Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi proteins. These piRNA complexes have been linked to both epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, particularly those in spermatogenesis. They are distinct from microRNA (miRNA) in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity.
It remains unclear how piRNAs are generated, but potential methods have been suggested, and it is certain their biogenesis pathway is distinct from miRNA and siRNA, while rasiRNAs are a piRNA subspecies.
piRNAs have been identified in both vertebrates and invertebrates, and although biogenesis and modes of action do vary somewhat between species, a number of features are conserved. piRNAs have no clear secondary structure motifs, the length of a piRNA is, by definition, between 26 and 31 nucleotides, and the bias for a 5’ uridine is common to piRNAs in both vertebrates and invertebrates. piRNAs in Caenorhabditis elegans have a 5’ monophosphate and a 3’ modification that acts to block either the 2’ or 3’ oxygen, and this has also been confirmed to exist in Drosophila melanogaster, zebrafish, mice and rats. This 3’ modification is a 2’-O-methylation; the reason for this modification is not clear, but it has been suggested to increase piRNA stability. It is thought that there are many hundreds of thousands of different piRNA species found in mammals. Thus far, over 50,000 unique piRNA sequences have been discovered in mice and more than 13,000 in D. melanogaster.
piRNAs are found in clusters throughout the genome; these clusters may contain as few as ten or up to many thousands of piRNAs and can vary in size from one to one hundred kb. The detection and annotation of piRNA clusters in genomes based on bioinformatic methods became more and more sophisticated during the past years. While the clustering of piRNAs is highly conserved across species, the sequences are not. While D. melanogaster and vertebrate piRNAs have been located in areas lacking any protein coding genes, piRNAs in C. elegans have been identified amidst protein coding genes.
In mammals, piRNAs are found both in testes and ovaries, although they only seem to be required in males. In invertebrates, piRNAs have been detected in both the male and female germlines.
The biogenesis of piRNAs is not yet fully understood, although possible mechanisms have been proposed. piRNAs show a significant strand bias, that is, they are derived from one strand of DNA only, and this may indicate that they are the product of long single stranded precursor molecules. A primary processing pathway is suggested to be the only pathway used to produce pachytene piRNAs; in this mechanism, piRNA precursors are transcribed resulting in piRNAs with a tendency to target 5’ uridines. Also proposed is a ‘Ping Pong’ mechanism wherein primary piRNAs recognise their complementary targets and cause the recruitment of piwi proteins. This results in the cleavage of the transcript at a point ten nucleotides from the 5’ end of the primary piRNA, producing the secondary piRNA. These secondary piRNAs are targeted toward sequences that possess an adenine at the tenth position. Since the piRNA involved in the ping pong cycle directs its attacks on transposon transcripts, the ping pong cycle acts only at the level of transcription. One or both of these mechanisms may be acting in different species; C. elegans, for instance, does have piRNAs, but does not appear to use the ping pong mechanism at all.
A significant number of piRNAs identified in zebrafish and D.melanogaster contain adenine at their tenth position, and this has been interpreted as possible evidence of a conserved biosynthetic mechanism across species. Ping-pong signatures have been identified in very primitive animals such as sponges and cnidarians, pointing to the existence of the ping-pong cycle already in the early branches of metazoans.
The piRNA Ping-Pong pathway was first proposed from studies in Drosophila where the piRNA associated with the two cytoplasmic Piwi proteins, Aubergine (Aub) and Argonaute-3 (Ago3) exhibited a high frequency of sequence complementarity over exactly 10 nucleotides at their 5' ends. This relationship is known as the "ping-pong signature" and is also observed in associated piRNA from Mili and Miwi2 proteins isolated from mouse testes. The proposed function of Ping-Pong in Drosophila or in mouse remains to be understood, but a leading hypothesis is that the interaction between Aub and Ago3 allows for a cyclic refinement of piRNA that are best suited to target active transposon sequences. Aub piRNA are primarily antisense to transposable element transcripts and are believed to be the main factor in targeting deleterious transcripts through complementarity. Conversely, Ago3 piRNA sequences are predominantly of sense orientation to transposable element transcripts and are derived from the product of Aub cleavage of transposon mRNA. As such, Ago3 piRNA lack the ability to target transposable element transcripts directly. Therefore, it was proposed that Ago3 piRNA guide the production of piRNA that are loaded into Aub by targeting newly exported piRNA cluster transcripts. Several lines of evidence support the effect of Ago3 on the production of Aub piRNA, in particular from examining the piRNA repertoire in Drosophila ovaries that are mutant for Ago3 and the Tudor-domain protein Kumo/Qin.
