Characterizing viral circRNAs and their application in identifying circRNAs in viruses

Mengting Niu; Ying Ju; Chen Lin; Quan Zou

doi:10.1093/bib/bbab404

Characterizing viral circRNAs and their application in identifying circRNAs in viruses

Brief Bioinform. 2022 Jan 17;23(1):bbab404. doi: 10.1093/bib/bbab404.

Authors

Mengting Niu^{1

2}, Ying Ju³, Chen Lin³, Quan Zou^{1

2}

Affiliations

¹ Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
² Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China.
³ School of Informatics, Xiamen University, Xiamen, China.

PMID: 34585234
DOI: 10.1093/bib/bbab404

Abstract

Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced formed by the reverse splicing mechanism, which play an important role in a variety of biological activities. Viruses can encode circRNA, and viral circRNAs have been found in multiple single-stranded and double-stranded viruses. However, the characteristics and functions of viral circRNAs remain unknown. Sequence alignment showed that viral circRNAs are less conserved than circRNAs in animal, indicating that the viral circRNAs may evolve rapidly. Through the analysis of the sequence characteristics of viral circRNAs and circRNAs in animal, it was found that viral circRNAs and animals circRNAs are similar in nucleic acid composition, but have obvious differences in secondary structure and autocorrelation characteristics. Based on these characteristics of viral circRNAs, machine learning algorithms were employed to construct a prediction model to identify viral circRNA. Additionally, analysis of the interaction between viral circRNA and miRNAs showed that viral circRNA is expected to interact with 518 human miRNAs, and preliminary analysis of the role of viral circRNA. And it has been also found that viral circRNAs may be involved in many KEGG pathways related to nervous system and cancer. We curated an online server, and the data and code are available: http://server.malab.cn/viral-CircRNA/.

Keywords: characteristic; conservation; function; identify; viral circRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Machine Learning
MicroRNAs* / genetics
MicroRNAs* / metabolism
RNA, Circular / genetics
Viruses* / genetics
Viruses* / metabolism

Substances

MicroRNAs
RNA, Circular