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PMID: 29114018 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2.

RNA (New York, N.Y.) ·Vol. 24 ·No. 2 ·2018-00-00 ·Pages 143-148

Busan S, Weeks KM

Abstract

Mutational profiling (MaP) enables detection of sites of chemical modification in RNA as sequence changes during reverse transcription (RT), subsequently read out by massively parallel sequencing. We introduce ShapeMapper 2, which integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to now identify RNA adduct sites as accurately as achieved by careful manual analysis of electrophoresis data, the prior highest-accuracy standard. MaP and ShapeMapper 2 provide a robust, experimentally concise, and accurate approach for reading out nucleic acid chemical probing experiments.

Keywords

1M6 1M7 5NIA NAI NMIA RING RNA structure modeling SHAPE correlated chemical probing dimethyl sulfate mutational profiling single molecule

MeSH Terms

Base Pairing High-Throughput Nucleotide Sequencing/methods Mutation RNA/chemistry Sequence Analysis, RNA/methods Software

Chemicals

RNA

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

Busan Steven

Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

Weeks Kevin M ORCID

Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA weeks@unc.edu.

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Article Info

Journal

RNA (New York, N.Y.)

Abbr.

RNA

ISSN

1469-9001

DOI

10.1261/rna.061945.117

weeks@unc.edu

Published

2018-00-00

Epub

2017-00-07

Pages

143-148

Language

English

Region

United States

NLM ID

9509184

PMCID

PMC5769742

Subset

Grants

NIAID NIH HHS · R01 AI068462 · United States

External Links

PubMed source DOI: 10.1261/rna.061945.117 PMC Full Text View journal details

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Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2.

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