{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T07:49:40Z","timestamp":1770968980367,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The massive spread of repetitive elements in the human genome presents a substantial challenge to the organism, as such elements may accidentally contain seemingly functional motifs. A striking example is offered by the roughly one million copies of Alu repeats in the genome, of which \u223c0.5% reside within genes\u2019 untranslated regions (UTRs), presenting \u223c30 000 novel potential targets for highly conserved microRNAs (miRNAs). Here, we examine the functionality of miRNA targets within Alu elements in 3\u2032UTRs in the human genome.<\/jats:p>\n               <jats:p>Results: Using a comprehensive dataset of miRNA overexpression assays, we show that mRNAs with miRNA targets within Alus are significantly less responsive to the miRNA effects compared with mRNAs that have the same targets outside Alus. Using Ago2-binding mRNA profiling, we confirm that the miRNA machinery avoids miRNA targets within Alus, as opposed to the highly efficient binding of targets outside Alus. We propose three features that prevent potential miRNA sites within Alus from being recognized by the miRNA machinery: (i) Alu repeats that contain miRNA targets and genuine functional miRNA targets appear to reside in distinct mutually exclusive territories within 3\u2032UTRs; (ii) Alus have tight secondary structure that may limit access to the miRNA machinery; and (iii) A-to-I editing of Alu-derived mRNA sequences may divert miRNA targets. The combination of these features is proposed to allow toleration of Alu insertions into mRNAs. Nonetheless, a subset of miRNA targets within Alus appears not to possess any of the aforementioned features, and thus may represent cases where Alu insertion in the genome has introduced novel functional miRNA targets.<\/jats:p>\n               <jats:p>Contact: moshe.oren@weizmann.ac.il or Pilpel@weizmann.ac.il<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt044","type":"journal-article","created":{"date-parts":[[2013,1,30]],"date-time":"2013-01-30T04:44:22Z","timestamp":1359521062000},"page":"894-902","source":"Crossref","is-referenced-by-count":30,"title":["The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery"],"prefix":"10.1093","volume":"29","author":[{"given":"Yonit","family":"Hoffman","sequence":"first","affiliation":[{"name":"1 Department of Molecular Genetics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel"},{"name":"1 Department of Molecular Genetics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dvir","family":"Dahary","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Genetics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debora Rosa","family":"Bublik","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Genetics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moshe","family":"Oren","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Genetics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yitzhak","family":"Pilpel","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Genetics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,1,29]]},"reference":[{"key":"2023020303310155300_btt044-B1","doi-asserted-by":"crossref","first-page":"e391","DOI":"10.1371\/journal.pbio.0020391","article-title":"Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome","volume":"2","author":"Athanasiadis","year":"2004","journal-title":"PLoS Biol."},{"key":"2023020303310155300_btt044-B2","doi-asserted-by":"crossref","first-page":"6905","DOI":"10.1093\/nar\/gkp729","article-title":"Evidence for large diversity in the human transcriptome created by Alu RNA editing","volume":"37","author":"Barak","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020303310155300_btt044-B3","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nrg798","article-title":"Alu repeats and human genomic diversity","volume":"3","author":"Batzer","year":"2002","journal-title":"Nat. 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Genet."},{"key":"2023020303310155300_btt044-B6","doi-asserted-by":"crossref","first-page":"e85","DOI":"10.1371\/journal.pbio.0030085","article-title":"Principles of microRNA-target recognition","volume":"3","author":"Brennecke","year":"2005","journal-title":"PLoS Biol"},{"key":"2023020303310155300_btt044-B7","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1093\/molbev\/msq315","article-title":"CpG Islands as a putative source for animal miRNAs: evolutionary and functional implications","volume":"28","author":"Dahary","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"2023020303310155300_btt044-B8","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1242\/jcs.055210","article-title":"Argonaute proteins at a glance","volume":"123","author":"Ender","year":"2010","journal-title":"J. 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