piRNAs in the Germ Line
Haifan Lin, et al.
Science 316, 397 (2007);
DOI: 10.1126/science.1137543

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SPECIALSECTION

piRNAs in the Germ Line
Haifan Lin
Small noncoding RNAs have emerged as potent regulators of gene expression at bothtranscriptional and posttranscriptional levels. Recently, a class of small RNAs that interactwith Piwi proteins has been discovered in the mammalian germ line and Drosophila. These
Piwi-interacting RNAs (piRNAs) represent a distinct small RNA pathway.
he importance of small noncoding
RNAs as regulators of transcription,RNA stability, and translation is becoming increasingly evident (1). The recently
discovered piRNAs differ from the known
small interfering RNAs (siRNAs) or microRNAs (miRNAs) in several ways (2–6). First,piRNAs interact with the Piwi, but not theArgonaute (Ago), subfamily of the Piwi-Ago
family proteins. Mouse Piwi (Miwi) is required for piRNA biogenesis and/or stability(7), whereas mouse Ago2 is required for thesiRNA pathway. Second, piRNAs are 24 to 31
nucleotides (nt) instead of ~21 nt. Third,piRNAs consist of more than 50,000 different
species, in contrast to several hundred speciesof miRNAs. Fourth, most piRNAs match to
the genome in clusters of 20 to 90 kbs in a
strand-specific manner, with each cluster
likely representing a long single-stranded
RNA precursor or, more often, two nonoverlapping and divergently transcribed precursors (Fig. 1A) (2). In contrast, siRNAs andmiRNAs are derived from double-stranded
and short-hairpin RNA precursors, respectively. Finally, some piRNAs might positively
regulate mRNA stability and translation (seebelow), in contrast to the negative effect of thesiRNAs and miRNAs.
In Drosophila, some piRNAs have beencalled repeat-associated siRNAs (“rasiRNAs”)(3, 4, 6). However, unlike siRNAs, theserasiRNAs bind to Piwi, Aubergine (Aub), andAgo3—three Piwi subfamily proteins, but notto Ago subfamily proteins. Moreover, their production requires neither Dicer-1 nor Dicer-2,
which generate miRNAs and siRNAs, respectively (3). Thus, by definition, these rasiRNAs
are piRNAs.
How are piRNAs produced? They arelikely produced from long single-stranded
precursors by yet-to-be-identified endonucleases. In Drosophila, Piwi, Aub, and Ago3
could be such endonucleases because they haveslicing activity (4, 6). For some transposon-T

Yale Stem Cell Center, Yale University School of Medicine,
New Haven, CT 06510, USA. E-mail: haifan.lin@yale.edu

derived piRNAs in Drosophila, an additional“Ping-Pong” mechanism might be involvedin accelerating their processing from precursors (5, 6) (Fig. 1B). This is possible because the Aub- and Piwi-associated piRNAs
match the antisense strand of DNA, showing
a strong bias for a uracyl (U) at the 5′ ends;
yet Ago3-associated piRNAs match the sense
strand and complement Aub- and Piwiassociated piRNAs in their first 10 nucleotides, showing a conserved adenine (A) at
position 10. Thus, the Ago3-piRNA complex
might guide and cleave the 5′ ends of Auband Piwi-associated piRNAs, whereas theAub-Piwi–piRNA complex might guide andADNABDNARNA pol
Aub5'AubUAubU

Aub/PiwipiRNA
precursor

AubUReferences

10-nt
complementary
sequence
AubU
A N9

Maternal
supply5' U

Aub5' U

5'

AcceleratedpiRNA
processing via
Ping-Pongmechanism

Aub?

Ago3
piRNA
precursor?
A N9 5'
Ago3

A N9 5'U

5'Ago3

A N9 5'Ago3

Maternal
supplyFig. 1. (A) A bidirectional piRNA cluster. (B) A
proposed piRNA biogenesis pathway. The
resulting piRNA-protein complexes then regulate gene expression at the epigenetic or posttranscriptional levels (not shown). N9, the 9th
nucleotide from A10 in Ago3-piRNA; the question mark (?), other nuclease.

www.sciencemag.org

SCIENCEcleave the 5′ ends of Ago3-associated piRNAs(Fig. 1B).
What are the roles of piRNAs in the germline? The genomic distribution of piRNAs andthe function of their Piwi proteins provide
important clues to this question. Most piRNAs
map to unique sites in the genome, includingintergenic, intronic, and exonic sequences.
For example, only 17 to 20% of mammalianpiRNAs map to annotated repeats, includingtransposons and retrotransposons (2). Thus,
piRNAs may have diverse functions fromepigenetic programming and repressing transposition to posttranscriptional regulation.
Each of these speculated roles is supportedby the known function of their partner Piwi
proteins. For instance, Piwi is an epigenetic
regulator (8). It colocalizes with Polycomb
group (PcG) proteins to cluster PcG responsesequences in the genome (9). Thus, somePIWI-associated piRNAs may be involved inepigenetic regulation. In fact, gypsy piRNAsin Drosophila have been shown to downregulate sense gypsy transcripts (10). Inaddition, Piwi prevents retrotransposon transposition in the testicular germ line (11), whichsuggests a second role of Piwi-associatedpiRNAs. Furthermore, Piwi and Aub appear
to positively regulate translation in early
Drosophila embryos (12, 13). Similarly, Miwi
promotes the stability (14) and, likely, translation of its target mRNAs (15). Thus, somepiRNAs may have a third role in positively
regulating translation and mRNA stability.
The discovery of piRNAs reveals a new
dimension of gene regulation. Future studies
on the biogenesis and the potentially diverse
functions of piRNAs should substantially advance our understanding of gene regulationthat defines the germ line.

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