{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T01:00:50Z","timestamp":1760230850205,"version":"build-2065373602"},"reference-count":90,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T00:00:00Z","timestamp":1660608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"A*STAR BMRC","award":["CDF 202D800013"],"award-info":[{"award-number":["CDF 202D800013"]}]},{"name":"A*STAR Investigatorship","award":["CDF 202D800013"],"award-info":[{"award-number":["CDF 202D800013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Most pandemics of recent decades can be traced to RNA viruses, including HIV, SARS, influenza, dengue, Zika, and SARS-CoV-2. These RNA viruses impose considerable social and economic burdens on our society, resulting in a high number of deaths and high treatment costs. As these RNA viruses utilize an RNA genome, which is important for different stages of the viral life cycle, including replication, translation, and packaging, studying how the genome folds is important to understand virus function. In this review, we summarize recent advances in computational and high-throughput RNA structure-mapping approaches and their use in understanding structures within RNA virus genomes. In particular, we focus on the genome structures of the dengue, Zika, and SARS-CoV-2 viruses due to recent significant outbreaks of these viruses around the world.<\/jats:p>","DOI":"10.3390\/v14081795","type":"journal-article","created":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T03:15:27Z","timestamp":1660706127000},"page":"1795","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9560-9633","authenticated-orcid":false,"given":"Siwy Ling","family":"Yang","sequence":"first","affiliation":[{"name":"Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo Delli","family":"Ponti","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Wan","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5093-5988","authenticated-orcid":false,"given":"Roland G.","family":"Huber","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/nature12060","article-title":"The global distribution and burden of dengue","volume":"496","author":"Bhatt","year":"2013","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1146\/annurev-med-120617-041310","article-title":"Is a universal influenza virus vaccine possible?","volume":"71","author":"Nachbagauer","year":"2020","journal-title":"Annu. Rev. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0140-6736(96)01029-X","article-title":"Global burden of the HIV pandemic","volume":"348","author":"Quinn","year":"1996","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e1498","DOI":"10.1002\/wrna.1498","article-title":"Unconventional RNA-binding proteins step into the virus-host battlefront","volume":"9","author":"Castello","year":"2018","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Embarc-Buh, A., Francisco-Velilla, R., and Martinez-Salas, E. (2021). RNA-binding proteins at the host-pathogen interface targeting viral regulatory elements. Viruses, 13.","DOI":"10.3390\/v13060952"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev-virology-092917-043315","article-title":"Physical and functional analysis of viral RNA genomes by SHAPE","volume":"6","author":"Boerneke","year":"2019","journal-title":"Annu. Rev. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/nrd.2018.93","article-title":"Principles for targeting RNA with drug-like small molecules","volume":"17","author":"Warner","year":"2018","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_8","unstructured":"World Health Organization (2009). Dengue Guidelines for Diagnosis, Treatment, Prevention and Control: New Edition, World Health Organization."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.ijid.2022.06.050","article-title":"Epidemiology and costs of dengue in Brazil: A systematic literature review","volume":"122","author":"Junior","year":"2022","journal-title":"Int. J. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/S1473-3099(20)30120-1","article-title":"An interactive web-based dashboard to track COVID-19 in real time","volume":"20","author":"Dong","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/j.dsx.2021.04.007","article-title":"Long COVID: An overview","volume":"15","author":"Raveendran","year":"2021","journal-title":"Diabetes Metab. Syndr. Clin. Res. Rev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.ajem.2020.12.080","article-title":"The burden of the pandemic on the non-SARS-CoV-2 emergencies: A multicenter study","volume":"42","author":"Steinman","year":"2021","journal-title":"Am. J. Emerg Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.virusres.2008.06.004","article-title":"Structure and function of HCV IRES domains","volume":"139","author":"Lukavsky","year":"2009","journal-title":"Virus Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nsb1004","article-title":"Structure of HCV IRES domain II determined by NMR","volume":"10","author":"Lukavsky","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"8006","DOI":"10.1093\/nar\/gkaa519","article-title":"Structure of the PCBP2\/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES","volume":"48","author":"Beckham","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S0042-6822(03)00544-0","article-title":"Enterovirus 71 contains a type I IRES element that functions when eukaryotic initiation factor eIF4G is