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

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Nucleic Acids Res. Jun 3, 2022: gkac435. doi: 10.1093/nar/gkac435. Online ahead of print.


RNA structures play an essential role in the regulation of gene expression in all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the field of RNA structure by allowing the evaluation of many structures in their native physiological context. Previously, we developed dimethyl sulfate-based mutation profiling and sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in RNA. We have used this approach to determine genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which has uncovered novel biology and identified therapeutic targets. Due to the simplicity and ease of the experimental procedure, DMS-MaPseq has been adopted by laboratories around the world. However, bioinformatics analysis remains a significant obstacle for laboratories that often lack the necessary IT infrastructure and expertise. Here we present a modern web 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 DMS-MaPseq analysis will greatly expand RNA structure studies and facilitate the design of structure-based therapies.

PMID:35657086 | DO I:10.1093/nar/gkac435