Web-based platform for analysis of RNA folding from high throughput chemical probing data

Authors

Christopher Jurich, University of Nebraska-LincolnFollow
Amir Brivanlou, Harvard Medical SchoolFollow
Silvi Rouskin, Harvard Medical SchoolFollow
Joseph D. Yesselman, University of Nebraska - LincolnFollow

ORCID IDs

Joseph D. Yesselman https://orcid.org/0000-0001-8878-8119

Date of this Version

2022

Citation

Nucleic Acids Research, 2022, Vol. 50, W266-W271

https://doi.org/10.1093/nar/gkac435

Comments

This is an Open Access article distributed under the terms of the Creative Commons Attribution License

Abstract

RNA structures play critical roles in regulating gene expression across all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and ease of the experimental procedure, DMS-MaPseq has been adopted by labs worldwide. However, bioinformatic analysis remains a substantial hurdle for labs that often lack the necessary infrastructure and computational expertise. Here we present a modern web-based interface that automates the analysis of chemical probing profiles from raw sequencing files (http://rnadreem.org). The availability of a simple web-based platform for DMSMaPseq analysis will dramatically expand studies of RNA structure and aid in the design of structurebased therapeutics.