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COMRADES determines in vivo RNA structures and interactions.

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.

SUBMITTER: Ziv O

PROVIDER: S-EPMC6168409 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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COMRADES determines in vivo RNA structures and interactions.

Ziv Omer O Gabryelska Marta M MM Lun Aaron T L ATL Gebert Luca F R LFR Sheu-Gruttadauria Jessica J Meredith Luke W LW Liu Zhong-Yu ZY Kwok Chun Kit CK Qin Cheng-Feng CF MacRae Ian J IJ Goodfellow Ian I Marioni John C JC Kudla Grzegorz G Miska Eric A EA

Nature methods 20180910 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 nonc ...[more]

PMID: 30202058

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