Piwi-interacting RNA

{{short description|Largest class of small non-coding RNA molecules in animals}} {{Redirect|piRNA|the software package|Partition function for Interacting RNAs}} '''Piwi-interacting RNA''' ('''piRNA''') is the largest class of small non-coding RNA molecules expressed in animal cells.<ref name="Molecular">{{cite journal |title=Molecular Biology Select |journal=Cell |date=July 2006 |volume=126 |issue=2 |pages=223–225 |doi=10.1016/j.cell.2006.07.012|doi-access=free }}</ref><ref name="Seto">{{cite journal | vauthors = Seto AG, Kingston RE, Lau NC | title = The coming of age for Piwi proteins | journal = Molecular Cell | volume = 26 | issue = 5 | pages = 603–609 | date = June 2007 | pmid = 17560367 | doi = 10.1016/j.molcel.2007.05.021 | doi-access = free }}</ref><ref name="Monga">{{cite journal | vauthors = Monga I, Banerjee I| title = Computational Identification of piRNAs Using Features Based on RNA Sequence, Structure, Thermodynamic and Physicochemical Properties | journal = Current Genomics | volume = 20 | issue = 7 | pages = 508–518 | date = November 2019 | pmid = 32655289| doi = 10.2174/1389202920666191129112705 | pmc = 7327968 }}</ref> piRNAs form RNA-protein complexes through interactions with piwi-subfamily Argonaute proteins. These piRNA complexes are mostly involved in the epigenetic and post-transcriptional silencing of transposable elements and other spurious or repeat-derived transcripts, but can also be involved in the regulation of other genetic elements in germ line cells.<ref name="siomi_review">{{cite journal | vauthors = Siomi MC, Sato K, Pezic D, Aravin AA | title = PIWI-interacting small RNAs: the vanguard of genome defence | journal = Nature Reviews Molecular Cell Biology | volume = 12 | issue = 4 | pages = 246–258 | date = April 2011 | pmid = 21427766 | doi = 10.1038/nrm3089 | s2cid = 5710813 }}</ref><ref name="rasirn">{{cite journal | vauthors = Dorner S, Eulalio A, Huntzinger E, Izaurralde E | title = Delving into the diversity of silencing pathways. Symposium on MicroRNAs and siRNAs: biological functions and mechanisms | journal = EMBO Reports | volume = 8 | issue = 8 | pages = 723–729 | date = August 2007 | pmid = 17599087 | pmc = 1978081 | doi = 10.1038/sj.embor.7401015 }}</ref><ref name="pmid17199040">{{cite journal | vauthors = Klattenhoff C, Bratu DP, McGinnis-Schultz N, Koppetsch BS, Cook HA, Theurkauf WE | title = Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an ATR/Chk2 DNA damage response | journal = Developmental Cell | volume = 12 | issue = 1 | pages = 45–55 | date = January 2007 | pmid = 17199040 | doi = 10.1016/j.devcel.2006.12.001 | doi-access = free }}</ref>

piRNAs are mostly created from loci that function as transposon traps which provide a kind of RNA-mediated adaptive immunity against transposon expansions and invasions.<ref name="Goriaux">{{cite journal | vauthors = Goriaux C, Théron E, Brasset E, Vaury C | title = History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster | journal = Frontiers in Genetics | volume = 5 | page = 257 | year = 2014 | pmid = 25136352 | pmc = 4120762 | doi = 10.3389/fgene.2014.00257 | doi-access = free }}</ref> They are distinct from microRNA (miRNA) in size (26–31 nucleotides as opposed to 21–24 nt), lack of sequence conservation, increased complexity, and independence of Dicer for biogenesis, at least in animals.<ref name="rasirn"/><ref name="Molecular" /><ref name="Seto" /> (Plant Dcl2 may play a role in rasi/piRNA biogenesis.)<ref name="rasi"/><ref>{{cite journal | vauthors = Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC | title = Genetic and functional diversification of small RNA pathways in plants | journal = PLOS Biology | volume = 2 | issue = 5 | article-number = E104 | date = May 2004 | pmid = 15024409 | pmc = 350667 | doi = 10.1371/journal.pbio.0020104 | doi-access = free }}</ref>

