{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:07:11Z","timestamp":1792786031404,"version":"4.5.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,7,24]],"date-time":"2021-07-24T00:00:00Z","timestamp":1627084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Walter Benjamin Fellowship","award":["GE 3407\/1-1"],"award-info":[{"award-number":["GE 3407\/1-1"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["GRK 2526\/1"],"award-info":[{"award-number":["GRK 2526\/1"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI\/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically influence piRNA populations in different evolutionary lineages. We launched the initial version of the piRNA cluster database to facilitate research on regulation and evolution of piRNA-producing loci across tissues und species. In recent years the amount of small RNA sequencing data that was generated and the abundance of species that were studied has grown rapidly. To keep up with this recent progress, we have released a major update for the piRNA cluster database (https:\/\/www.smallrnagroup.uni-mainz.de\/piRNAclusterDB), expanding it from 12 to a total of 51 species with hundreds of new datasets, and revised its overall structure to enable easy navigation through this large amount of data.<\/jats:p>","DOI":"10.1093\/nar\/gkab622","type":"journal-article","created":{"date-parts":[[2021,7,7]],"date-time":"2021-07-07T15:44:33Z","timestamp":1625672673000},"page":"D259-D264","source":"Crossref","is-referenced-by-count":50,"title":["piRNAclusterDB 2.0: update and expansion of the piRNA cluster database"],"prefix":"10.1093","volume":"50","author":[{"given":"David","family":"Rosenkranz","sequence":"first","affiliation":[{"name":"Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany"},{"name":"Senckenberg Centre for Human Genetics, Facharztzentrum Frankfurt-Nordend gGmbH, Frankfurt am Main 60314, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans","family":"Zischler","sequence":"additional","affiliation":[{"name":"Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6159-3231","authenticated-orcid":false,"given":"Daniel","family":"Gebert","sequence":"additional","affiliation":[{"name":"Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany"},{"name":"Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,24]]},"reference":[{"key":"2022010507333913500_B1","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/nature04916","article-title":"A novel class of small RNAs bind to MILI protein in mouse testes","volume":"442","author":"Aravin","year":"2006","journal-title":"Nature"},{"key":"2022010507333913500_B2","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature04917","article-title":"A germline-specific class of small RNAs binds mammalian Piwi proteins","volume":"442","author":"Girard","year":"2006","journal-title":"Nature"},{"key":"2022010507333913500_B3","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1101\/gad.1434406","article-title":"A novel class of small RNAs in mouse spermatogenic cells","volume":"20","author":"Grivna","year":"2006","journal-title":"Genes Dev."},{"key":"2022010507333913500_B4","doi-asserted-by":"crossref","first-page":"1732","DOI":"10.1101\/gad.1425706","article-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","volume":"20","author":"Watanabe","year":"2006","journal-title":"Genes Dev."},{"key":"2022010507333913500_B5","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1126\/science.1142612","article-title":"Developmentally regulated piRNA clusters implicate MILI in transposon control","volume":"316","author":"Aravin","year":"2007","journal-title":"Science"},{"key":"2022010507333913500_B6","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","article-title":"Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila","volume":"128","author":"Brennecke","year":"2007","journal-title":"Cell"},{"key":"2022010507333913500_B7","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1038\/cr.2014.41","article-title":"Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis","volume":"24","author":"Gou","year":"2014","journal-title":"Cell Res."},{"key":"2022010507333913500_B8","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/cr.2015.4","article-title":"MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes","volume":"25","author":"Zhang","year":"2015","journal-title":"Cell Res."},{"key":"2022010507333913500_B9","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1101\/gad.260455.115","article-title":"piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis","volume":"29","author":"Goh","year":"2015","journal-title":"Genes Dev."},{"key":"2022010507333913500_B10","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1261\/rna.046482.114","article-title":"The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes","volume":"21","author":"Pantano","year":"2015","journal-title":"RNA"},{"key":"2022010507333913500_B11","doi-asserted-by":"crossref","first-page":"e0124860","DOI":"10.1371\/journal.pone.0124860","article-title":"piRNAs from pig testis provide evidence for a conserved role of the Piwi pathway in post-transcriptional gene regulation in mammals","volume":"10","author":"Gebert","year":"2015","journal-title":"PLoS One"},{"key":"2022010507333913500_B12","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1101\/gr.180802.114","article-title":"Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline","volume":"25","author":"Watanabe","year":"2015","journal-title":"Genome Res."},{"key":"2022010507333913500_B13","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1016\/j.molcel.2008.09.003","article-title":"A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice","volume":"31","author":"Aravin","year":"2008","journal-title":"Mol. Cell"},{"key":"2022010507333913500_B14","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1126\/science.1140494","article-title":"A slicer-mediated mechanism for repeat-associated siRNA 5\u2032 end formation in Drosophila","volume":"315","author":"Gunawardane","year":"2007","journal-title":"Science"},{"key":"2022010507333913500_B15","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/s41559-017-0403-4","article-title":"Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements","volume":"2","author":"Lewis","year":"2018","journal-title":"Nat. Ecol. Evol."},{"key":"2022010507333913500_B16","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s42003-018-0141-4","article-title":"PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation","volume":"1","author":"Jehn","year":"2018","journal-title":"Commun. Biol."