{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T12:07:31Z","timestamp":1759579651858},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Over the past decade, deciphering the roles of microRNAs (miRNAs) has relied heavily upon the identification of their targets. Most of the targets that were computationally and experimentally characterized were evolutionarily conserved \u2018seed\u2019 targets, containing a perfect 6\u20138 nt match between the miRNA 5\u2032-region and the messenger RNA (mRNA). Gradually, it has become evident that other types of miRNA binding can confer target regulation, but their characterization has been lagging behind.<\/jats:p>\n               <jats:p>Results: Here, we complement the putative evolutionarily-conserved seed-containing targets by a wide repertoire of putative targets exhibiting a variety of miRNA binding patterns, predicted by our algorithm RepTar. These include non-conserved sites, \u2018seed\u2019 binding sites with G:U-wobbles within the seed, \u20183\u2032 compensatory\u2019 sites and \u2018centered\u2019 sites. Apart from the centered sites, we demonstrate the functionality of these sites and characterize the target profile of a miRNA by the types of binding sites predicted in its target 3\u2032 UTRs. We find that different miRNAs have individual target profiles, with some more inclined to seed binding and others more inclined to binding through 3\u2032 compensatory sites. This diversity in targeting patterns is also evident within several miRNA families (defined by common seed sequences), leading to divergence in the target sets of members of the same family. The prediction of non-conventional miRNA targets is also beneficial in the search for targets of the non-conserved viral miRNAs. Analyzing the cellular targets of viral miRNAs, we show that viral miRNAs use various binding patterns to exploit cellular miRNA binding sites and suggest roles for these targets in virus\u2013host interactions.<\/jats:p>\n               <jats:p>Availability: All RepTar's predictions are available for simple and advanced querying at http:\/\/reptar.ekmd.huji.ac.il<\/jats:p>\n               <jats:p>Contact: \u00a0hanahm@ekmd.huji.ac.il<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr534","type":"journal-article","created":{"date-parts":[[2011,9,28]],"date-time":"2011-09-28T06:46:31Z","timestamp":1317192391000},"page":"3093-3101","source":"Crossref","is-referenced-by-count":26,"title":["A wide repertoire of miRNA binding sites: prediction and functional implications"],"prefix":"10.1093","volume":"27","author":[{"given":"Naama","family":"Elefant","sequence":"first","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel"}]},{"given":"Yael","family":"Altuvia","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel"}]},{"given":"Hanah","family":"Margalit","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel"}]}],"member":"286","published-online":{"date-parts":[[2011,9,27]]},"reference":[{"key":"2023012511320763900_B1","doi-asserted-by":"crossref","first-page":"3049","DOI":"10.1093\/bioinformatics\/btp565","article-title":"Lost in translation: an assessment and perspective for computational microRNA target identification","volume":"25","author":"Alexiou","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511320763900_B2","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/msb.2010.24","article-title":"Target mRNA abundance dilutes microRNA and siRNA activity","volume":"6","author":"Arvey","year":"2010","journal-title":"Mol. 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