Selvan, Mathanakumara Ealam and Lim, Kai Shen and Teo, Chee How and Lim, Yat-Yuen (2022) In Silico identification and characterization of circRNAs during host-pathogen interactions. Jove-Journal of Visualized Experiments (188). ISSN 1940-087X, DOI https://doi.org/10.3791/64565.
Full text not available from this repository.Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via backsplicing. These circRNAs are predominantly studied for their roles as regulators of various biological processes. Notably, emerging evidence demonstrates that host circRNAs can be differentially expressed (DE) upon infection with pathogens (e.g., influenza and coronaviruses), suggesting a role for circRNAs in regulating host innate immune responses. However, investigations on the role of circRNAs during pathogenic infections are limited by the knowledge and skills required to carry out the necessary bioinformatic analysis to identify DE circRNAs from RNA sequencing (RNA-seq) data. Bioinformatics prediction and identification of circRNAs is crucial before any verification, and functional studies using costly and time-consuming wetlab techniques. To solve this issue, a step-by-step protocol of in Silico prediction and characterization of circRNAs using RNA-seq data is provided in this manuscript. The protocol can be divided into four steps: 1) Prediction and quantification of DE circRNAs via the CIRIquant pipeline; 2) Annotation via circBase and characterization of DE circRNAs; 3) CircRNA-miRNA interaction prediction through Circr pipeline; 4) functional enrichment analysis of circRNA parental genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). This pipeline will be useful in driving future in vitro and in vivo research to further unravel the role of circRNAs in host-pathogen interactions.
| Item Type: | Article |
|---|---|
| Funders: | Fundamental Research Grant Scheme [FRGS/1/2020/SKK0/UM/02/15], University of Malaya High Impact Research Grant [UM.C/625/1/HIR/MOE/CHAN/02/07] |
| Uncontrolled Keywords: | Computational Biology; Gene Expression Profiling; Host-Pathogen Interactions; MicroRNAs; RNA, Circular; Sequence Analysis, RNA |
| Subjects: | S Agriculture > S Agriculture (General) |
| Divisions: | Faculty of Science > Institute of Biological Sciences Deputy Vice Chancellor (Research & Innovation) Office > Centre for Research in Biotechnology for Agriculture |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 15 Jul 2024 03:23 |
| Last Modified: | 15 Jul 2024 03:23 |
| URI: | http://eprints.um.edu.my/id/eprint/40406 |
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