Genome-scale deconvolution of RNA structure ensembles

Edoardo Morandi; Ilaria Manfredonia; Lisa M Simon; Francesca Anselmi; Martijn J van Hemert; Salvatore Oliviero; Danny Incarnato

doi:10.1038/s41592-021-01075-w

Genome-scale deconvolution of RNA structure ensembles

Edoardo Morandi
, Ilaria Manfredonia
, Lisa M Simon
, Francesca Anselmi
, Martijn J van Hemert
, Salvatore Oliviero^*
, Danny Incarnato^*

^*Corresponding author for this work

Molecular Genetics

Research output: Contribution to journal › Article › Academic › peer-review

94 Citations (Scopus)

155 Downloads (Pure)

Abstract

RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3' untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.

Original language	English
Article number	s41592-021-01075-w
Pages (from-to)	249-252
Number of pages	4
Journal	Nature Methods
Volume	18
Early online date	22-Feb-2021
DOIs	https://doi.org/10.1038/s41592-021-01075-w
Publication status	Published - Feb-2021

Keywords

RNA Structure
DRACO
chemical probing
SARS-CoV-2 genome
RNA structurome

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10.1038/s41592-021-01075-w

Genome-scale deconvolution of RNA structure ensemblesFinal publisher's version, 2.09 MBLicence: Taverne

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Structurele schakelaars als middel tegen COVID-19
Incarnato, D.
24/02/2021
1 item of Media coverage
Press/Media: Other › Popular
New technique reveals switches in RNA
Incarnato, D.
22/02/2021
3 items of Media coverage
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Nieuwe techniek onthult schakelaars in virus-RNA - Structurele schakelaars vormen mogelijk doelwit voor middel tegen coronavirus
Incarnato, D.
22/02/2021
1 item of Media coverage
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Cite this

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title = "Genome-scale deconvolution of RNA structure ensembles",

abstract = "RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3' untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.",

keywords = "RNA Structure, DRACO, chemical probing, SARS-CoV-2 genome, RNA structurome",

author = "Edoardo Morandi and Ilaria Manfredonia and Simon, \{Lisa M\} and Francesca Anselmi and \{van Hemert\}, \{Martijn J\} and Salvatore Oliviero and Danny Incarnato",

year = "2021",

month = feb,

doi = "10.1038/s41592-021-01075-w",

language = "English",

volume = "18",

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journal = "Nature Methods",

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AU - Morandi, Edoardo

AU - Manfredonia, Ilaria

AU - Simon, Lisa M

AU - Anselmi, Francesca

AU - van Hemert, Martijn J

AU - Oliviero, Salvatore

AU - Incarnato, Danny

PY - 2021/2

Y1 - 2021/2

N2 - RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3' untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.

AB - RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3' untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.

KW - RNA Structure

KW - DRACO

KW - chemical probing

KW - SARS-CoV-2 genome

KW - RNA structurome

U2 - 10.1038/s41592-021-01075-w

DO - 10.1038/s41592-021-01075-w

M3 - Article

C2 - 33619392

SN - 1548-7105

VL - 18

SP - 249

EP - 252

JO - Nature Methods

JF - Nature Methods

M1 - s41592-021-01075-w

ER -

Genome-scale deconvolution of RNA structure ensembles

Abstract

Keywords

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Press/Media

Structurele schakelaars als middel tegen COVID-19

New technique reveals switches in RNA

Nieuwe techniek onthult schakelaars in virus-RNA - Structurele schakelaars vormen mogelijk doelwit voor middel tegen coronavirus

Cite this