1. High affinity of host human microRNAs to SARS-CoV-2 genome: An in silico analysis
- Author
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Saeideh Jafarinejad-Farsangi, Farzaneh Rostamzadeh, Morteza Hadizadeh, and Maryam Moazzam Jazi
- Subjects
0301 basic medicine ,miR-29 ,lcsh:QH426-470 ,In silico ,viruses ,MiRNA binding ,Computational biology ,Biology ,Genome ,Biochemistry ,MiRBase ,Article ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,Genetics ,Binding site ,Gene ,Molecular Biology ,Biochemistry, medical ,SARS-CoV-2 ,Biochemistry (medical) ,COVID-19 ,biology.organism_classification ,lcsh:Genetics ,030104 developmental biology ,030220 oncology & carcinogenesis ,miR-21 ,Betacoronavirus - Abstract
Background Coronavirus disease 2019 (COVID-19) caused by a novel betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted top health concerns worldwide within a few months after its appearance. Since viruses are highly dependent on the host small RNAs (microRNAs) for their replication and propagation, in this study, top miRNAs targeting SARS-CoV-2 genome and top miRNAs targeting differentially expressed genes (DEGs) in lungs of patients infected with SARS-CoV-2, were predicted. Methods All human mature miRNA sequences were acquired from miRBase database. MiRanda tool was used to predict the potential human miRNA binding sites on the SARS-CoV-2 genome. EdgeR identified differentially expressed genes (DEGs) in response to SARS-CoV-2 infection from GEO147507 data. Gene Set Enrichment Analysis (GSEA) and DEGs annotation analysis were performed using ToppGene and Metascape tools. Results 160 miRNAs with a perfect matching in the seed region were identified. Among them, there was 15 miRNAs with more than three binding sites and 12 miRNAs with a free energy binding of −29 kCal/Mol. MiR-29 family had the most binding sites (11 sites) on the SARS-CoV-2 genome. MiR-21 occupied four binding sites and was among the top miRNAs that targeted up-regulated DEGs. In addition to miR-21, miR-16, let-7b, let-7e, and miR-146a were the top miRNAs targeting DEGs. Conclusion Collectively, more experimental studies especially miRNA-based studies are needed to explore detailed molecular mechanisms of SARS-CoV-2 infection. Moreover, the role of DEGs including STAT1, CCND1, CXCL-10, and MAPKAPK2 in SARS-CoV-2 should be investigated to identify the similarities and differences between SARS-CoV-2 and other respiratory viruses., Highlights • miR-29 family had 11 binding site on the SARS-COV-2 genome. • miR-29a/b, 21, 761, 3130, 3167 and miR-3175 bound to the spike coding sequence. • miR-16, 146a, 21, 615 and let-7b/e targeted SARS-CoV-2 induced DEGs. • miR-146a, 203a, 24, 615 and miR-16 targeted DEGs involved in viral prosesess
- Published
- 2020