RNABP COGEST: a resource for investigating functional RNAs.

Sohini Bhattacharya,Rahul Paul,Abhijit Mitra,Swati Panigrahi,Purshotam Sharma,Shriyaa Mittal,Preethi S P,Sukanya Halder,Dhananjay Bhattacharyya,Antarip Halder

doi:10.1093/database/bav011

Abstract

Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. ‘RNA Base Pair Count, Geometry and Stability’ (http://bioinf.iiit.ac.in/RNABPCOGEST) brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. The database is designed to enable the QM community, on the one hand, to identify appropriate biologically relevant model systems and also enable the biology community to easily sift through diverse computational results to gain theoretical insights which could promote hypothesis driven biological research.Database URL: http://bioinf.iiit.ac.in/RNABPCOGEST

Highlights

There is a remarkable growth in the ranks of newly discovered non-(protein)-coding RNAs [1,2,3,4,5,6,7] that regulate diverse cellular processes
We observe a lot of activity in two distinct research fields: quantum mechanical (QM) computations of interaction energies in nucleic acids and RNA structural bioinformatics [11]
Unlike double helical DNA which is characterized by canonical A-T/U and G-C base pairs, a variety of nc base pairs are observed in RNA, as single-stranded RNA molecule folds on itself and open up possibilities for the constituent nucleotide bases to interact with others through any of their three distinct edges in either cis or trans glycosidic bond orientation

Summary

Introduction

There is a remarkable growth in the ranks of newly discovered non-(protein)-coding RNAs (ncRNAs) [1,2,3,4,5,6,7] that regulate diverse cellular processes This has been accompanied by a rapid increase in efforts toward characterizing and understanding their complex structures and functionalities, at the molecular level. Structural bioinformatics of RNA has evolved in response to the rapidly accumulating evidence that ncRNAs, which constitute a major proportion of the transcriptome, play critical roles in gene regulation and expression Important developments in this area include the identification and characterization of the nc base pairs, higher order structures and recurrent 3D motifs involving them. RNA Base Pair Count, Geometry and Stability (RNABP COGEST) addresses this issue of effective communication across domains, by annotating and systematically organizing validated QM analysis data, in a manner relevant for understanding functionalities of ncRNA at the molecular level

Materials and methods

Result and discussion

Findings

Future work