ArticlePloS one2020
Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 2 of them syntheses that pooled it.
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Who cites it
25 citing papers in PubMed, 2 syntheses or guidelines pooled it, 37 citations in OpenAlex.
- The role of microRNAs in modulating SARS-CoV-2 infection in human cells: a systematic review.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Pooled it
- Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review.European journal of medical research · 2021Pooled it
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- Macrophage Activation Syndrome in Coinciding Pandemics of Obesity and COVID-19: Worse than Bad.Advances in experimental medicine and biology · 2024Review
- Clinically informative microRNAs for SARS-CoV-2 infection.Epigenomics · 2023Review
- A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.NAR genomics and bioinformatics · 2023Article
- L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on "neutralist-selectionist" debate.Computers in biology and medicine · 2023Article
- CovInter: interaction data between coronavirus RNAs and host proteins.Nucleic acids research · 2023Article
- Gene Network Analysis of the Transcriptome Impact of SARS-CoV-2 Interacting MicroRNAs in COVID-19 Disease.International journal of molecular sciences · 2022Review
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- miRNAs: The Key Regulator of COVID-19 Disease.International journal of cell biology · 2022Review
- RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment.Methods in molecular biology (Clifton, N.J.) · 2022Article
- MicroRNAs as the Potential Regulators of SARS-CoV-2 Infection and Modifiers of the COVID-19 Clinical Features.Molecular biology · 2022Article
- Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures.Science advances · 2021Article
- Article
- COVIDOUTCOME-estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome.Database : the journal of biological databases and curation · 2021Article
- Review
- Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan.PloS one · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV-2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5' and 3' untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon.
methodsTo have an idea of the global changes in 5' and 3'-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV-2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by 'RBPmap' and 'RNA22 v2' respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue.
resultsWe identified 28 unique variants in SARS-CoV-2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5'-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3'UTR among most of the continents. Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs.
conclusionOur results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future.
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