cleaved","volume":"315","author":"Thompson","year":"2003","journal-title":"Virology"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/0092-8674(89)90124-4","article-title":"Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot","volume":"57","author":"Brierley","year":"1989","journal-title":"Cell"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5995","DOI":"10.1074\/jbc.M108972200","article-title":"In vitro evidence for a long range pseudoknot in the 5\u2032-untranslated and matrix coding regions of HIV-1 genomic RNA","volume":"277","author":"Paillart","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.3390\/v3091739","article-title":"Functional RNA elements in the dengue virus genome","volume":"3","author":"Gebhard","year":"2011","journal-title":"Viruses"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Reuter, J.S., and Mathews, D.H. (2010). RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-129"},{"key":"ref_21","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":"ref_22","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/0022-2836(71)90341-X","article-title":"Self-complementary oligoribonucleotides: Adenylic acid-uridylic acid block copolymers","volume":"57","author":"Martin","year":"1971","journal-title":"J. Mol. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5498","DOI":"10.1073\/pnas.1219988110","article-title":"Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots","volume":"110","author":"Hajdin","year":"2013","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1261\/rna.1643609","article-title":"Improved RNA secondary structure prediction by maximizing expected pair accuracy","volume":"15","author":"Lu","year":"2009","journal-title":"RNA"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nmeth.3029","article-title":"RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)","volume":"11","author":"Siegfried","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1038\/nature07749","article-title":"A hierarchical model for evolution of 23S ribosomal RNA","volume":"457","author":"Bokov","year":"2009","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., and Stadler, P.F. (2008). RNAalifold: Improved consensus structure prediction for RNA alignments. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-474"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Harmanci, A.O., Sharma, G., and Mathews, D.H. (2011). TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-108"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"13939","DOI":"10.1093\/nar\/gku1172","article-title":"Dynalign II: Common secondary structure prediction for RNA homologs with domain insertions","volume":"42","author":"Fu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1093\/bioinformatics\/btq726","article-title":"Multilign: An algorithm to predict secondary structures conserved in multiple RNA sequences","volume":"27","author":"Xu","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1093\/bioinformatics\/btm049","article-title":"Multiple structural alignment and clustering of RNA sequences","volume":"23","author":"Torarinsson","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"D593","DOI":"10.1093\/nar\/gkr859","article-title":"ViPR: An open bioinformatics database and analysis resource for virology research","volume":"40","author":"Pickett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nmeth.4066","article-title":"A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs","volume":"14","author":"Rivas","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41467-019-09391-8","article-title":"Structure mapping of dengue and Zika viruses reveals functional long-range interactions","volume":"10","author":"Huber","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/nature08237","article-title":"Architecture and secondary structure of an entire HIV-1 RNA genome","volume":"460","author":"Watts","year":"2009","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14263","article-title":"Structural imprints in vivo decode RNA regulatory mechanisms","volume":"519","author":"Spitale","year":"2015","journal-title":"Nature"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nmeth.4057","article-title":"DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo","volume":"14","author":"Zubradt","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.molcel.2016.04.028","article-title":"In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation","volume":"62","author":"Aw","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1016\/j.cell.2016.04.028","article-title":"RNA duplex map in living cells reveals higher-order transcriptome structure","volume":"165","author":"Lu","year":"2016","journal-title":"Cell"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s41592-018-0121-0","article-title":"COMRADES determines in vivo RNA structures and interactions","volume":"15","author":"Ziv","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3917","DOI":"10.1038\/s41467-021-22785-x","article-title":"The architecture of the SARS-CoV-2 RNA genome inside virion","volume":"12","author":"Cao","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/s41576-018-0034-x","article-title":"High-throughput determination of RNA structures","volume":"19","author":"Strobel","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/s41586-020-2253-5","article-title":"Determination of RNA structural diversity and its role in HIV-1 RNA splicing","volume":"582","author":"Tomezsko","year":"2020","journal-title":"Nature"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.molcel.2016.04.030","article-title":"Global