{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T20:11:22Z","timestamp":1777493482378,"version":"3.51.4"},"reference-count":50,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T00:00:00Z","timestamp":1704844800000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["K01 ES032048 K99 ES034429 R00 ES022221"],"award-info":[{"award-number":["K01 ES032048 K99 ES034429 R00 ES022221"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007270","name":"University of Michigan","doi-asserted-by":"publisher","award":["ES007062"],"award-info":[{"award-number":["ES007062"]}],"id":[{"id":"10.13039\/100007270","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"crossref","award":["R01 ES026877 R35 ES031686"],"award-info":[{"award-number":["R01 ES026877 R35 ES031686"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIEHS Core Center","award":["P30 ES017885 U01 ES 026697"],"award-info":[{"award-number":["P30 ES017885 U01 ES 026697"]}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["K01 ES032048 K99 ES034429 R00 ES022221"],"award-info":[{"award-number":["K01 ES032048 K99 ES034429 R00 ES022221"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007270","name":"University of Michigan","doi-asserted-by":"publisher","award":["ES007062"],"award-info":[{"award-number":["ES007062"]}],"id":[{"id":"10.13039\/100007270","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"crossref","award":["R01 ES026877 R35 ES031686"],"award-info":[{"award-number":["R01 ES026877 R35 ES031686"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIEHS Core Center","award":["P30 ES017885 U01 ES 026697"],"award-info":[{"award-number":["P30 ES017885 U01 ES 026697"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2\u02b9-O-methylation signature at the 3\u02b9 end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and while overall expression was lower than that of the germline, unique characteristics suggested tissue-specific functions of this class. While currently available databases commonly use length and association with PIWI proteins to identify piRNA, few have included a chemical oxidation method that detects piRNA based on its 3\u02b9 modification. This method leads to reproducible and rigorous data processing when coupled with next-generation sequencing and bioinformatics analysis. Here, we introduce piOxi DB, a user-friendly web resource that provides a comprehensive analysis of piRNA, generated exclusively through sodium periodate treatment of small RNA. The current version of piOxi DB includes 435\u2009749 germline and 9828 somatic piRNA sequences robustly identified from M. musculus, M. fascicularis and H. sapiens. The database provides species- and tissue-specific data that are further analyzed according to chromosome location and correspondence to gene and repetitive elements. piOxi DB is an informative tool to assist broad research applications in the fields of RNA biology, cancer biology, environmental toxicology and beyond.<\/jats:p>\n               <jats:p>Database URL: \u00a0https:\/\/pioxidb.dcmb.med.umich.edu\/<\/jats:p>","DOI":"10.1093\/database\/baad096","type":"journal-article","created":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T19:21:15Z","timestamp":1704914475000},"source":"Crossref","is-referenced-by-count":8,"title":["piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation"],"prefix":"10.1093","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8541-7563","authenticated-orcid":false,"given":"Kai","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bambarendage P U","family":"Perera","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachel K","family":"Morgan","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kimberley","family":"Sala-Hamrick","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viviana","family":"Geron","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurie K","family":"Svoboda","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"},{"name":"Department of Pharmacology, School of Medicine, University of Michigan , 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9749-9658","authenticated-orcid":false,"given":"Christopher","family":"Faulk","sequence":"additional","affiliation":[{"name":"Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota , 1988 Fitch Avenue, Saint Paul, MN 55108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dana C","family":"Dolinoy","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"},{"name":"Department of Nutritional Sciences, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"},{"name":"Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan , 100 Washtenaw Ave, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maureen A","family":"Sartor","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan , 100 Washtenaw Ave, Ann Arbor, MI 48109, USA"},{"name":"Department of Biostatistics, School of Public Health, University of Michigan , 1415 Washington Heights, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,1,10]]},"reference":[{"key":"2024062912154846500_R1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1080\/09723757.2016.11886278","article-title":"piRNAs and their functions in the brain","volume":"16","author":"Zuo","year":"2016","journal-title":"Int. J. Human Genet."},{"key":"2024062912154846500_R2","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1002\/mrd.22195","article-title":"Untangling the web: the diverse functions of the PIWI\/piRNA pathway","volume":"80","author":"Mani","year":"2013","journal-title":"Mol. Reprod. Dev."},{"key":"2024062912154846500_R3","doi-asserted-by":"crossref","DOI":"10.1126\/science.1137543","article-title":"piRNAs in the germ line","volume":"316","author":"Lin","year":"2007","journal-title":"Science"},{"key":"2024062912154846500_R4","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":"2024062912154846500_R5","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.devcel.2007.03.001","article-title":"MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline","volume":"12","author":"Carmell","year":"2007","journal-title":"Dev. Cell"},{"key":"2024062912154846500_R6","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.tibs.2015.12.008","article-title":"One loop to rule them all: the ping-pong cycle and piRNA-guided silencing","volume":"41","author":"Czech","year":"2016","journal-title":"Trends Biochem. Sci."