COMRADES determines in vivo RNA structures and interactions

Nat Methods. 2018 Oct;15(10):785-788. doi: 10.1038/s41592-018-0121-0. Epub 2018 Sep 10.


The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs.

Publication types

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

MeSH terms

  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Nucleic Acid Conformation*
  • RNA, Viral / chemistry*
  • RNA, Viral / metabolism*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Sequence Analysis, RNA / methods
  • Transcriptome
  • Zika Virus / isolation & purification
  • Zika Virus / physiology*
  • Zika Virus Infection / genetics
  • Zika Virus Infection / metabolism*
  • Zika Virus Infection / virology


  • RNA, Viral
  • RNA-Binding Proteins