A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools

RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essent...

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Bibliographic Details
Published in:Briefings in bioinformatics 2023-11, Vol.25 (1)
Main Authors: Tieng, Francis Yew Fu, Abdullah-Zawawi, Muhammad-Redha, Md Shahri, Nur Alyaa Afifah, Mohamed-Hussein, Zeti-Azura, Lee, Learn-Han, Mutalib, Nurul-Syakima Ab
Format: Article
Language:English
Subjects:
Algorithms
Computational Biology - methods
Genomics
Humans
Nucleic Acid Conformation
Review
RNA - metabolism
RNA Folding
RNA, Untranslated - genetics
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Summary:RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbad421