title: RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA.
abstract: Dengue virus is a growing global health threat. Dengue and other flaviviruses commandeer the host cell's RNA degradation machinery to generate the small flaviviral RNA (sfRNA), a noncoding RNA that induces cytopathicity and pathogenesis. Host cell exonuclease Xrn1 likely loads on the 5' end of viral genomic RNA and degrades processively through ∼10 kB of RNA, halting near the 3' end of the viral RNA. The surviving RNA is the sfRNA. We interrogated the architecture of the complete Dengue 2 sfRNA, identifying five independently-folded RNA structures, two of which quantitatively confer Xrn1 resistance. We developed an assay for real-time monitoring of Xrn1 resistance that we used with mutagenesis and RNA folding experiments to show that Xrn1-resistant RNAs adopt a specific fold organized around a three-way junction. Disrupting the junction's fold eliminates the buildup of disease-related sfRNAs in human cells infected with a flavivirus, directly linking RNA structure to sfRNA production. DOI: http://dx.doi.org/10.7554/eLife.01892.001.
authors.affiliation: Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States.
authors.forename: Erich G
authors.initials: EG
authors.lastname: Chapman
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: Moon
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Wilusz
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Kieft
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D003716:Dengue Virus / Q000235:genetics* / Q000472:pathogenicity*; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011994:Recombinant Proteins / Q000378:metabolism; D013329:Structure-Activity Relationship
chemical_list: D020413:3' Untranslated Regions; D012367:RNA, Viral; D011994:Recombinant Proteins; D005095:Exoribonucleases
keywords: 3′UTR; Xrn1; dengue virus; exonuclease resistance; small flavivirus RNA; xrRNA