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.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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High-Throughput Nucleotide Sequencing / methods*
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Humans
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Nucleic Acid Conformation*
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RNA, Viral / chemistry*
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RNA, Viral / metabolism*
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RNA-Binding Proteins / chemistry
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RNA-Binding Proteins / metabolism*
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Sequence Analysis, RNA / methods
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Transcriptome
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Zika Virus / isolation & purification
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Zika Virus / physiology*
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Zika Virus Infection / genetics
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Zika Virus Infection / metabolism*
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Zika Virus Infection / virology
Substances
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RNA, Viral
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RNA-Binding Proteins