The molecular mechanism that underpins Ping-Pong likely involves several piRNA pathway associated factors. Kumo/Qin was reported to coordinate the loading of Ago3 with piRNA, in addition to interacting with both Aub and Ago3. However, the Tudor protein, Krimper, was also shown to interact with both Aub and Ago3 through its Tudor domains while also binding itself through its N-terminal Krimper domain. Specifically, Krimper interacts with Ago3 in its piRNA-unloaded state, while its interaction with Aub is dependent on the symmetrical dimethylation of arginine residues in the N-terminal region of Aub. In Silkmoth germ cells, it was proposed that Vasa protein coordinates the Ping-Pong mechanism of Silkmoth Aub (Siwi) and Ago3. It is likely that the mechanism of Ping-Pong is primarily coordinated by Krimper but factors such as Kumo/Qin and Vasa, in addition to other factors have necessary functions in the Ping-Pong mechanism.
The Drosophila piRNA pathway can be separated into two branches: the cytoplasmic branch consisting of Aub and Ago3 operating the Ping-Pong mechanism, and the nuclear branch, pertaining to the co-transcriptional silencing of genomic loci by Piwi in the nucleus. Through complementary strategies, two studies show that Aub and Ago3 target cleavage triggers the 'phased' loading of piRNA into Piwi. Phasing begins with the targeting and cleavage of a complementary target by either Aub or Ago3 associated with a 'responder' piRNA. Once cleaved, the targeted transcript is then processed further by a mechanism believed to require the mitochondrial-associated endonuclease, Zucchini, which leads to the loading of Piwi protein with sequential fragments of the targeted transcript. In this way, the Aub or Ago3 'responder' piRNA sequence cleaves a complementary target that is then sliced at periodic intervals of approximately 27 nucleotides that are sequentially loaded into Piwi protein. Once loaded with piRNA, Piwi then enters the germ cell nucleus to co-transcriptionally silence nascent transcripts with complementarity to it's piRNA guide. It is currently unknown whether phasing occurs in other organisms.
The wide variation in piRNA sequences and piwi function over species contributes to the difficulty in establishing the functionality of piRNAs. However, like other small RNAs, piRNAs are thought to be involved in gene silencing, specifically the silencing of transposons. The majority of piRNAs are antisense to transposon sequences, suggesting that transposons are the piRNA target. In mammals it appears that the activity of piRNAs in transposon silencing is most important during the development of the embryo, and in both C. elegans and humans, piRNAs are necessary for spermatogenesis.
piRNA has a role in RNA silencing via the formation of an RNA-induced silencing complex (RISC). piRNAs interact with piwi proteins that are part of a family of proteins called the Argonautes. These are active in the testes of mammals and are required for germ-cell and stem-cell development in invertebrates. Three piwi subfamily proteins - MIWI, MIWI2 and MILI - have been found to be essential for spermatogenesis in mice. piRNAs direct the piwi proteins to their transposon targets. A decrease or absence of PIWI protein expression is correlated with an increased expression of transposons. Transposons have a high potential to cause deleterious effect on their host, and, in fact, mutations in piRNA pathways are found to reduce fertility in D.melanogaster. However, piRNA pathway mutations in mice do not demonstrate reduced fertility; this may indicate redundancies to the piRNA system. Further, it is thought that piRNA and endogenous small interfering RNA (endo-siRNA) may have comparable and even redundant functionality in transposon control in mammalian oocytes.
piRNAs appear to have an impact on particular methyltransferases that perform the methylations which are required to recognise and silence transposons, but this relationship is not well understood.
piRNAs can be transmitted maternally, and based on research in D. melanogaster, piRNAs may be involved in maternally derived epigenetic effects. The activity of specific piRNAs in the epigenetic process also requires interactions between piwi proteins and HP1a, as well as other factors.
