{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T12:21:43Z","timestamp":1768479703351,"version":"3.49.0"},"posted":{"date-parts":[[2019,4,11]]},"group-title":"Genomics","reference-count":61,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2019,4,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Dengue virus (DENV) and Zika virus (ZIKV) are both positive sense single-stranded RNA viruses. They are packaged within the virion with a capsid (C) protein to form the nucleocapsid. Based on cryo-electron microscopy imaging, the nucleocapsid has been described as lacking symmetry, whilst there is distinguishable separation of the C proteins from the viral RNA (vRNA) genome. Here, to elucidate the architecture of the nucleocapsid of DENV serotype 2 and ZIKV, we used a nuclease digestion assay and next-generation sequencing to map the respective vRNA genome wide association with the C protein\n                  <jats:italic>in vitro<\/jats:italic>\n                  . The C protein exhibited non-uniform binding along the vRNA, and as C protein concentration increased, the normalized read counts also increased. A saturation point of 1:100 (vRNA:C protein monomers) was found, and binding regions showed variable saturation patterns. We also observed that C protein had a preference for G-rich sequences for both viruses. Taken together, we demonstrate that the DENV 2 and ZIKV C proteins bind vRNA in a non-uniform manner with distinct patterns of association.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Singificance Statement<\/jats:title>\n                  <jats:p>Our study demonstrates that flavivirus capsid proteins associate with the viral genome at specific sites rather than in a uniform manner as commonly expected. We estimate the number of capsid proteins binding to a single genomic RNA. We proceed to locate the capsid binding sites along the viral genomes of Dengue and Zika viruses. We characterize the binding sites in terms of affinity and analyze the nucleotide composition and sequence motifs at binding sites. We cross-reference binding sites against SHAPE reactivity data corresponding to local RNA secondary structure, which allows us to identify structural motifs of capsid binding sites. As capsid proteins are essential for viral packaging, these interactions may form attractive targets for therapeutic intervention.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/606905","type":"posted-content","created":{"date-parts":[[2019,4,11]],"date-time":"2019-04-11T21:25:20Z","timestamp":1555017920000},"source":"Crossref","is-referenced-by-count":3,"title":["Genome-wide Associations of Flavivirus Capsid Proteins"],"prefix":"10.64898","author":[{"given":"P. L.S.","family":"Boon","sequence":"first","affiliation":[]},{"given":"A. S.","family":"Martins","sequence":"additional","affiliation":[]},{"given":"F. J.","family":"Enguita","sequence":"additional","affiliation":[]},{"given":"X. N.","family":"Lim","sequence":"additional","affiliation":[]},{"given":"N. C.","family":"Santos","sequence":"additional","affiliation":[]},{"given":"P. T.","family":"Matsudaira","sequence":"additional","affiliation":[]},{"given":"I. C.","family":"Martins","sequence":"additional","affiliation":[]},{"given":"W.","family":"Yue","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2900-098X","authenticated-orcid":false,"given":"P. J.","family":"Bond","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5093-5988","authenticated-orcid":false,"given":"R. G.","family":"Huber","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019041312151802000_606905v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(16)00026-"},{"key":"2019041312151802000_606905v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nature12060"},{"key":"2019041312151802000_606905v1.3","doi-asserted-by":"crossref","unstructured":"Calvet, G. , R.S. Aguiar , A.S.O. Melo , S.A. Sampaio , I. de Filippis , A. Fabri , E.S.M. Araujo , P.C. de Sequeira , M.C.L. de Mendon\u00e7a , L. de Oliveira , D.A. Tschoeke , C.G. Schrago , F.L. Thompson , P. Brasil , F.B. dos Santos , R.M.R. Nogueira , A. Tanuri , and A.M.B. de Filippis . 2016. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect. Dis..","DOI":"10.1016\/S1473-3099(16)00095-5"},{"key":"2019041312151802000_606905v1.4","doi-asserted-by":"crossref","unstructured":"Mlakar, J. , M. Korva , N. Tul , M. Popovic , M. Poljsak-Prijatelj , J. Mraz , M. Kolenc , K. Resman Rus , T. Vipotnik , V. Vodusek , A. Vizjak , J. Pizem , M. Petrovec , and T.A. Zupanc . 2016. Zika Virus Associated with Microcephaly. N. Engl. J. Med..","DOI":"10.1056\/NEJMoa1600651"},{"key":"2019041312151802000_606905v1.5","doi-asserted-by":"crossref","unstructured":"Cao-Lormeau, V.M. , A. Blake , S. Mons , S. Last\u00e8re , C. Roche , J. Vanhomwegen , T. Dub , L. Baudouin , A. Teissier , P. Larre , A.L. Vial , C. Decam , V. Choumet , S.K. Halstead , H.J. Willison , L. Musset , J.C. Manuguerra , P. Despres , E. Fournier , H.P. Mallet , D. Musso , A. Fontanet , J. Neil , and F. Ghawch\u00e9 . 