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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions.
Ealam Selvan, Mathanakumara; Lim, Kai Shen; Teo, Chee How; Lim, Yat-Yuen.
  • Ealam Selvan M; Institute of Biological Sciences, Faculty of Science, Universiti Malaya.
  • Lim KS; Institute of Biological Sciences, Faculty of Science, Universiti Malaya.
  • Teo CH; Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya; cheehow.teo@um.edu.my.
  • Lim YY; Institute of Biological Sciences, Faculty of Science, Universiti Malaya; yatyuen.lim@um.edu.my.
J Vis Exp ; (188)2022 10 21.
Article in English | MEDLINE | ID: covidwho-2110320
ABSTRACT
Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. 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 wet-lab 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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: MicroRNAs / RNA, Circular Type of study: Prognostic study Language: English Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: MicroRNAs / RNA, Circular Type of study: Prognostic study Language: English Year: 2022 Document Type: Article