Double-stranded RNAs capable of silencing repeat elements, then known as '''repeat associated small interfering RNA''' (rasiRNA), were proposed in ''Drosophila'' in 2001.<ref name="aravin">{{cite journal | vauthors = Aravin AA, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM, Gvozdev VA | title = Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline | journal = Current Biology | volume = 11 | issue = 13 | pages = 1017–1027 | date = July 2001 | pmid = 11470406 | doi = 10.1016/S0960-9822(01)00299-8| s2cid = 14767819 | doi-access = free | bibcode = 2001CBio...11.1017A }}</ref> By 2008, it was still unclear how piRNAs are generated, but potential methods had been suggested, and it was certain their biogenesis pathway is distinct from miRNA and siRNA, while rasiRNA is now considered a piRNA subspecies.<ref name="Klattenhoff">{{cite journal | vauthors = Klattenhoff C, Theurkauf W | title = Biogenesis and germline functions of piRNAs | journal = Development | volume = 135 | issue = 1 | pages = 3–9 | date = January 2008 | pmid = 18032451 | doi = 10.1242/dev.006486 | doi-access = free }}</ref>

==Characteristics== frame|right|Proposed piRNA structure, with the 3′ end 2′-O-methylation 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,<ref name="Molecular" /><ref name="madurai1982">{{cite journal | vauthors = Carmen L, Michela B, Rosaria V, Gabriella M | year = 2009| title = Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens| journal = Journal of Bioinformatics and Sequence Analysis | volume = 1 | issue = 2 | pages = 031–040 }}</ref> due to the fact that the length of a piRNA varies between species (from 21 to 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;<ref name="Ruby">{{cite journal | vauthors = Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP | title = Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans | journal = Cell | volume = 127 | issue = 6 | pages = 1193–1207 | date = December 2006 | pmid = 17174894 | doi = 10.1016/j.cell.2006.10.040 | s2cid = 16838469 | doi-access = free }}</ref> this has also been confirmed to exist in ''Drosophila melanogaster'',<ref name="Vagin">{{cite journal | vauthors = Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD | title = A distinct small RNA pathway silences selfish genetic elements in the germline | journal = Science | volume = 313 | issue = 5785 | pages = 320–324 | date = July 2006 | pmid = 16809489 | doi = 10.1126/science.1129333 | bibcode = 2006Sci...313..320V | s2cid = 40471466 }}</ref> zebrafish,<ref name="Houwing">{{cite journal | vauthors = Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RH, Hannon GJ, Draper BW, Ketting RF | display-authors = 6 | title = A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish | journal = Cell | volume = 129 | issue = 1 | pages = 69–82 | date = April 2007 | pmid = 17418787 | doi = 10.1016/j.cell.2007.03.026 | hdl = 11858/00-001M-0000-0012-E169-6 | s2cid = 13373509 | hdl-access = free }}</ref> mice,<ref name="Kirino">{{cite journal | vauthors = Kirino Y, Mourelatos Z | title = Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini | journal = Nature Structural & Molecular Biology | volume = 14 | issue = 4 | pages = 347–348 | date = April 2007 | pmid = 17384647 | doi = 10.1038/nsmb1218 | s2cid = 31193964 }}</ref> and rats.<ref name="Houwing" /> This 3' modification is a 2'-O-methylation; the reason for this modification is not clear, but it has been suggested that it increases piRNA stability.<ref name="Houwing" /><ref name="Faehnle">{{cite journal | vauthors = Faehnle CR, Joshua-Tor L | title = Argonautes confront new small RNAs | journal = Current Opinion in Chemical Biology | volume = 11 | issue = 5 | pages = 569–577 | date = October 2007 | pmid = 17928262 | pmc = 2077831 | doi = 10.1016/j.cbpa.2007.08.032 }}</ref>

More than 50,000 unique piRNA sequences have been discovered in mice and more than 13,000 in ''D. melanogaster''.<ref name="Lin">{{cite journal | vauthors = Lin H, Yin H, Beyret E, Findley S, Deng W | title = The role of the piRNA pathway in stem cell self-renewal. | journal = Developmental Biology | date = 2008 | issue = 2 | volume = 319 | page = 479 | doi = 10.1016/j.ydbio.2008.05.048 | doi-access = }}</ref> It is thought that there are many hundreds of thousands of different piRNA species in mammals.<ref name="Das">{{cite journal | vauthors = Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavaré S, Miska EA | title = Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline | journal = Molecular Cell | volume = 31 | issue = 1 | pages = 79–90 | date = July 2008 | pmid = 18571451 | pmc = 3353317 | doi = 10.1016/j.molcel.2008.06.003 }}</ref>

