Small RNAs associate with Argonaute proteins and serve as sequence-specific guides to regulate messenger RNA stability, protein synthesis, chromatin organization and genome structure1,2,3. In animals, Argonaute proteins segregate into two subfamilies4. The Argonaute subfamily acts in RNA interference and in microRNA-mediated gene regulation using 21–22-nucleotide RNAs as guides. The Piwi subfamily is involved in germline-specific events such as germline stem cell maintenance and meiosis. However, neither the biochemical function of Piwi proteins nor the nature of their small RNA guides is known. Here we show that MIWI, a murine Piwi protein, binds a previously uncharacterized class of ∼29–30-nucleotide RNAs that are highly abundant in testes. We have therefore named these Piwi-interacting RNAs (piRNAs). piRNAs show distinctive localization patterns in the genome, being predominantly grouped into 20–90-kilobase clusters, wherein long stretches of small RNAs are derived from only one strand. Similar piRNAs are also found in human and rat, with major clusters occurring in syntenic locations. Although their function must still be resolved, the abundance of piRNAs in germline cells and the male sterility of Miwi mutants suggest a role in gametogenesis.
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We thank N. Sheth for help with the informatics analysis of piRNA populations, and W. R. McCombie for pilot sequencing. C. Cordon-Cardo and M. Golding provided tissue samples. We thank C. Mello, L. Murchison, S. Cheloufi and O. Tam for helpful discussions. This work was supported in part by grants from the NIH (G.J.H.). A.G. is a Florence Gould Fellow of the Watson School of Biological Sciences. G.J.H. is an Investigator of the Howard Hughes Medical Institute.
The GenBank accession numbers for piR-1, piR-2 and piR-3 are DQ539889, DQ539890 and DQ539891, respectively. Mouse piRNA accession numbers range from DQ539889 to DQ569912; human piRNA accession numbers range from DQ569913 to DQ601958; and rat piRNA accession numbers range from DQ601959 to DQ628526. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.
Full description of the materials and methods used in this study. (DOC 29 kb)
Supplementary Table 1 indicates the number of piRNA clones mapping to each category of sequences in the mouse genome. Supplementary Tables 2, 3 and 4 describe the piRNA clusters in mouse, human and rat, respectively. (DOC 901 kb)
Supplementary Figure 1 shows that piRNAs are degraded by RNaseA, but not DNase I. Supplementary Figure 2 describes the general features of the mouse piRNA clones. (PDF 228 kb)
Supplementary Figures 3, 4, 5 and 6 represent the density of mouse piRNAs along chromosomes 1 and 2, 3 and 4, 5 and 6, 7 and 8, respectively. (PDF 3383 kb)
Supplementary Figures 7, 8, 9, 10 and 11 represent the density of mouse piRNAs along chromosomes 9 and 10, 11 and 12, 13 and 14, 15 and 16, 18 and 19, respectively. (PDF 3145 kb)
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Girard, A., Sachidanandam, R., Hannon, G. et al. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006). https://doi.org/10.1038/nature04917
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