A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures

Gianfrotta, Coline; Reinharz, Vladimir; Barth, Dominique; Denise, Alain

doi:10.4230/lipics.sea.2021.19

Cited by 1 publication

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Generally, all the motifs are defined based on hydrogen bonding interactions [6,[9][10][11][12], hydrophobic stacking interactions [13][14][15], or both of them [16][17][18][19]. The structural context matters for RNA tertiary motifs formation and can be leveraged for the prediction of their location [20,21].…”

Section: Introductionmentioning

confidence: 99%

“…The databases that include long-range motifs are often focused on these described types [34,35]. The majority of existing approaches consider only motifs formed by base-pairing interactions and completely ignore other hydrogen bonds or stacking interactions [21,35,36]. Therefore, the annotation of the motifs relies on the automatic annotation of the base-pairing interactions, which is usually performed with one of the five standard tools [37][38][39][40][41].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Bohdan

Voronina

Bujnicki

et al. 2022

Preprint

View full text Add to dashboard Cite

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.

show abstract