Recent discovery also show, the existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens.
Accessory Proteins of the piRNA Pathway
Genetic screens examining fertility defects identified a number of proteins that are not Piwi-clade Argonautes, yet produce the same sterility phenotypes as Piwi mutants.
Drosophila Tudor Domain Proteins
Many factors required for the piRNA pathway in Drosophila contain Tudor domains that are known to bind symmetrically dimethylated arginine residues (sDMA) present in methylation motifs of Piwi proteins. Piwi proteins are symmetrically dimethylated by the PRMT5 methylosome complex, consisting of Valois (MEP50) and Capsulèen (dart5; PRMT5).
- Yb (fs(1)Yb)
Non-Tudor Drosophila piRNA pathway proteins
Drosophila Nuclear piRNA pathway proteins
- Rhino (HP1D)
- SetDB1 (Eggless)
Major advances in the piRNA field have been achieved thanks to the use of next-generation sequencing techniques, such as Solexa and 454. These techniques allow analysis of highly complex and heterogeneous RNA populations like piRNAs. Due to their small size, expression and amplification of small RNAs can be challenging, so specialised PCR-based methods have been developed in response to this difficulty.
- Molecular Biology Select. Cell, 2006. 126(2): p. 223, 225-223, 225.
- Seto, A.G., R.E. Kingston, and N.C. Lau, The Coming of Age for Piwi Proteins. Molecular Cell, 2007. 26(5): p. 603-609.
- Siomi MC, Sato K, Pezic D, Aravin AA: PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 2011, 12:246-258.
- Klattenhoff, C. and W. Theurkauf, Biogenesis and germline functions of piRNAs. Development, 2008. 135(1): p. 3-9.
- Kandhavelu M,* Lammi C, Buccioni M, Dal Ben D, Volpini R, Marucci G (2009). "Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens". Journal of Bioinformatics and Sequence Analysis 1 (2): 031–040.
- Ruby, J.G., et al., Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans. 2006. 127(6): p. 1193-1207.
- Vagin, V.V., et al., A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline. Science, 2006. 313(5785): p. 320-324.
- Houwing, S., et al., A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish. Cell, 2007. 129(1): p. 69-82.
- Kirino, Y. and Z. Mourelatos, Mouse Piwi-interacting RNAs are 2[prime]-O-methylated at their 3[prime] termini. Nat Struct Mol Biol, 2007. 14(4): p. 347-348.
- Faehnle, C.R. and L. Joshua-Tor, Argonautes confront new small RNAs. Current Opinion in Chemical Biology, 2007. 11(5): p. 569-577.
- Das, P.P., et al., Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline. Molecular Cell, 2008. 31(1): p. 79-90.
- Lin, H., et al., The role of the piRNA pathway in stem cell self-renewal. Developmental Biology, 2008. 319(2): p. 479-479.
- O'Donnell, K.A. and J.D. Boeke, Mighty Piwis Defend the Germline against Genome Intruders. Cell, 2007. 129(1): p. 37-44.
- Rosenkranz, David; Zischler, Hans (10 January 2012). "proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis". BMC Bioinformatics 13 (5). doi:10.1186/1471-2105-13-5.
- Malone, C.D. and G.J. Hannon, Small RNAs as Guardians of the Genome. Cell, 2009. 136(4): p. 656-668.
- Brennecke, J., et al., An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing. Science, 2008. 322(5906): p. 1387-1392.
- Aravin, A., et al., A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 2006. 442(7099): p. 203-207.
- Tam, O. H. et al. (2008). "Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes". Nature 453: 534–538. doi:10.1038/nature06904.