2016. Guillain-Barr\u00e9 Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study. Lancet..","DOI":"10.1016\/S0140-6736(16)00562-6"},{"key":"2019041312151802000_606905v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.07.005"},{"key":"2019041312151802000_606905v1.7","doi-asserted-by":"crossref","unstructured":"Guzman, A. , and R.E. Ist\u00fariz . 2010. Update on the global spread of dengue. Int. J. Antimicrob. Agents..","DOI":"10.1016\/j.ijantimicag.2010.06.018"},{"key":"2019041312151802000_606905v1.8","doi-asserted-by":"publisher","DOI":"10.1126\/science.329.5993.736"},{"key":"2019041312151802000_606905v1.9","first-page":"19676","article-title":"First two autochthonous dengue virus infections in metropolitan France, September 2010","volume":"15","year":"2010","journal-title":"Euro Surveill"},{"key":"2019041312151802000_606905v1.10","unstructured":"Gjenero-Margan, I. , B. Aleraj , D. Krajcar , V. Lesnikar , A. Klobu\u010dar , I. Pem-Novosel , S. Kure\u010di\u0107-Filipovi\u0107 , S. Komparak , R. Marti\u0107 , S. Duri\u010di\u0107 , L. Betica-Radi\u0107 , J. Okmad\u017ei\u0107 , T. Vilibi\u0107-\u010cavlek , A. Babi\u0107-Erceg , B. Turkovi\u0107 , T. Avsi\u0107-\u017dupanc , I. Radi\u0107 , M. Ljubi\u0107 , K. Sarac , N. Beni\u0107 , and G. Mlinari\u0107-Galinovi\u0107 . 2011. Autochthonous dengue fever in Croatia, August-September 2010. Euro Surveill. 16."},{"key":"2019041312151802000_606905v1.11","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES2013.18.50.20661"},{"key":"2019041312151802000_606905v1.12","doi-asserted-by":"crossref","unstructured":"Alves, M.J. , P.L. Fernandes , F. Amaro , H. Os\u00f3rio , T. Luz , P. Parreira , G. Andrade , L. Z\u00e9-Z\u00e9 , and H. Zeller . 2013. Clinical presentation and laboratory findings for the first autochthonous cases of dengue fever in Madeira Island, Portugal, October 2012. Eurosurveillance..","DOI":"10.2807\/ese.18.06.20398-en"},{"key":"2019041312151802000_606905v1.13","unstructured":"Burke, D.S. , L. Billings , D.A.T. Cummings , I.B. Schwartz , and L.B. Shaw . 2005. Dynamic effects of antibody-dependent enhancement on the fitness of viruses. Proc. Natl. Acad. Sci.."},{"key":"2019041312151802000_606905v1.14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004398"},{"key":"2019041312151802000_606905v1.15","doi-asserted-by":"crossref","unstructured":"Hadinegoro, S.R. , J.L. Arredondo-Garc\u00eda , M.R. Capeding , C. Deseda , T. Chotpitayasunondh , R. Dietze , H.I.H.M. Ismail , H. Reynales , K. Limkittikul , D.M. Rivera-Medina , H.N. Tran , A. Bouckenooghe , D. Chansinghakul , M. Cort\u00e9s , K. Fanouillere , R. Forrat , C. Frago , S. Gailhardou , N. Jackson , F. Noriega , E. Plennevaux , T.A. Wartel , B. Zambrano , and M. Saville . 2015. Efficacy and Long-Term Safety of a Dengue Vaccine in Regions of Endemic Disease. N. Engl. J. Med..","DOI":"10.1056\/NEJMoa1506223"},{"key":"2019041312151802000_606905v1.16","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1411037"},{"key":"2019041312151802000_606905v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.06.036"},{"key":"2019041312151802000_606905v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2463"},{"key":"2019041312151802000_606905v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(02)00660-8"},{"key":"2019041312151802000_606905v1.20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004604"},{"key":"2019041312151802000_606905v1.21","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01647-08"},{"key":"2019041312151802000_606905v1.22","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00197-13"},{"key":"2019041312151802000_606905v1.23","doi-asserted-by":"publisher","DOI":"10.1002\/bip.22266"},{"key":"2019041312151802000_606905v1.24","doi-asserted-by":"publisher","DOI":"10.1007\/s00705-009-0350-8"},{"key":"2019041312151802000_606905v1.25","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0305892101"},{"key":"2019041312151802000_606905v1.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2011.06.038"},{"key":"2019041312151802000_606905v1.27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000632"},{"key":"2019041312151802000_606905v1.28","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.virol.2013.07.023","article-title":"Non-encapsidation activities of the capsid proteins of positive-strand RNA viruses","volume":"446","year":"2013","journal-title":"Virology"},{"key":"2019041312151802000_606905v1.29","doi-asserted-by":"publisher","DOI":"10.3391\/mbi.2016.7.1.01"},{"key":"2019041312151802000_606905v1.30","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.06796-11"},{"key":"2019041312151802000_606905v1.31","doi-asserted-by":"publisher","DOI":"10.1042\/BJ20112219"},{"key":"2019041312151802000_606905v1.32","doi-asserted-by":"publisher","DOI":"10.1016\/j.virusres.2016.10.005"},{"key":"2019041312151802000_606905v1.33","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.05431-11"},{"key":"2019041312151802000_606905v1.34","doi-asserted-by":"publisher","DOI":"10.1111\/febs.12078"},{"key":"2019041312151802000_606905v1.35","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02641-13"},{"key":"2019041312151802000_606905v1.36","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-virology-110615-042334"},{"key":"2019041312151802000_606905v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.3352"},{"key":"2019041312151802000_606905v1.38","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1016\/j.jmb.2018.02.006","article-title":"Crystal