Sim, AYL, Huber, RG, Lim, XN, Ng, WC, Chawla, T, Aw, J, Lim, SY, Shen, Y, Boon, K, Choy, MM, Wilm, A, de Sessions, PF, Hibberd, M, Nagarajan, N, Ooi, EE, Bond, PJ, Sessions, OM and Wan, Y. 2019. Genome organization of dengue and Zika viruses. [Online]. NCBI Gene Expression Omnibus. Available from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106483
Sim, AYL, Huber, RG, Lim, XN, Ng, WC, Chawla, T, Aw, J, Lim, SY, Shen, Y, Boon, K, Choy, MM, Wilm, A, de Sessions, PF, Hibberd, M, Nagarajan, N, Ooi, EE, Bond, PJ, Sessions, OM and Wan, Y. Genome organization of dengue and Zika viruses [Internet]. NCBI Gene Expression Omnibus; 2019. Available from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106483
Sim, AYL, Huber, RG, Lim, XN, Ng, WC, Chawla, T, Aw, J, Lim, SY, Shen, Y, Boon, K, Choy, MM, Wilm, A, de Sessions, PF, Hibberd, M, Nagarajan, N, Ooi, EE, Bond, PJ, Sessions, OM and Wan, Y (2019). Genome organization of dengue and Zika viruses. [Data Collection]. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106483
Description
Dengue and Zika are closely related members of the Flaviviridae family of positive, single-stranded RNA viruses and are of global clinical importance. These viruses utilize an 11kb RNA genome for translation and replication, and much remains to be learnt about how the entire genome folds to enable virus function. Here, we performed high throughput RNA secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains within their virus particles. We identified structures that are associated with translation pausing, and are evolutionary conserved by integrating synonymous mutation rates into our analysis. Genome-wide interaction mapping revealed alternative structures, as well as extensive long-range RNA interactions – including the known circularization signals– within the virus particles. Many of these long-range interactions are conserved across the viruses and/or clustered into “hubs” that are shown to be functionally important. This comprehensive structural resource of dengue and Zika viruses reveals that viral genome organization is much more complex than previously appreciated and deepens our understanding of the molecular basis for viral pathogenesis.
Keywords
Data capture method | Experiment |
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Date (Date published in a 3rd party system) | 30 May 2019 |
Language(s) of written materials | English |
Data Creators | Sim, AYL, Huber, RG, Lim, XN, Ng, WC, Chawla, T, Aw, J, Lim, SY, Shen, Y, Boon, K, Choy, MM, Wilm, A, de Sessions, PF, Hibberd, M, Nagarajan, N, Ooi, EE, Bond, PJ, Sessions, OM and Wan, Y |
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LSHTM Faculty/Department | Faculty of Infectious and Tropical Diseases > Dept of Immunology and Infection |
Participating Institutions | London School of Hygiene & Tropical Medicine, London, United Kingdom |
Date Deposited | 16 Sep 2020 08:50 |
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Last Modified | 08 Jul 2021 12:49 |
Publisher | NCBI Gene Expression Omnibus |