Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

Zhang, Yupeng; Zhang, Yikan; Liu, Zhong‐Yu; Cheng, Meng‐Li; Ma, Junfeng; Wang, Yan; Qin, Cheng‐Feng; Fang, Xianyang

doi:10.15252/embr.201847016

Title: Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

Journal Article · Tue Sep 10 00:00:00 EDT 2019 · EMBO Reports

DOI:https://doi.org/10.15252/embr.201847016· OSTI ID:1578208

Zhang, Yupeng ^[1]; Zhang, Yikan ^[1]; Liu, Zhong‐Yu ^[2]; Cheng, Meng‐Li ^[3]; Ma, Junfeng ^[1]; Wang, Yan ^[1]; Qin, Cheng‐Feng ^[3];

^[1]

Tsinghua Univ., Beijing (China)
Beijing Institute of Microbiology and Epidemiology (China); Guangzhou Medical University (China); Sun Yat-Sen Univ., Guangzhou (China)
Beijing Institute of Microbiology and Epidemiology (China)

Most mosquito-borne flaviviruses, including Zika virus (ZIKV), Dengue virus (DENV), and West Nile virus (WNV), produce long non-coding subgenomic RNAs (sfRNAs) in infected cells that link to pathogenicity and immune evasion. Until now, the structural characterization of these lncRNAs remains limited. Here, we studied the 3D structures of individual and combined subdomains of sfRNAs, and visualized the accessible 3D conformational spaces of complete sfRNAs from DENV2, ZIKV, and WNV by small angle X-ray scattering (SAXS) and computational modeling. The individual xrRNA1s and xrRNA2s adopt similar structures in solution as the crystal structure of ZIKV xrRNA1, and all xrRNA1-2s form compact structures with reduced flexibility. While the DB12 of DENV2 is extended, the DB12s of ZIKV and WNV are compact due to the formation of intertwined double pseudoknots. All 3' stem-loops (3'SLs) share similar rod-like structures. Complete sfRNAs are extended and sample a large conformational space in solution. Our work not only provides structural insight into the function of flavivirus sfRNAs, but also highlights strategies of visualizing other lncRNAs in solution by SAXS and computational methods.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC); National Key Research and Development Project of China; National Natural Science Foundation of China (NSFC)

Grant/Contract Number:: AC02-06CH11357; 2016YFA0500700; 2016YFD0500304; 2018ZX09711003; 81522025; 81621005; 31770190

OSTI ID:: 1578208

Journal Information:: EMBO Reports, Vol. 20, Issue 11; ISSN 1469-221X

Publisher:: European Molecular Biology OrganizationCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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59 BASIC BIOLOGICAL SCIENCES
3D structure
computational modeling
long non-coding RNA
small angle X-ray scattering
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Title: Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

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References (80)

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