==History and loci== In the early 1980s, it was discovered that a single mutation in the fruit fly genome could specifically activate all copies of a retrovirus-like element called ''Gypsy'' in the female germline. The site of the mutations that made these Gypsies "dance" was thus called the ''flamenco locus''. In 2001, Aravin ''et al.'' proposed that double-stranded (ds) RNA-mediated silencing is implicated in the control of retrotransposons in the germline and by 2003 the idea had emerged that vestiges of transposons might produce dsRNAs required for the silencing of "live" transposons.<ref name="aravin"/> Sequencing of the 200,000-bp flamenco locus was difficult, as it turned out to be packed with transposable element fragments (104 insertions of 42 different transposons, including multiple Gypsies), all facing the same direction. Indeed, piRNAs are all found in clusters throughout animal genomes; these clusters may contain as few as ten or many thousands of piRNAs matching different, phased transposon fragments. This led to the idea in 2007 that in germlines a pool of primary piRNAs is processed from long single-stranded transcripts encoded by piRNA clusters in the opposite orientation of the transposons, so that the piRNAs can anneal to and complement the transposon-encoded transcripts, thereby triggering their degradation. Any transposon landing in the correct orientation in such a cluster will make the individual more or less immune to that transposon, and such an advantageous mutation will spread quickly through the population. The original mutations in the flamenco locus inhibited the transcription of the master transcript, thereby deactivating this defense system.<ref name="Goriaux" /><ref name="Brennecke" /><ref name="Molecular" /><ref name="ODonnell">{{cite journal | vauthors = O'Donnell KA, Boeke JD | title = Mighty Piwis defend the germline against genome intruders | journal = Cell | volume = 129 | issue = 1 | pages = 37–44 | date = April 2007 | pmid = 17418784 | pmc = 4122227 | doi = 10.1016/j.cell.2007.03.028 }}</ref><ref name="Malone">{{cite journal | vauthors = Malone CD, Hannon GJ | title = Small RNAs as guardians of the genome | journal = Cell | volume = 136 | issue = 4 | pages = 656–668 | date = February 2009 | pmid = 19239887 | pmc = 2792755 | doi = 10.1016/j.cell.2009.01.045 }}</ref>

A historical example of invasion and Piwi response is known: the P-element transposon invaded a ''Drosophila melanogaster'' genome in the mid-20th century, and, through interbreeding, within decades all wild fruit flies worldwide (though not the reproductively isolated lab strains) contained the same P-element. Repression of further P-element activity, spreading near-simultaneously, appears to have occurred by the Piwi-interacting RNA pathway.<ref>{{cite journal | vauthors = Kelleher ES | title = Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing | journal = Genetics | volume = 203 | issue = 4 | pages = 1513–1531 | date = August 2016 | pmid = 27516614 | pmc = 4981261 | doi = 10.1534/genetics.115.184119 }}</ref>

piRNA clusters in genomes can now readily be detected via bioinformatics methods.<ref name="Rosenkranz">{{cite journal | vauthors = Rosenkranz D, Zischler H | title = proTRAC—a software for probabilistic piRNA cluster detection, visualization and analysis | journal = BMC Bioinformatics | volume = 13 | issue = 5 | article-number = 5 | date = January 2012 | pmid = 22233380 | pmc = 3293768 | doi = 10.1186/1471-2105-13-5 | doi-access = free }}</ref> While ''D. melanogaster'' and vertebrate piRNAs have been located in areas lacking any protein-coding genes,<ref name="Klattenhoff" /><ref name="Brennecke">{{cite journal | vauthors = Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ | title = An epigenetic role for maternally inherited piRNAs in transposon silencing | journal = Science | volume = 322 | issue = 5906 | pages = 1387–1392 | date = November 2008 | pmid = 19039138 | pmc = 2805124 | doi = 10.1126/science.1165171 | bibcode = 2008Sci...322.1387B }}</ref> piRNAs in ''C. elegans'' have been identified amidst protein-coding genes.<ref name="Ruby" />

In mammals, piRNAs are found both in testes<ref name="Aravin">{{cite journal | vauthors = Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T | title = A novel class of small RNAs bind to MILI protein in mouse testes | journal = Nature | volume = 442 | issue = 7099 | pages = 203–207 | date = July 2006 | pmid = 16751777 | doi = 10.1038/nature04916 | bibcode = 2006Natur.442..203A | s2cid = 4379895 }}</ref> and ovaries,<ref name="Tam">{{cite journal | vauthors = Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ | title = Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes | journal = Nature | volume = 453 | issue = 7194 | pages = 534–538 | date = May 2008 | pmid = 18404147 | pmc = 2981145 | doi = 10.1038/nature06904 | bibcode = 2008Natur.453..534T }}</ref> although they only seem to be required in males.<ref name="siomi_review" /> In invertebrates, piRNAs have been detected in both the male and female germlines.<ref name="Houwing" /><ref name="Das" />

