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COMRADES determines in vivo RNA structures and interactions.

Omer Ziv1,2, Marta M Gabryelska3, Aaron T L Lun4

  • 1Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK. omer.ziv@gurdon.cam.ac.uk.

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Researchers developed a new method, cross-linking of matched RNAs and deep sequencing (COMRADES), to study RNA structures within cells. This technique revealed the Zika virus RNA genome

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Area of Science:

  • Molecular Biology
  • Virology
  • Genomics

Background:

  • RNA structural flexibility is crucial for biological functions.
  • Existing methods lack the ability to explore multiple RNA conformations in vivo.
  • Understanding RNA architecture in its cellular context is essential.

Purpose of the Study:

  • To develop a novel method for capturing RNA conformations within living cells.
  • To investigate the in vivo structural ensemble of the Zika virus RNA genome.
  • To identify interactions between viral RNA and host noncoding RNAs.

Main Methods:

  • Development of cross-linking of matched RNAs and deep sequencing (COMRADES).
  • Creation of a computational pipeline for RNA structural ensemble retrieval.
  • Application of COMRADES to study the Zika virus RNA genome in human cells.

Main Results:

  • COMRADES successfully captured in vivo RNA conformations.
  • The study elucidated the architecture of the Zika virus RNA genome.
  • Multiple site-specific interactions between Zika virus RNA and human noncoding RNAs were identified.

Conclusions:

  • COMRADES is a powerful tool for exploring RNA structural dynamics in vivo.
  • The findings provide insights into Zika virus RNA structure and its interactions with host factors.
  • This method has broad implications for understanding RNA biology and viral pathogenesis.