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Updated: Sep 21, 2025
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
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Web-based platform for analysis of RNA folding from high throughput chemical probing data
Christopher P Jurich1, Amir Brivanlou2, Silvi Rouskin2
1Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Nucleic Acids Research
|June 3, 2022
Summary
RNA structure analysis is crucial for gene regulation. A new web tool (RNA-DREAM) simplifies Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq) data analysis, making RNA structure studies more accessible.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- RNA structures are vital for gene expression regulation in all organisms.
- Chemical probing coupled with sequencing (e.g., DMS-MaPseq) allows RNA structure determination in native cellular environments.
- Previous methods like DMS-MaPseq have revealed new biological insights and therapeutic targets for viruses like HIV-1 and SARS-CoV-2.
Purpose of the Study:
- To address the bioinformatic challenges hindering the widespread adoption of DMS-MaPseq.
- To present a user-friendly, web-based platform for automated analysis of DMS-MaPseq data.
- To facilitate broader research into RNA structure and structure-based therapeutic development.
Main Methods:
- Development of a web-based interface (http://rnadreem.org) for automated analysis.
- Processing of raw sequencing files from chemical probing experiments.
- Utilizing Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq) for RNA structure profiling.
Main Results:
- A functional web platform automating DMS-MaPseq data analysis is now available.
- The platform simplifies the interpretation of chemical probing profiles.
- This automation lowers the barrier for researchers lacking extensive bioinformatics expertise.
Conclusions:
- The RNA-DREAM web platform significantly enhances accessibility to RNA structure analysis.
- Wider adoption of DMS-MaPseq will accelerate RNA structure research.
- This tool supports the discovery and design of novel structure-based therapeutics.
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