Structure of the Capsid Protein from Zika Virus","volume":"430","year":"2018","journal-title":"J. Mol. Biol"},{"key":"2019041312151802000_606905v1.39","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx584"},{"key":"2019041312151802000_606905v1.40","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","year":"2019","journal-title":"Nat. Commun"},{"key":"2019041312151802000_606905v1.41","doi-asserted-by":"crossref","unstructured":"Kikin, O. , L. D\u2019Antonio , and P.S. Bagga . 2006. QGRS Mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res..","DOI":"10.1093\/nar\/gkl253"},{"key":"2019041312151802000_606905v1.42","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-359"},{"key":"2019041312151802000_606905v1.43","doi-asserted-by":"crossref","unstructured":"Hadfield, J.D. 2010. MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package. J. Stat. Softw. 33.","DOI":"10.18637\/jss.v033.i02"},{"key":"2019041312151802000_606905v1.44","doi-asserted-by":"crossref","unstructured":"Venables, W.N. , and B.D. Ripley . 2002. Modern Applied Statistics with S Fourth edition by.","DOI":"10.1007\/978-0-387-21706-2"},{"key":"2019041312151802000_606905v1.45","unstructured":"Fox, J. , and S. Weisberg . 2011. An R companion to applied regression."},{"key":"2019041312151802000_606905v1.46","doi-asserted-by":"crossref","unstructured":"Wickham, H. 2009. ggplot2. New York, NY: Springer New York.","DOI":"10.1007\/978-0-387-98141-3"},{"key":"2019041312151802000_606905v1.47","doi-asserted-by":"crossref","unstructured":"Sarkar, D. 2008. Lattice, Multivariate Data Visualization with R.","DOI":"10.1007\/978-0-387-75969-2"},{"key":"2019041312151802000_606905v1.48","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv416"},{"key":"2019041312151802000_606905v1.49","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","year":"1994","journal-title":"Proceedings. Int. Conf. Intell. Syst. Mol. Biol"},{"key":"2019041312151802000_606905v1.50","doi-asserted-by":"crossref","first-page":"2267","DOI":"10.1111\/febs.13274","article-title":"Rethinking the capsid proteins of enveloped viruses: multifunctionality from genome packaging to genome transfection","volume":"282","year":"2015","journal-title":"FEBS J"},{"key":"2019041312151802000_606905v1.51","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/cdg270"},{"key":"2019041312151802000_606905v1.52","doi-asserted-by":"publisher","DOI":"10.1038\/nsb990"},{"key":"2019041312151802000_606905v1.53","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku999"},{"key":"2019041312151802000_606905v1.54","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm1051"},{"key":"2019041312151802000_606905v1.55","doi-asserted-by":"crossref","unstructured":"Eddy, S.R. 2014. Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes. Annu. Rev. Biophys..","DOI":"10.1146\/annurev-biophys-051013-022950"},{"key":"2019041312151802000_606905v1.56","doi-asserted-by":"crossref","unstructured":"Kofler, R.M. , F.X. Heinz , and C.W. Mandl . 2002. Capsid Protein C of Tick-Borne Encephalitis Virus Tolerates Large Internal Deletions and Is a Favorable Target for Attenuation of Virulence. J. Virol..","DOI":"10.1128\/JVI.76.7.3534-3543.2002"},{"key":"2019041312151802000_606905v1.57","doi-asserted-by":"crossref","unstructured":"Kofler, R.M. , A. Leitner , G. O\u2019Riordain , F.X. Heinz , and C.W. Mandl . 2003. Spontaneous mutations restore the viability of Tick-borne encephalitis virus mutants with large deletions in protein C. J. Virol..","DOI":"10.1128\/JVI.77.1.443-451.2003"},{"key":"2019041312151802000_606905v1.58","doi-asserted-by":"crossref","unstructured":"Patkar, C.G. , C.T. Jones , Y.-h. Chang , R. Warrier , and R.J. Kuhn . 2007. Functional Requirements of the Yellow Fever Virus Capsid Protein. J. Virol..","DOI":"10.1128\/JVI.02241-07"},{"key":"2019041312151802000_606905v1.59","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1204357109"},{"key":"2019041312151802000_606905v1.60","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0105875"},{"key":"2019041312151802000_606905v1.61","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2014.11.010"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/606905","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T22:57:07Z","timestamp":1768431427000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/606905"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,11]]},"references-count":61,"URL":"https:\/\/doi.org\/10.1101\/606905","relation":{},"subject":[],"published":{"date-parts":[[2019,4,11]]},"subtype":"preprint"}}