mapping of human RNA-RNA interactions","volume":"62","author":"Sharma","year":"2016","journal-title":"Mol. cell"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/s41586-020-2249-1","article-title":"RIC-seq for global in situ profiling of RNA-RNA spatial interactions","volume":"582","author":"Cai","year":"2020","journal-title":"Nature"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3692","DOI":"10.1073\/pnas.1416266112","article-title":"Functionally conserved architecture of hepatitis C virus RNA genomes","volume":"112","author":"Mauger","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e6136","DOI":"10.7717\/peerj.6136","article-title":"ScanFold: An approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV","volume":"6","author":"Andrews","year":"2018","journal-title":"PeerJ"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.molcel.2020.12.041","article-title":"Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms","volume":"81","author":"Huston","year":"2021","journal-title":"Mol. Cell"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"5113","DOI":"10.1038\/s41467-021-25357-1","article-title":"Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions","volume":"12","author":"Yang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"4925","DOI":"10.1093\/nar\/gkh839","article-title":"A comparative method for finding and folding RNA secondary structures within protein-coding regions","volume":"32","author":"Pedersen","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"878679","DOI":"10.3389\/fviro.2022.878679","article-title":"RNAvigator: A Pipeline to Identify Candidates for Functional RNA Structure Elements","volume":"2","author":"Wang","year":"2022","journal-title":"Front. Virol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1038\/s41467-022-28603-2","article-title":"Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells","volume":"13","author":"Lan","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1093\/bioinformatics\/btv523","article-title":"SHAPE directed RNA folding","volume":"32","author":"Lorenz","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.ymeth.2010.06.007","article-title":"SHAPE-directed RNA secondary structure prediction","volume":"52","author":"Low","year":"2010","journal-title":"Methods"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1073\/pnas.0806929106","article-title":"Accurate SHAPE-directed RNA structure determination","volume":"106","author":"Deigan","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Zarringhalam, K., Meyer, M.M., Dotu, I., Chuang, J.H., and Clote, P. (2012). Integrating chemical footprinting data into RNA secondary structure prediction. PloS ONE, 7.","DOI":"10.1371\/journal.pone.0045160"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"4261","DOI":"10.1093\/nar\/gks009","article-title":"RNA folding with soft constraints: Reconciliation of probing data and thermodynamic secondary structure prediction","volume":"40","author":"Washietl","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"e35","DOI":"10.1093\/nar\/gkw1094","article-title":"A high-throughput approach to profile RNA structure","volume":"45","author":"Marti","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"i354","DOI":"10.1093\/bioinformatics\/btz395","article-title":"ShaKer: RNA SHAPE prediction using graph kernel","volume":"35","author":"Mautner","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"11270","DOI":"10.1093\/nar\/gkaa864","article-title":"Structural analysis of SARS-CoV-2 genome and predictions of the human interactome","volume":"48","author":"Vandelli","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Delli Ponti, R., and Mutwil, M. (2021). Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07638-7"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/j.stem.2016.02.016","article-title":"Zika virus infects human cortical neural progenitors and attenuates their growth","volume":"18","author":"Tang","year":"2016","journal-title":"Cell Stem Cell"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"De Falco, L., Silva, N.M., Santos, N.C., Huber, R.G., and Martins, I.C. (2021). The pseudo-circular genomes of flaviviruses: Structures, mechanisms, and functions of circularization. Cells, 10.","DOI":"10.3390\/cells10030642"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1016\/j.chom.2018.10.011","article-title":"Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity","volume":"24","author":"Li","year":"2018","journal-title":"Cell Host Microbe."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"11513","DOI":"10.1073\/pnas.1716689115","article-title":"Pervasive tertiary structure in the dengue virus RNA genome","volume":"115","author":"Dethoff","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41579-018-0118-9","article-title":"Origin and evolution of pathogenic coronaviruses","volume":"17","author":"Cui","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2394","DOI":"10.1016\/j.cell.2021.03.012","article-title":"Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions","volume":"184","author":"Flynn","year":"2021","journal-title":"Cell"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1016\/j.cell.2021.02.008","article-title":"In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs","volume":"184","author":"Sun","year":"2021","journal-title":"Cell"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1021\/acscentsci.0c00984","article-title":"Targeting the SARS-CoV-2 RNA genome with small molecule binders and ribonuclease targeting chimera (RIBOTAC) degraders","volume":"6","author":"Haniff","year":"2020","journal-title":"ACS Cent. Sci."