At the cellular level, piRNAs have been found within both the nucleus and cytoplasm, suggesting that piRNA pathways may function in both of these areas<ref name="Klattenhoff" /> and, therefore, may have multiple effects.<ref name="Ruvkun">{{cite journal | vauthors = Ruvkun G | title = Tiny RNA: Where do we come from? What are we? Where are we going? | journal = Trends in Plant Science | volume = 13 | issue = 7 | pages = 313–316 | date = July 2008 | pmid = 18562240 | doi = 10.1016/j.tplants.2008.05.005 | doi-access = free | bibcode = 2008TPS....13..313R }}</ref>

==Classification==  There are at least three Argonaute (Ago) subfamilies that have been found in eukaryotes. Unlike the Ago subfamily which is present in animals, plants, and fission yeast, the Piwi subfamily has only been found in animals.<ref name="pmid17418787">{{cite journal | vauthors = Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RH, Hannon GJ, Draper BW, Ketting RF | author-link10=Cecilia Moens | title = A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish | journal = Cell | volume = 129 | issue = 1 | pages = 69–82 | date = April 2007 | pmid = 17418787 | doi = 10.1016/j.cell.2007.03.026 | hdl = 11858/00-001M-0000-0012-E169-6 | s2cid = 13373509 | hdl-access = free }}</ref> RasiRNA has been observed in ''Drosophila'' and some unicellular eukaryotes but its presence in mammals has not been determined, unlike piRNA which has been observed in many species of invertebrates and vertebrates including mammals;<ref name="pmid16751776">{{cite journal | vauthors = Girard A, Sachidanandam R, Hannon GJ, Carmell MA | title = A germline-specific class of small RNAs binds mammalian Piwi proteins | journal = Nature | volume = 442 | issue = 7099 | pages = 199–202 | date = July 2006 | pmid = 16751776 | doi = 10.1038/nature04917 | bibcode = 2006Natur.442..199G | s2cid = 3185036 }}</ref> however, since proteins which associate with rasiRNA are found in both vertebrates and invertebrates, it is possible that active rasiRNA exist and have yet to be observed in other animals. RasiRNAs have been observed in ''Schizosaccharomyces pombe'', a species of yeast, as well in some plants, neither of which have been observed to contain the Piwi subfamily of Argonaute proteins.<ref name="rasi">{{cite journal | vauthors = Aravin A, Tuschl T | title = Identification and characterization of small RNAs involved in RNA silencing | journal = FEBS Letters | volume = 579 | issue = 26 | pages = 5830–5840 | date = October 2005 | pmid = 16153643 | doi = 10.1016/j.febslet.2005.08.009 | doi-access = free | bibcode = 2005FEBSL.579.5830A }}</ref> It has been observed that both rasiRNA and piRNA are maternally linked, but more specifically it is the Piwi protein subfamily that is maternally linked and therefore leads to the observation that rasiRNA and piRNA are maternally linked.{{clarify |date=August 2019 |reason=reads like a donut }}<ref name="pmid15035985">{{cite journal | vauthors = Tomari Y, Du T, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE, Zamore PD | title = RISC assembly defects in the Drosophila RNAi mutant armitage | journal = Cell | volume = 116 | issue = 6 | pages = 831–841 | date = March 2004 | pmid = 15035985 | doi = 10.1016/S0092-8674(04)00218-1| s2cid = 17588448 | doi-access = free }}</ref>

==Biogenesis== thumb|The ping-pong mechanism for the biogenesis of the 5′ end of rasiRNA. 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,<ref name="Molecular" /> and this may indicate that they are the product of long single stranded precursor molecules.<ref name="Seto" /> 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.<ref name="Aravin2">{{cite journal | vauthors = Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ | title = A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice | journal = Molecular Cell | volume = 31 | issue = 6 | pages = 785–799 | date = September 2008 | pmid = 18922463 | pmc = 2730041 | doi = 10.1016/j.molcel.2008.09.003 }}</ref><ref name="Brennecke2">{{cite journal | vauthors = Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ | title = Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila | journal = Cell | volume = 128 | issue = 6 | pages = 1089–1103 | date = March 2007 | pmid = 17346786 | doi = 10.1016/j.cell.2007.01.043 | s2cid = 2246942 | url = https://authors.library.caltech.edu/95370/2/1-s2.0-S0092867407002577-mmc1.pdf | doi-access = free }}</ref> 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.<ref name="Brennecke2" /> These secondary piRNAs are targeted toward sequences that possess an adenine at the tenth position.<ref name="Aravin2" /> 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.<ref name="Malone" /> 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.<ref name="Das" />

