{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:41:49Z","timestamp":1765485709422},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1262,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine\u2013Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints.<\/jats:p>\n               <jats:p>Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3\u2032-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data.<\/jats:p>\n               <jats:p>Contact: \u00a0brave.oval.pan@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt184","type":"journal-article","created":{"date-parts":[[2013,4,20]],"date-time":"2013-04-20T02:09:34Z","timestamp":1366423774000},"page":"1488-1491","source":"Crossref","is-referenced-by-count":54,"title":["rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments"],"prefix":"10.1093","volume":"29","author":[{"given":"Patrick B. F.","family":"O\u2019Connor","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry, University College Cork, Cork, Ireland and 2Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA"}]},{"given":"Gene-Wei","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University College Cork, Cork, Ireland and 2Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA"}]},{"given":"Jonathan S.","family":"Weissman","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University College Cork, Cork, Ireland and 2Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA"}]},{"given":"John F.","family":"Atkins","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University College Cork, Cork, Ireland and 2Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA"}]},{"given":"Pavel V.","family":"Baranov","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University College Cork, Cork, Ireland and 2Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,4,19]]},"reference":[{"key":"2023012810441363800_btt184-B1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1093\/embo-reports\/kvf065","article-title":"Release factor 2 frameshifting sites in different bacteria","volume":"3","author":"Baranov","year":"2002","journal-title":"EMBO Rep."},{"key":"2023012810441363800_btt184-B2","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0405s35","article-title":"Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite","author":"Borodovsky","year":"2011","journal-title":"Curr. 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Microbiol."},{"key":"2023012810441363800_btt184-B4","doi-asserted-by":"crossref","first-page":"W70","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012810441363800_btt184-B5","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/nature09267","article-title":"Mammalian microRNAs predominantly act to decrease target mRNA levels","volume":"466","author":"Guo","year":"2010","journal-title":"Nature"},{"key":"2023012810441363800_btt184-B6","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012810441363800_btt184-B7","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"2023012810441363800_btt184-B8","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","article-title":"Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes","volume":"147","author":"Ingolia","year":"2011","journal-title":"Cell"},{"key":"2023012810441363800_btt184-B9","doi-asserted-by":"crossref","first-page":"6842","DOI":"10.1128\/jb.176.22.6842-6851.1994","article-title":"rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift","volume":"176","author":"Larsen","year":"1994","journal-title":"J. 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Correlation between the 3'-terminal-polypyrimidine sequence of 16-S RNA and translational specificity of the ribosome","volume":"57","author":"Shine","year":"1975","journal-title":"Eur. J. Biochem."},{"key":"2023012810441363800_btt184-B14","doi-asserted-by":"crossref","first-page":"2063","DOI":"10.1261\/rna.02890211","article-title":"Wobble base-pairing slows in vivo translation elongation in metazoans","volume":"17","author":"Stadler","year":"2011","journal-title":"RNA"},{"key":"2023012810441363800_btt184-B15","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1101\/SQB.1987.052.01.078","article-title":"Slippery runs, shifty stops, backward steps, and forward hops: \u22122, \u22121, +1, +2, +5, and +6 ribosomal frameshifting","volume":"52","author":"Weiss","year":"1987","journal-title":"Cold Spring Harb. Symp. Quant. 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