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

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...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research Vol. 51; no. 16; pp. 8367 - 8382
Main Authors: Bohdan, Davyd R, Voronina, Valeria V, Bujnicki, Janusz M, Baulin, Eugene F
Format: Journal Article
Language:English
Published: England Oxford University Press 08.09.2023
Subjects:
Data Resources and Analyses
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. Along with the prevalent canonical A-minor interactions, a large number of previously undescribed staple interactions were observed. The most frequent long-range motifs were found to belong to three main motif families: planar staples, tilted staples, and helical packing motifs. Graphical Abstract Graphical Abstract
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkad605