RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA

• Published in: eLife Vol. 3; p. e01892
• Main Authors: Chapman, Erich G, Moon, Stephanie L, Wilusz, Jeffrey, Kieft, Jeffrey S
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 01-04-2014; eLife Sciences Publications, Ltd
• Subjects: 3' Untranslated Regions; 3′UTR; Base Sequence; Biochemistry; Dengue fever; dengue virus; Dengue Virus - genetics; Dengue Virus - pathogenicity; Disease control; Enzymes; Exonuclease; exonuclease resistance; Exoribonucleases - genetics; Exoribonucleases - metabolism; Infections; Kinetics; Microbiology and Infectious Disease; Molecular Sequence Data; Mutagenesis; Mutation; Nucleic Acid Conformation; Recombinant Proteins - metabolism; Ribonucleic acid; RNA; RNA Stability; RNA viruses; RNA, Viral - chemistry; RNA, Viral - genetics; RNA, Viral - metabolism; small flavivirus RNA; Sodium; Structure-Activity Relationship; Viral infections; Viruses; Xrn1; xrRNA; small flavivirus RNA; xrRNA; Xrn1; 3′UTR; dengue virus; exonuclease resistance
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.01892

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.