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RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
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Comparison of SHAPE reagents for mapping RNA structures inside living cells
Byron Lee1, Ryan A Flynn1, Anastasia Kadina2
1Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.
RNA (New York, N.Y.)
|November 24, 2016
Summary
Acylimidazole reagents NAI and NAI-N3 provide superior signals for in vivo RNA structure analysis compared to 1M7. These findings enhance high-throughput sequencing of the RNA structurome.
Area of Science:
- Molecular Biology
- Biochemistry
- Genomics
Background:
- Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) technology enables transcriptome-wide RNA secondary structure analysis.
- Recent SHAPE methods like icSHAPE (NAI-N3) and SHAPE-MaP (1M7) aim to measure in vivo RNA structure using high-throughput sequencing.
Purpose of the Study:
- To directly compare the performance of various in vivo SHAPE acylation reagents on an unbiased, raw-signal level.
- To determine the most effective reagent for in vivo RNA structurome analysis.
Main Methods:
- Direct comparison of in vivo SHAPE acylation reagents.
- Utilizing the simple primer extension assay.
- Analysis of raw signal levels and background noise.
Main Results:
- Acylimidazole reagents NAI and NAI-N3 demonstrated significantly greater signals compared to the 1M7 reagent.
- NAI and NAI-N3 exhibited lower background noise for in vivo RNA structure measurements.
- While multiple SHAPE technologies are effective for in vitro RNA analysis, NAI and NAI-N3 show superior performance in vivo.
Conclusions:
- NAI and NAI-N3 are more effective than 1M7 for in vivo measurement of the RNA structurome.
- These acylimidazole reagents offer improved signal-to-noise ratio for high-throughput sequencing-based RNA structure determination.