A significant number of piRNAs identified in zebrafish and ''D. melanogaster'' contain adenine at their tenth position,<ref name="Klattenhoff" /> and this has been interpreted as possible evidence of a conserved biosynthetic mechanism across species.<ref name="Faehnle" /> 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.<ref name="Grimson">{{cite journal | vauthors = Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP | title = Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals | journal = Nature | volume = 455 | issue = 7217 | pages = 1193–1197 | date = October 2008 | pmid = 18830242 | pmc = 3837422 | doi = 10.1038/nature07415 | bibcode = 2008Natur.455.1193G }}</ref>

===Ping Pong=== 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.<ref name="Brennecke2" /><ref name="Gunawardane">{{cite journal | vauthors = Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC | title = A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila | journal = Science | volume = 315 | issue = 5818 | pages = 1587–1590 | date = March 2007 | pmid = 17322028 | doi = 10.1126/science.1140494 | bibcode = 2007Sci...315.1587G | s2cid = 11513777 | doi-access = free }}</ref> 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.<ref name="LiZamore">{{cite journal | vauthors = Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich MD, Syrzycka M, Honda BM, Kittler EL, Zapp ML, Klattenhoff C, Schulz N, Theurkauf WE, Weng Z, Zamore PD | title = Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies | journal = Cell | volume = 137 | issue = 3 | pages = 509–521 | date = May 2009 | pmid = 19395009 | pmc = 2768572 | doi = 10.1016/j.cell.2009.04.027 }}</ref><ref name="ZhangZamore1">{{cite journal | vauthors = Zhang Z, Xu J, Koppetsch BS, Wang J, Tipping C, Ma S, Weng Z, Theurkauf WE, Zamore PD | title = Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains | journal = Molecular Cell | volume = 44 | issue = 4 | pages = 572–584 | date = November 2011 | pmid = 22099305 | pmc = 3236501 | doi = 10.1016/j.molcel.2011.10.011 }}</ref>

The molecular mechanism that underpins Ping-Pong likely involves several piRNA pathway associated factors. ''Qin'' was reported to coordinate the loading of Ago3 with piRNA, in addition to interacting with both Aub and Ago3.<ref name="ZhangZamore1" /> However, the Tudor protein ''krimper'' ({{UniProt|A1ZAC4}}) was also shown to interact with both Aub and Ago3 through its Tudor domains while also binding itself through its N-terminal Krimper domain.<ref name="WebsterAravin">{{cite journal | vauthors = Webster A, Li S, Hur JK, Wachsmuth M, Bois JS, Perkins EM, Patel DJ, Aravin AA | title = Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper | journal = Molecular Cell | volume = 59 | issue = 4 | pages = 564–575 | date = August 2015 | pmid = 26295961 | pmc = 4545750 | doi = 10.1016/j.molcel.2015.07.017 }}</ref> 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.<ref name="WebsterAravin" /><ref name="SatoSiomi">{{cite journal | vauthors = Sato K, Iwasaki YW, Shibuya A, Carninci P, Tsuchizawa Y, Ishizu H, Siomi MC, Siomi H | title = Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline | journal = Molecular Cell | volume = 59 | issue = 4 | pages = 553–563 | date = August 2015 | pmid = 26212455 | doi = 10.1016/j.molcel.2015.06.024 | doi-access = free }}</ref> In Silkmoth germ cells, it was proposed that Vasa protein coordinates the Ping-Pong mechanism of Silkmoth Aub (Siwi) and Ago3.<ref name="XiolPillai">{{cite journal | vauthors = Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Couté Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS | title = RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts | journal = Cell | volume = 157 | issue = 7 | pages = 1698–1711 | date = June 2014 | pmid = 24910301 | doi = 10.1016/j.cell.2014.05.018 | doi-access = free }}</ref>

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.

===piRNA Phasing=== 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.<ref name="MohnBrennecke">{{cite journal | vauthors = Mohn F, Handler D, Brennecke J | title = Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis | journal = Science | volume = 348 | issue = 6236 | pages = 812–817 | date = May 2015 | pmid = 25977553 | pmc = 4988486 | doi = 10.1126/science.aaa1039 }}</ref><ref name="HanZamore">{{cite journal | vauthors = Han BW, Wang W, Li C, Weng Z, Zamore PD | title = Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production | journal = Science | volume = 348 | issue = 6236 | pages = 817–821 | date = May 2015 | pmid = 25977554 | pmc = 4545291 | doi = 10.1126/science.aaa1264 }}</ref> 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 its piRNA guide.<ref name="LeThomas">{{cite journal | vauthors = Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Tóth KF | title = Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state | journal = Genes & Development | volume = 27 | issue = 4 | pages = 390–399 | date = February 2013 | pmid = 23392610 | pmc = 3589556 | doi = 10.1101/gad.209841.112 }}</ref> It is currently unknown whether phasing occurs in other organisms.

