{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T06:35:15Z","timestamp":1771655715950,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Edmond J. Safra Center for Bioinformatics"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MicroRNAs (miRNAs) are short (\u223c24nt), non-coding RNAs, which downregulate gene expression in many species and physiological processes. Many details regarding the mechanism which governs miRNA-mediated repression continue to elude researchers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We elucidate the interplay between the coding sequence and the 3\u2032UTR, by using elastic net regularization and incorporating translation-related features to predict miRNA-mediated repression. We find that miRNA binding sites at the end of the coding sequence contribute to repression, and that weak binding sites are linked to effective de-repression, possibly as a result of competing with stronger binding sites. Furthermore, we propose a recycling model for miRNAs dissociated from the open reading frame (ORF) by traversing ribosomes, explaining the observed link between increased ribosome density\/traversal speed and increased repression. We uncover a novel layer of interaction between the coding sequence and the 3\u2032UTR (untranslated region) and suggest the ORF has a larger role than previously thought in the mechanism of miRNA-mediated repression.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code is freely available at https:\/\/github.com\/aescrdni\/miRNA_model.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1021","type":"journal-article","created":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T13:37:04Z","timestamp":1606311424000},"page":"5398-5404","source":"Crossref","is-referenced-by-count":3,"title":["New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6013-2214","authenticated-orcid":false,"given":"Shaked","family":"Bergman","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, Tel-Aviv University , 69978 Tel Aviv, Israel"}]},{"given":"Alon","family":"Diament","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Tel-Aviv University , 69978 Tel Aviv, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4194-7068","authenticated-orcid":false,"given":"Tamir","family":"Tuller","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Tel-Aviv University , 69978 Tel Aviv, Israel"},{"name":"The Sagol School of Neuroscience, Tel-Aviv University , 69978 Tel Aviv, Israel"}]}],"member":"286","published-online":{"date-parts":[[2020,12,27]]},"reference":[{"key":"2023062707303379200_btaa1021-B1","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"Elife"},{"key":"2023062707303379200_btaa1021-B2","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","article-title":"MicroRNAs: target recognition and regulatory functions","volume":"136","author":"Bartel","year":"2009","journal-title":"Cell"},{"key":"2023062707303379200_btaa1021-B3","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cell.2018.03.006","article-title":"Metazoan MicroRNAs","volume":"173","author":"Bartel","year":"2018","journal-title":"Cell"},{"key":"2023062707303379200_btaa1021-B4","doi-asserted-by":"crossref","first-page":"e1001508","DOI":"10.1371\/journal.pbio.1001508","article-title":"Positively charged residues are the major determinants of ribosomal velocity","volume":"11","author":"Charneski","year":"2013","journal-title":"PLoS Biol"},{"key":"2023062707303379200_btaa1021-B5","doi-asserted-by":"crossref","first-page":"D296","DOI":"10.1093\/nar\/gkx1067","article-title":"miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions","volume":"46","author":"Chou","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062707303379200_btaa1021-B6","doi-asserted-by":"crossref","first-page":"5947","DOI":"10.1038\/srep05947","article-title":"Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types","volume":"4","author":"Clark","year":"2014","journal-title":"Sci. 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