{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T01:12:54Z","timestamp":1790644374652,"version":"4.1.0"},"reference-count":166,"publisher":"MDPI AG","issue":"20","license":[{"start":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T00:00:00Z","timestamp":1634342400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP24248034"],"award-info":[{"award-number":["JP24248034"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Fellowship of the Japan Society for the Promotion of Science Postdoctoral Fellowship for Overseas Researchers","award":["P20395"],"award-info":[{"award-number":["P20395"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.<\/jats:p>","DOI":"10.3390\/ijms222011166","type":"journal-article","created":{"date-parts":[[2021,10,17]],"date-time":"2021-10-17T23:05:47Z","timestamp":1634511947000},"page":"11166","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans"],"prefix":"10.3390","volume":"22","author":[{"given":"Songqian","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8247-9443","authenticated-orcid":false,"given":"Kazutoshi","family":"Yoshitake","sequence":"additional","affiliation":[{"name":"Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuichi","family":"Asakawa","sequence":"additional","affiliation":[{"name":"Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,10,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1038\/457974b","article-title":"Molecular biology: The long and short of RNAs","volume":"457","author":"Carninci","year":"2009","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1093\/bioinformatics\/btr016","article-title":"A k-mer scheme to predict piRNAs and characterize locust piRNAs","volume":"27","author":"Zhang","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"i364","DOI":"10.1093\/bioinformatics\/btu441","article-title":"Towards a piRNA prediction using multiple kernel fusion and support vector machine","volume":"30","author":"Brayet","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1016\/S0960-9822(01)00299-8","article-title":"Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline","volume":"11","author":"Aravin","year":"2001","journal-title":"Curr. 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