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"19191","DOI":"10.1002\/anie.202103693","article-title":"Exploring the druggability of conserved RNA regulatory elements in the SARS-CoV-2 genome","volume":"60","author":"Sreeramulu","year":"2021","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s41592-021-01075-w","article-title":"Genome-scale deconvolution of RNA structure ensembles","volume":"18","author":"Morandi","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nchembio.596","article-title":"Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble","volume":"7","author":"Stelzer","year":"2011","journal-title":"Nat. Chem. Biol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/s41392-022-00916-0","article-title":"Cryo-EM advances in RNA structure determination","volume":"7","author":"Ma","year":"2022","journal-title":"Signal Transduct. Target."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/s41594-021-00653-y","article-title":"Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome","volume":"28","author":"Zhang","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Sun, Y.-T., and Varani, G. (2022). Structure of the Dengue Virus RNA Promoter. bioRxiv, 2022.04.15.488410.","DOI":"10.1101\/2022.04.15.488410"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"12436","DOI":"10.1093\/nar\/gkaa1053","article-title":"Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements","volume":"48","author":"Manfredonia","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"e34","DOI":"10.1093\/nar\/gkaa1255","article-title":"A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy","volume":"49","author":"Marinus","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1038\/nprot.2016.011","article-title":"Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE","volume":"11","author":"Flynn","year":"2016","journal-title":"Nat. Protoc."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/j.molcel.2020.11.004","article-title":"The short- and long-range RNA-RNA interactome of SARS-CoV-2","volume":"80","author":"Ziv","year":"2020","journal-title":"Mol. Cell"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1038\/s41564-019-0513-7","article-title":"The structure of the influenza A virus genome","volume":"4","author":"Dadonaite","year":"2019","journal-title":"Nat. Microb."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"5695","DOI":"10.1038\/s41467-021-25999-1","article-title":"In vivo structure and dynamics of the SARS-CoV-2 RNA genome","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"13858","DOI":"10.1073\/pnas.1407306111","article-title":"Single-molecule correlated chemical probing of RNA","volume":"111","author":"Homan","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/s41587-020-0712-z","article-title":"Determination of isoform-specific RNA structure with nanopore long reads","volume":"39","author":"Aw","year":"2021","journal-title":"Nat. Biotech."},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Pollom, E., Dang, K.K., Potter, E.L., Gorelick, R.J., Burch, C.L., Weeks, K.M., and Swanstrom, R. (2013). Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs. PLoS Pathog., 9.","DOI":"10.1371\/journal.ppat.1003294"},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Lavender, C.A., Gorelick, R.J., and Weeks, K.M. (2015). Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes. PLOS Comput. Biol., 11.","DOI":"10.1371\/journal.pcbi.1004230"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"11670","DOI":"10.1128\/JVI.01560-13","article-title":"Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity","volume":"87","author":"Burrill","year":"2013","journal-title":"J. Virol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.molcel.2016.01.024","article-title":"The coding region of the HCV genome contains a network of regulatory RNA structures","volume":"62","author":"Pirakitikulr","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"107823","DOI":"10.1016\/j.celrep.2020.107823","article-title":"Mapping of influenza virus RNA-RNA interactions reveals a flexible network","volume":"31","author":"Kanarek","year":"2020","journal-title":"Cell Rep."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1016\/j.cell.2020.04.011","article-title":"The architecture of SARS-CoV-2 transcriptome","volume":"181","author":"Kim","year":"2020","journal-title":"Cell"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Sanders, W., Fritch, E.J., Madden, E.A., Graham, R.L., Vincent, H.A., Heise, M.T., Baric, R.S., and Moorman, N.J. (2020). Comparative analysis of coronavirus genomic RNA structure reveals conservation in SARS-like coronaviruses. Biorxiv Prepr. Serv. Biol., 2020.06.15.153197.","DOI":"10.1101\/2020.06.15.153197"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/8\/1795\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:10:47Z","timestamp":1760141447000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/8\/1795"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,16]]},"references-count":90,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,8]]}},"alternative-id":["v14081795"],"URL":"https:\/\/doi.org\/10.3390\/v14081795","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2022,8,16]]}}}