},{"key":"2024062912154846500_R7","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":"2024062912154846500_R8","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2012.02.057","article-title":"A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity","volume":"149","author":"Rajasethupathy","year":"2012","journal-title":"Cell"},{"key":"2024062912154846500_R9","doi-asserted-by":"crossref","DOI":"10.1098\/rsob.180181","article-title":"Rapid evolution and conserved function of the piRNA pathway","volume":"9","author":"Parhad","year":"2019","journal-title":"Open Biol."},{"key":"2024062912154846500_R10","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1080\/15592294.2019.1600389","article-title":"Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA","volume":"14","author":"Perera","year":"2019","journal-title":"Epigenetics"},{"key":"2024062912154846500_R11","doi-asserted-by":"crossref","DOI":"10.1186\/s12943-019-1052-9","article-title":"The emerging role of the piRNA\/piwi complex in cancer","volume":"18","author":"Liu","year":"2019","journal-title":"Mol. Cancer"},{"key":"2024062912154846500_R12","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/aps.2018.30","article-title":"miRNAS in cardiovascular diseases: potential biomarkers, therapeutic targets and challenges","volume":"39","author":"Zhou","year":"2018","journal-title":"Acta Pharmacol. Sin."},{"key":"2024062912154846500_R13","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1146\/annurev.pathol.4.110807.092222","article-title":"MicroRNAs in cancer","volume":"4","author":"Lee","year":"2009","journal-title":"Annu. Rev. Pathol."},{"key":"2024062912154846500_R14","doi-asserted-by":"crossref","DOI":"10.1016\/j.taap.2020.115306","article-title":"Arsenic-induced changes in miRNA expression in cancer and other diseases","volume":"409","author":"Ferragut Cardoso","year":"2020","journal-title":"Toxicol. Appl. 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Toxicol."},{"key":"2024062912154846500_R23","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1002\/em.22311","article-title":"The role of environmental exposures and the epigenome in helath and disease","volume":"61","author":"Perera","year":"2019","journal-title":"Environ. Mol. Mutagen."},{"key":"2024062912154846500_R24","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1007\/s40572-022-00372-6","article-title":"PIWI-interacting RNA (piRNA) and epigenetic editing in environmental health sciences","volume":"9","author":"Perera","year":"2022","journal-title":"Curr. Environ. Health Rep."},{"key":"2024062912154846500_R25","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1016\/j.celrep.2015.02.062","article-title":"Piwi proteins and piRNAs in mammalian oocytes and early embryos","volume":"10","author":"Roovers","year":"2015","journal-title":"Cell Rep."},{"key":"2024062912154846500_R26","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0044542","article-title":"Novel small noncoding RNAs in mouse spermatozoa, zygotes and early embryos","volume":"7","author":"Kawano","year":"2012","journal-title":"PLoS One"},{"key":"2024062912154846500_R27","doi-asserted-by":"crossref","first-page":"D265","DOI":"10.1093\/nar\/gkab1012","article-title":"piRBase: integrating piRNA annotation in all aspects","volume":"50","author":"Wang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024062912154846500_R28","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1080\/15476286.2021.2010960","article-title":"piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species","volume":"19","author":"Ghosh","year":"2022","journal-title":"RNA Biol."},{"key":"2024062912154846500_R29","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 Lakshmi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2024062912154846500_R30","doi-asserted-by":"crossref","first-page":"D259","DOI":"10.1093\/nar\/gkab622","article-title":"piRNAclusterDB 2.0: update and expansion of the piRNA cluster database","volume":"50","author":"Rosenkranz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024062912154846500_R31","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1159\/000519237","article-title":"Non-coding RNAs: lncRNAs, miRNAs, and piRNAs in sexual development","volume":"15","author":"Burgos","year":"2021","journal-title":"Sex Dev."},{"key":"2024062912154846500_R32","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.jprot.2017.09.010","article-title":"Environmental toxicology and omics: a question of sex","volume":"172","author":"Liang","year":"2018","journal-title":"J. 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(Berl)"},{"key":"2024062912154846500_R46","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-021-93885-3","article-title":"Human placental piwi-interacting RNA transcriptome is characterized by expression from the DLK1-DIO3 imprinted region","volume":"11","author":"Martinez","year":"2021","journal-title":"Sci. Rep."},{"key":"2024062912154846500_R47","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1007\/s12539-021-00428-5","article-title":"Computational methods and online resources for identification of piRNA-related molecules","volume":"13","author":"Liu","year":"2021","journal-title":"Interdiscip. Sci."},{"key":"2024062912154846500_R48","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1016\/j.csbj.2022.02.026","article-title":"Identification of piRNA disease associations using deep learning","volume":"20","author":"Ali","year":"2022","journal-title":"Comput. Struct. Biotechnol. 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