},{"key":"2022010507333913500_B17","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1111\/j.1525-142X.2010.00413.x","article-title":"Piwi expression in archeocytes and choanocytes in demosponges: insights into the stem cell system in demosponges","volume":"12","author":"Funayama","year":"2010","journal-title":"Evol. Dev."},{"key":"2022010507333913500_B18","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1073\/pnas.1320965111","article-title":"PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells","volume":"111","author":"Juliano","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2022010507333913500_B19","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.cell.2009.03.040","article-title":"Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary","volume":"137","author":"Malone","year":"2009","journal-title":"Cell"},{"key":"2022010507333913500_B20","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.molcel.2013.02.016","article-title":"An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes","volume":"50","author":"Li","year":"2013","journal-title":"Mol. Cell"},{"key":"2022010507333913500_B21","doi-asserted-by":"crossref","first-page":"7079","DOI":"10.1073\/pnas.0900523106","article-title":"Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution","volume":"106","author":"Assis","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2022010507333913500_B22","doi-asserted-by":"crossref","first-page":"e1005652","DOI":"10.1371\/journal.pgen.1005652","article-title":"Conserved piRNA expression from a distinct set of piRNA cluster loci in eutherian mammals","volume":"11","author":"Chirn","year":"2015","journal-title":"PLoS Genet."},{"key":"2022010507333913500_B23","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1093\/gbe\/evz060","article-title":"Primate piRNA cluster evolution suggests limited relevance of pseudogenes in piRNA-mediated gene regulation","volume":"11","author":"Gebert","year":"2019","journal-title":"Genome Biol. Evol."},{"key":"2022010507333913500_B24","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/s41559-019-1065-1","article-title":"Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans","volume":"4","author":"\u00d6zata","year":"2020","journal-title":"Nat. Ecol. Evol."},{"key":"2022010507333913500_B25","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1080\/15476286.2017.1349048","article-title":"Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis","volume":"14","author":"Praher","year":"2017","journal-title":"RNA Biol."},{"key":"2022010507333913500_B26","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1002\/jez.b.22815","article-title":"Diversity of piRNA expression patterns during the ontogeny of the German cockroach","volume":"330","author":"Llonga","year":"2018","journal-title":"J. Exp. Zool. B. Mol. Dev. Evol."},{"key":"2022010507333913500_B27","doi-asserted-by":"crossref","first-page":"D223","DOI":"10.1093\/nar\/gkv1265","article-title":"piRNA cluster database: a web resource for piRNA producing loci","volume":"44","author":"Rosenkranz","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507333913500_B28","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/s42003-017-0001-7","article-title":"Non-coding RNA fragments account for the majority of annotated piRNAs expressed in somatic non-gonadal tissues","volume":"1","author":"Tosar","year":"2018","journal-title":"Commun. Biol."},{"key":"2022010507333913500_B29","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-13-5","article-title":"proTRAC-a software for probabilistic piRNA cluster detection, visualization and analysis","volume":"13","author":"Rosenkranz","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2022010507333913500_B30","doi-asserted-by":"crossref","first-page":"D173","DOI":"10.1093\/nar\/gkm696","article-title":"piRNABank: a web resource on classified and clustered Piwi-interacting RNAs","volume":"36","author":"Sai\u00a0Lakshmi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2022010507333913500_B31","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1186\/1471-2164-15-555","article-title":"piRNAQuest: searching the piRNAome for silencers","volume":"15","author":"Sarkar","year":"2014","journal-title":"BMC Genomics"},{"key":"2022010507333913500_B32","doi-asserted-by":"crossref","first-page":"D175","DOI":"10.1093\/nar\/gky1043","article-title":"piRBase: a comprehensive database of piRNA sequences","volume":"47","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507333913500_B33","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkr854","article-title":"The Sequence Read Archive: explosive growth of sequencing data","volume":"40","author":"Kodama","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022010507333913500_B34","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1186\/s12864-017-4031-9","article-title":"unitas: the universal tool for annotation of small RNAs","volume":"18","author":"Gebert","year":"2017","journal-title":"BMC Genomics"},{"key":"2022010507333913500_B35","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2022010507333913500_B36","doi-asserted-by":"crossref","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","article-title":"Database resources of the national center for biotechnology information","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507333913500_B37","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.molcel.2011.10.011","article-title":"Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains","volume":"44","author":"Zhang","year":"2011","journal-title":"Mol. Cell"},{"key":"2022010507333913500_B38","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1126\/science.1130164","article-title":"Characterization of the piRNA complex from rat testes","volume":"313","author":"Lau","year":"2006","journal-title":"Science"},{"key":"2022010507333913500_B39","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1101\/gad.345041.120","article-title":"piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline","volume":"35","author":"Chen","year":"2021","journal-title":"Genes Dev."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D259\/42057856\/gkab622.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D259\/42057856\/gkab622.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T02:53:40Z","timestamp":1641351220000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D259\/6327686"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,24]]},"references-count":39,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,7,24]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab622","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,7,24]]}}}