SHAPE-guided RNA structure homology search and motif discovery

Edoardo Morandi, Martijn J. Hemert and Danny Incarnato ()
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Edoardo Morandi: University of Groningen
Martijn J. Hemert: Leiden University Medical Center
Danny Incarnato: University of Groningen

Nature Communications, 2022, vol. 13, issue 1, 1-7

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-29398-y

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