{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T08:48:49Z","timestamp":1791362929869,"version":"4.3.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T00:00:00Z","timestamp":1671494400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001656","name":"Helmholtz Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001656","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["948636"],"award-info":[{"award-number":["948636"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Helmholtz Young Investigator","award":["VH-NG-1347"],"award-info":[{"award-number":["VH-NG-1347"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The RNA genome of SARS-CoV-2 contains a frameshift stimulatory element (FSE) that allows access to an alternative reading frame through \u22121 programmed ribosomal frameshifting (PRF). \u22121PRF in the 1a\/1b gene is essential for efficient viral replication and transcription of the viral genome. \u22121PRF efficiency relies on the presence of conserved RNA elements within the FSE. One of these elements is a three-stemmed pseudoknot, although alternative folds of the frameshift site might have functional roles as well. Here, by complementing ensemble and single-molecule structural analysis of SARS-CoV-2 frameshift RNA variants with functional data, we reveal a conformational interplay of the 5\u2032 and 3\u2032 immediate regions with the FSE and show that the extended FSE exists in multiple conformations. Furthermore, limiting the base pairing of the FSE with neighboring nucleotides can favor or impair the formation of the alternative folds, including the pseudoknot. Our results demonstrate that co-existing RNA structures can function together to fine-tune SARS-CoV-2 gene expression, which will aid efforts to design specific inhibitors of viral frameshifting.<\/jats:p>","DOI":"10.1093\/nar\/gkac1184","type":"journal-article","created":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T08:52:56Z","timestamp":1671526376000},"page":"728-743","source":"Crossref","is-referenced-by-count":39,"title":["<i>Cis<\/i>-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function"],"prefix":"10.1093","volume":"51","author":[{"given":"Lukas","family":"Pekarek","sequence":"first","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI-HZI) , W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias M","family":"Zimmer","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI-HZI) , W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Sophie","family":"Gribling-Burrer","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI-HZI) , W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Buck","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI-HZI) , W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Redmond","family":"Smyth","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI-HZI) , W\u00fcrzburg, Germany"},{"name":"Medical Faculty, Julius-Maximilians University W\u00fcrzburg ,\u00a0W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0435-4757","authenticated-orcid":false,"given":"Neva","family":"Caliskan","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI-HZI) , W\u00fcrzburg, Germany"},{"name":"Medical Faculty, Julius-Maximilians University W\u00fcrzburg ,\u00a0W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,20]]},"reference":[{"key":"2023012711445302700_B1","doi-asserted-by":"crossref","first-page":"842261","DOI":"10.3389\/fmolb.2022.842261","article-title":"Thinking outside the frame: impacting genomes capacity by programmed ribosomal frameshifting","volume":"9","author":"Riegger","year":"2022","journal-title":"Front. Mol. Biosci."},{"key":"2023012711445302700_B2","first-page":"7007","article-title":"Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use","volume":"44","author":"Atkins","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023012711445302700_B3","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1099\/vir.0.042499-0","article-title":"Non-canonical translation in RNA viruses","volume":"93","author":"Firth","year":"2012","journal-title":"J. Gen. Virol."},{"key":"2023012711445302700_B4","doi-asserted-by":"crossref","first-page":"veaa009","DOI":"10.1093\/ve\/veaa009","article-title":"Properties and abundance of overlapping genes in viruses","volume":"6","author":"Schlub","year":"2020","journal-title":"Virus. 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