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

Elife. 2014 Apr 1:3:e01892. 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.

Keywords: 3′UTR; Xrn1; dengue virus; exonuclease resistance; small flavivirus RNA; xrRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions
  • Base Sequence
  • Dengue Virus / genetics*
  • Dengue Virus / pathogenicity*
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism*
  • Kinetics
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • RNA Stability*
  • RNA, Viral / chemistry
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism
  • Recombinant Proteins / metabolism
  • Structure-Activity Relationship


  • 3' Untranslated Regions
  • RNA, Viral
  • Recombinant Proteins
  • Exoribonucleases