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bioRxiv · 10.1101/2022.11.01.514747

A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures

Bohdan, D. R.·Voronina, V. V.·Bujnicki, J. M.·Baulin, E. F.
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Abstract

Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D structure is modular and can be seen as a composition of building blocks of various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops and helical regions are largely less studied than the local motifs determined by the RNA secondary structure. We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures. A new dataset of annotated LOng-RAnge RNA 3D modules (LORA) was built using an approach that does not rely on the automatic annotations of non-canonical interactions. An original algorithm, ARTEM, was developed for annotation-, sequence- and topology-independent superposition of two arbitrary RNA 3D modules. The proposed methods allowed us to identify and describe the most common long-range RNA tertiary motifs. Three basic interaction types were identified to be recurrent in the long-range RNA 3D modules: ribose-ribose interactions, canonical Type I and Type II A-minor interactions, and previously undescribed staple interactions. These three interaction types were found to be different building blocks of the same complex staple motifs common to non-coding RNA 3D structures.

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Bohdan, D. R., Voronina, V. V., Bujnicki, J. M., Baulin, E. F.. 2022-11-02. A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. https://doi.org/10.1101/2022.11.01.514747

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