SHAPE-guided RNA structure homology search and motif discovery

Edoardo Morandi; Martijn J van Hemert; Danny Incarnato

doi:10.1038/s41467-022-29398-y

SHAPE-guided RNA structure homology search and motif discovery

Nat Commun. 2022 Mar 31;13(1):1722. doi: 10.1038/s41467-022-29398-y.

Authors

Edoardo Morandi¹, Martijn J van Hemert², Danny Incarnato³

Affiliations

¹ Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
² Department of Medical Microbiology, Molecular Virology Laboratory, Leiden University Medical Center, Leiden, The Netherlands.
³ Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands. d.incarnato@rug.nl.

Abstract

The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared and conserved RNA structural features within transcriptomes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Humans
Nucleic Acid Conformation
RNA / chemistry
RNA / genetics
Sequence Analysis, RNA / methods
Zika Virus Infection*
Zika Virus* / genetics

Substances

RNA