- Ruvkun, G (2008). "Tiny RNA: Where do we come from? What are we? Where are we going?". Trends in Plant Science 13 (7): 313–316. doi:10.1016/j.tplants.2008.05.005.
- Aravin, A.A. et al. (2008). "A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice". Molecular Cell 31 (6): 785–799. doi:10.1016/j.molcel.2008.09.003.
- Brennecke, J. et al. (2007). ", Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila". Cell 128 (6): 1089–1103. doi:10.1016/j.cell.2007.01.043.
- Grimson, A.; Srivastava, M.; Fahey, B.; Woodcroft, B.J.; Chiang, H.R.; King, N.; Degnan, B.M.; Rokhsar, D.S.; Bartel, D.P. (2008). "Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals". Nature 455: 1193–1197. doi:10.1038/nature07415.
- Gunawardane, L. et al. (2007). "A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila". Science 215 (5818): 1587–1590. doi:10.1126/science.1140494.
- Li, C. et al. (2009). "Collapse of Germlin piRNAs in the Absense of Argonaute3 Reveals Somatic piRNAs in Flies". Cell 137 (3): 509–521. doi:10.1016/j.cell.2009.04.027.
- Zhang, Z. et al. (2011). "Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3 Ligase and Tudor Domains". Molecular Cell 44 (4): 572–584. doi:10.1016/j.molcel.2011.10.011.
- Webster, A. et al. (2015). "Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper.". Molecular Cell 59 (4): 564–575. doi:10.1016/j.molcel.2015.07.017.
- Sato, K. et al. (2015). "Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline.". Molecular Cell 59 (4): 553–563. doi:10.1016/j.molcel.2015.06.024.
- Xiol, J. et al. (2014). "RNA Clamping by Vasa Assembles a piRNA Amplifier Complex on Transposon Transcripts.". Cell 157 (7): 1698–1711. doi:10.1016/j.cell.2014.05.018.
- Mohn, F. et al. (2015). "piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis.". Science 348 (6236): 812–817. doi:10.1126/science.aaa1039.
- Han, B.W. et al. (2015). "piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production.". Science 348 (6236): 817–821. doi:10.1126/science.aaa1264.
- Le Thomas, A. et al. (2013). "Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state.". Genes & Development (27): 390–399. doi:10.1101/gad.209841.112.
- Wang, G. and V. Reinke, A C. elegans Piwi, PRG-1, Regulates 21U-RNAs during Spermatogenesis. Current Biology, 2008. 18(12): p. 861-867.
- Ro, S., et al., A PCR-based method for detection and quantification of small RNAs. Biochemical and Biophysical Research Communications, 2006. 351(3): p. 756-763.
- Tang, F., et al., A sensitive multiplex assay for piRNA expression. Biochemical and Biophysical Research Communications, 2008. 369(4): p. 1190-1194.
- Lau, N.C. et al. (2006). "Characterization of the piRNA Complex from Rat Testes". Science 313: 363–367. doi:10.1126/science.1130164.
- Kim, V.N. (2006). "Small RNAs Just Got Bigger: Piwi-Interacting RNAs (piRNAs) in Mammalian Testes". Genes Dev 20: 1993–1997. doi:10.1101/gad.1456106.
- Girard, A. et al. (2006). "A Germline-Specific Class of Small RNAs Binds Mammalian Piwi Proteins". Nature 442: 199. doi:10.1038/nature04917.
- Grivna, S.T. et al. (2006). "A Novel Class of Small RNAs in Mouse Spermatogenic Cells". Genes Dev 20: 1709–1714. doi:10.1101/gad.1434406.
- Watanabe, T. et al. (2006). "Identification and characterization of two novel classes of small RNAs in the mouse germline". Genes Dev 20: 1732–1743. doi:10.1101/gad.1425706.
- Carmell, M.A. et al. (2007). "MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline". Dev Cell. 12: 503–514. doi:10.1016/j.devcel.2007.03.001.
- PingPongPro - a software for finding ping-pong signatures and ping-pong cycle activity
- piRNA Bank A web resource on classified and clustered piRNAs
- proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
- piRNA cluster - database