==Function== The wide variation in piRNA sequences and piwi function across species contributes to the difficulty in establishing the functionality of piRNAs.<ref name="Wang">{{cite journal | vauthors = Wang G, Reinke V | title = A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis | journal = Current Biology | volume = 18 | issue = 12 | pages = 861–867 | date = June 2008 | pmid = 18501605 | pmc = 2494713 | doi = 10.1016/j.cub.2008.05.009 | bibcode = 2008CBio...18..861W }}</ref> However, like other small RNAs, piRNAs are thought to be involved in gene silencing,<ref name="Molecular" /> specifically the silencing of transposons.<ref name="pmid30446728">{{cite journal | vauthors=Ozata DM, Gainetdinov I, Zoch A, Phillip D, Zamore PD | title=PIWI-interacting RNAs: small RNAs with big functions | journal=Nature Reviews Genetics | volume=20 | issue=2 | pages=89–108 | year=2019 | doi = 10.1038/s41576-018-0073-3| pmid=30446728| s2cid=53565676 | url=https://www.pure.ed.ac.uk/ws/files/78781529/PIWI_interacting_RNAs_AAM_zata_et_al._Revised_v2.3.pdf }}</ref> The majority of piRNAs are antisense to transposon sequences,<ref name="Monga"/><ref name="Malone" /> suggesting that transposons are targets of the piRNAs. In mammals, it appears that the activity of piRNAs in transposon silencing is most important during the development of the embryo,<ref name="Aravin2" /> and in both ''C. elegans'' and humans, piRNAs are necessary for spermatogenesis.<ref name="Wang" />

===RNA silencing=== 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.<ref name="Aravin2" /> A decrease or absence of PIWI gene expression is correlated with an increased expression of transposons.<ref name="Klattenhoff" /><ref name="Aravin2" /> Transposons have a high potential to cause deleterious effects on their hosts<ref name="ODonnell" /> and, in fact, mutations in piRNA pathways have been found to reduce fertility in ''D. melanogaster''.<ref name="Brennecke" /> 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.<ref name="Malone" />

piRNAs appear to affect particular methyltransferases that perform the methylations which are required to recognise and silence transposons,<ref name="Aravin2" /> but this relationship is not well understood.

