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

doi:10.1038/s41592-018-0121-0

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

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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 language	English
Pages (from-to)	785-788
Number of pages	4
Journal	NATURE METHODS
Volume	15
Issue number	10
DOIs	https://doi.org/10.1038/s41592-018-0121-0
Publication status	Published - Oct 2018
Externally published	Yes

Keywords

RNA structure
COMRADES
in vivo
Zika virus
RNA Interactomics
cells

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10.1038/s41592-018-0121-0Licence: In Copyright

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title = "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.",

keywords = "RNA structure, COMRADES, in vivo, Zika virus, RNA Interactomics, cells",

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

year = "2018",

month = oct,

doi = "10.1038/s41592-018-0121-0",

language = "English",

volume = "15",

pages = "785--788",

journal = "NATURE METHODS",

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T1 - COMRADES determines in vivo RNA structures and interactions

AU - Ziv, Omer

AU - Gabryelska, Marta M.

AU - Lun, Aaron T.L.

AU - Gebert, Luca F.R.

AU - Sheu-Gruttadauria, Jessica

AU - Meredith, Luke W.

AU - Liu, Zhong Yu

AU - Kwok, Chun Kit

AU - Qin, Cheng Feng

AU - MacRae, Ian J.

AU - Goodfellow, Ian

AU - Marioni, John C.

AU - Kudla, Grzegorz

AU - Miska, Eric A.

PY - 2018/10

Y1 - 2018/10

N2 - 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.

AB - 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.

KW - RNA structure

KW - COMRADES

KW - in vivo

KW - Zika virus

KW - RNA Interactomics

KW - cells

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DO - 10.1038/s41592-018-0121-0

M3 - Article

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AN - SCOPUS:85053497270

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SP - 785

EP - 788

JO - NATURE METHODS

JF - NATURE METHODS

SN - 1548-7091

IS - 10

ER -

COMRADES determines in vivo RNA structures and interactions

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Keywords

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