Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2
- Corresponding author: weeks{at}unc.edu
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
- SHAPE
- RING
- 1M7
- NMIA
- 1M6
- 5NIA
- NAI
- dimethyl sulfate
- single molecule
- correlated chemical probing
- mutational profiling
- RNA structure modeling
Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.061945.117.
- Received April 28, 2017.
- Accepted November 5, 2017.
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