COMRADES determines in vivo RNA structures and interactions

Omer Ziv, Marta M. Gabryelska, Aaron T.L. Lun, Luca F.R. Gebert, Jessica Sheu-Gruttadauria, Luke W. Meredith, Zhong Yu Liu, Chun Kit Kwok, Cheng Feng Qin, Ian J. MacRae, Ian Goodfellow, John C. Marioni, Grzegorz Kudla, Eric A. Miska

Research output: Contribution to journalArticlepeer-review

84 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)785-788
Number of pages4
JournalNATURE METHODS
Volume15
Issue number10
DOIs
Publication statusPublished - Oct 2018
Externally publishedYes

Keywords

  • RNA structure
  • COMRADES
  • in vivo
  • Zika virus
  • RNA Interactomics
  • cells

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