIWI1, HIWI2 and HIWI3 in humans [1]. Although the biogenesis and function of piRNAs are not well understood, evidence strongly suggests that piRNAs play a key role in germ line development.

Mature piRNAs are short, single-stranded RNA molecules approximately 26-32 nucleotides in length. piRNAs consist of more than 50,000 different species in mouse testes[2], in contrast to several hundred species of miRNAs. Individual piRNAs are poorly conserved even between closely related species, and are strikingly different from microRNAs in their length, expression pattern, and genomic organization.

 

Unlike siRNAs and miRNAs, piRNAs are not generated from dsRNA precursors. Rather, piRNAs are likely produced from a primary transcript that traverses an entire piRNA cluster and is subsequently processed into mature piRNAs. The detail mechanism of this process is not well understood. However, evidence from flies demonstrates that the first 10 nucleotides of piRNAs bound to Aub or Piwi, which typically begin with uridine, are often complementary to the first 10 nucleotides of piRNAs bound to Ago3, which usually contain an adenosine at position 10. These observations led to the proposal of the "ping-pong" model, in which new piRNAs are generated by amplification mediated by this complementarity[3].

 

Fig.1 The "ping-pong" model for piRNA biogenesis. Complementarity between piRNA sequences causes amplification of new piRNA molecules[3].

The mammalian piRNAs can be divided into two classes, pre-pachytene and pachytene piRNAs, depending on the stage of meiosis at which they are expressed in developing spermatocytes[2]. They may have distinct functions according to their sequence features[1].

Numerous lines of evidence indicate that piRNAs have indispensable roles in spermatogenesis. * Spermatogenesis: Complete loss of Miwi and Mili causes meiotic arrest during spermatogenesis, leading to seminiferous tubules devoid of sperm.

•   Regulation of translation: Miwi and piRNAs associate with the cap binding complex and modulate mRNA stability during the production of proteins required for spermatogenesis[5].

•   Preservation of genomic integrity: Mili-and Miwi-2 null mice have increased activity of retrotransposons, suggesting that piRNAs protect the germline genome from deleterious transposon insertions[6].

 

Although piRNAs have been discovered in multiple species over the past 8 years, we still do not know how a new piRNA response is initiated, and the exact function of piRNAs in development remains elusive. There are many open questions in the piRNA field ripe for further study. Due to the large number of piRNAs, characterization of individual piRNAs is more challenging than that of single miRNAs. However, the refinement of microarray and high-throughput sequencing techniques will enable researchers to learn much more about the biological roles of individual piRNAs in the near future.

 

Arraystar's scientists have developed piRNA microarrays for human, mouse and rat species to evaluate the global expression of piRNAs. piRNA sequences from all three organisms are downloaded from the NCBI database, and mapped to the genome sequences (HG19, MM9 and RN4) using UCSC Blat. Acceptable strategies are employed to select the proper piRNAs. Then, antisense 60-mer oligonucleotide probes are designed using a duplex method. Using our proprietary piRNA arrays (table 1), we offer integrated services, from sample preparations to comprehensive data analysis. 

Microarray	Species	Database	Format	Detected piRNAs
Arraystar Human piRNA Array	Human	HG19	4 * 44K	23,677
Arraystar Mouse piRNA Array	Mouse	MM9	4 * 44K	43,537
Arraystar Rat piRNA Array	Rat	RN4	4 * 44K	39,727