===Antiviral effects=== In Dipterans viral-derived piRNAs derived from positive-sense RNA viruses were first identified in ''Drosophila'' ovarian somatic sheet (OSS) cells.<ref name="pmid20080648">{{cite journal| author=Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX | display-authors=etal| title=Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. | journal=Proc Natl Acad Sci U S A | year= 2010 | volume= 107 | issue= 4 | pages= 1606–11 | pmid=20080648 | doi=10.1073/pnas.0911353107 | pmc=2824396 | bibcode=2010PNAS..107.1606W| doi-access=free}}</ref> Subsequent experimental studies have demonstrated that the piRNA pathway is not required for antiviral defence in ''Drosophila melanogaster''.<ref name="pmid27357659">{{cite journal| author=Petit M, Mongelli V, Frangeul L, Blanc H, Jiggins F, Saleh MC| title=piRNA pathway is not required for antiviral defense in ''Drosophila melanogaster''. | journal=Proc Natl Acad Sci U S A | year= 2016 | volume= 113 | issue= 29 | pages= E4218-27 | pmid=27357659 | doi=10.1073/pnas.1607952113 | pmc=4961201 | doi-access=free | bibcode=2016PNAS..113E4218P }}</ref> However, in mosquitoes the PIWI family of proteins has expanded<ref name="pmid18801182">{{cite journal| author=Campbell CL, Black WC, Hess AM, Foy BD| title=Comparative genomics of small RNA regulatory pathway components in vector mosquitoes. | journal=BMC Genomics | year= 2008 | volume= 9 | issue= | article-number= 425 | pmid=18801182 | doi=10.1186/1471-2164-9-425 | pmc=2566310 | doi-access=free }}</ref> and some PIWI proteins have been identified as antiviral such as Piwi4.<ref name="pmid28497119">{{cite journal| author=Varjak M, Maringer K, Watson M, Sreenu VB, Fredericks AC, Pondeville E | display-authors=etal| title=Aedes aegypti Piwi4 Is a Noncanonical PIWI Protein Involved in Antiviral Responses. | journal=mSphere | year= 2017 | volume= 2 | issue= 3 | article-number=e00144-17| pmid=28497119 | doi=10.1128/mSphere.00144-17 | doi-access=free| pmc=5415634 }}</ref> As such virus infections in mosquitoes commonly produce virus-derived piRNAs in diverse positive-sense RNA,<ref name="pmid28033427">{{cite journal| author=Miesen P, Joosten J, van Rij RP| title=PIWIs Go Viral: Arbovirus-Derived piRNAs in Vector Mosquitoes. | journal=PLOS Pathog | year= 2016 | volume= 12 | issue= 12 | article-number= e1006017 | pmid=28033427 | doi=10.1371/journal.ppat.1006017 | pmc=5198996 | doi-access=free }}</ref> negative-sense RNA<ref name="pmid29950416">{{cite journal| author=Parry R, Asgari S| title=Aedes Anphevirus: an Insect-Specific Virus Distributed Worldwide in Aedes aegypti Mosquitoes That Has Complex Interplays with Wolbachia and Dengue Virus Infection in Cells. | journal=J Virol | year= 2018 | volume= 92 | issue= 17 | article-number=e00224-18 | pmid=29950416 | doi=10.1128/JVI.00224-18 | pmc=6096813 }}</ref><ref name="pmid28497119"/> and single-stranded DNA viruses.<ref name="pmid30583288">{{cite journal| author=Parry R, Bishop C, De Hayr L, Asgari S| title=Density-dependent enhanced replication of a densovirus in Wolbachia-infected Aedes cells is associated with production of piRNAs and higher virus-derived siRNAs. | journal=Virology | year= 2019 | volume= 528 | issue= | pages= 89–100 | pmid=30583288 | doi=10.1016/j.virol.2018.12.006 | pmc= | s2cid=58572380 | doi-access=free }}</ref>

===Epigenetic effects=== piRNAs can be transmitted maternally,<ref name="Houwing" /> and based on research in ''D. melanogaster'', piRNAs may be involved in maternally derived epigenetic effects.<ref name="Brennecke" /> The activity of specific piRNAs in the epigenetic process also requires interactions between piwi proteins and HP1a, as well as other factors.<ref name="Lin" />

==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).<ref>{{cite journal |vauthors=Kirino Y, Kim N, de Planell-Saguer M, Khandros E, Chiorean S, Klein PS, Rigoutsos I, Jongens TA, Mourelatos Z |title=Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability |journal=Nat. Cell Biol. |volume=11 |issue=5 |pages=652–8 |date=May 2009 |pmid=19377467 |pmc=2746449 |doi=10.1038/ncb1872 }}</ref><ref>{{cite journal |vauthors=Anne J, Mechler BM |title=Valois, a component of the nuage and pole plasm, is involved in assembly of these structures, and binds to Tudor and the methyltransferase Capsuléen |journal=Development |volume=132 |issue=9 |pages=2167–77 |date=May 2005 |pmid=15800004 |doi=10.1242/dev.01809 |s2cid=6810484 |doi-access= }}</ref> * Tudor (Tud) * Qin/Kumo * Spindle-E (SpnE) * Krimper * Tejas (Tej) * Vreteno (Vret) * Papi * Yb (''fs(1)Yb'') * Brother of Yb (BoYB) * Sister of Yb (SoYB)

===Non-Tudor ''Drosophila'' piRNA pathway proteins=== * Vasa * Maelstrom (Mael)

===''Drosophila'' nuclear piRNA pathway proteins=== * Rhino (HP1D) * Deadlock * Cutoff * SetDB1 (Eggless) * SuVar3–9

==Investigation== Major advances in the study of piRNA have been achieved thanks to the use of next-generation sequencing techniques, such as Solexa, 454, and Illumina platform sequencing. 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.<ref name="Ro">{{cite journal | vauthors = Ro S, Park C, Jin J, Sanders KM, Yan W | title = A PCR-based method for detection and quantification of small RNAs | journal = Biochemical and Biophysical Research Communications | volume = 351 | issue = 3 | pages = 756–763 | date = December 2006 | pmid = 17084816 | pmc = 1934510 | doi = 10.1016/j.bbrc.2006.10.105 | bibcode = 2006BBRC..351..756R }}</ref><ref name="Tang">{{cite journal | vauthors = Tang F, Hayashi K, Kaneda M, Lao K, Surani MA | title = A sensitive multiplex assay for piRNA expression | journal = Biochemical and Biophysical Research Communications | volume = 369 | issue = 4 | pages = 1190–1194 | date = May 2008 | pmid = 18348866 | pmc = 3855189 | doi = 10.1016/j.bbrc.2008.03.035 | bibcode = 2008BBRC..369.1190T }}</ref> However, research has also revealed that a number of annotated piRNAs may be false positives; for instance, a majority of piRNAs that were expressed in somatic non-gonadal tissues were considered to derive from non-coding RNA fragments.<ref>{{cite journal | vauthors = Tosar JP, Rovira C, Cayota A | title = Non-coding RNA fragments account for the majority of annotated piRNAs expressed in somatic non-gonadal tissues | language = En | journal = Communications Biology | volume = 1 | issue = 1 | article-number = 2 | date = 2018-01-22 | pmid = 30271890 | pmc = 6052916 | doi = 10.1038/s42003-017-0001-7 }}</ref>

==References== {{Reflist|32em}}

==Further reading== {{refbegin|32em}} * {{cite journal | vauthors = Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE | title = Characterization of the piRNA complex from rat testes | journal = Science | volume = 313 | issue = 5785 | pages = 363–367 | date = July 2006 | pmid = 16778019 | doi = 10.1126/science.1130164 | bibcode = 2006Sci...313..363L | s2cid = 21150160 }} * {{cite journal | vauthors = Kim VN | title = Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes | journal = Genes & Development | volume = 20 | issue = 15 | pages = 1993–1997 | date = August 2006 | pmid = 16882976 | doi = 10.1101/gad.1456106 | doi-access = free }} * {{cite journal | vauthors = Girard A, Sachidanandam R, Hannon GJ, Carmell MA | title = A germline-specific class of small RNAs binds mammalian Piwi proteins | journal = Nature | volume = 442 | issue = 7099 | pages = 199–202 | date = July 2006 | pmid = 16751776 | doi = 10.1038/nature04917 | bibcode = 2006Natur.442..199G | s2cid = 3185036 }} * {{cite journal | vauthors = Grivna ST, Beyret E, Wang Z, Lin H | title = A novel class of small RNAs in mouse spermatogenic cells | journal = Genes & Development | volume = 20 | issue = 13 | pages = 1709–1714 | date = July 2006 | pmid = 16766680 | pmc = 1522066 | doi = 10.1101/gad.1434406 }} * {{cite journal | vauthors = Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H | title = Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes | journal = Genes & Development | volume = 20 | issue = 13 | pages = 1732–1743 | date = July 2006 | pmid = 16766679 | pmc = 1522070 | doi = 10.1101/gad.1425706 }} * {{cite journal | vauthors = Carmell MA, Girard A, van de Kant HJ, Bourc'his D, Bestor TH, de Rooij DG, Hannon GJ | title = MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline | journal = Developmental Cell | volume = 12 | issue = 4 | pages = 503–514 | date = April 2007 | pmid = 17395546 | doi = 10.1016/j.devcel.2007.03.001 | doi-access = free }} * {{cite journal | vauthors = Le Thomas A, Tóth KF, Aravin AA | title = To be or not to be a piRNA: genomic origin and processing of piRNAs | journal = Genome Biology | volume = 15 | issue = 1 | article-number = 204 | date = January 2014 | pmid = 24467990 | pmc = 4053809 | doi = 10.1186/gb4154 | doi-access = free }} * {{cite journal | vauthors = Weick EM, Miska EA | title = piRNAs: from biogenesis to function | journal = Development | volume = 141 | issue = 18 | pages = 3458–3471 | date = September 2014 | pmid = 25183868 | doi = 10.1242/dev.094037 | doi-access = free }} {{refend}}

==External links== * [https://sourceforge.net/projects/pingpongpro/ PingPongPro] – a software for finding ping-pong signatures and ping-pong cycle activity * [https://web.archive.org/web/20110824125015/http://pirnabank.ibab.ac.in/ piRNA Bank] – a web resource on classified and clustered piRNAs * [http://www.biomedcentral.com/1471-2105/13/5 proTRAC] – a software for probabilistic piRNA cluster detection, visualization, and analysis * [http://www.uni-mainz.de/FB/Biologie/Anthropologie/492_ENG_HTML.php piRNA cluster – database] {{Webarchive|url=https://web.archive.org/web/20141011035001/http://www.uni-mainz.de/FB/Biologie/Anthropologie/492_ENG_HTML.php |date=2014-10-11 }}

{{DEFAULTSORT:Piwi-Interacting Rna}} Category:RNA Category:Non-coding RNA