Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation.
Amino Acid Sequence
Betacoronavirus
/ genetics
Binding Sites
COVID-19
Computational Biology
/ methods
Coronavirus Infections
/ virology
CpG Islands
Gene Expression Regulation, Viral
Genome, Viral
Humans
Nucleotide Motifs
Open Reading Frames
Pandemics
Pneumonia, Viral
/ virology
Promoter Regions, Genetic
Protein Binding
SARS-CoV-2
Transcription Factors
/ genetics
Transcription Initiation Site
Viral Proteins
/ genetics
COVID-19
CpG Island
Motif
Promoter
SARS-CoV-2
Transcription factor
Journal
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
ISSN: 1567-7257
Titre abrégé: Infect Genet Evol
Pays: Netherlands
ID NLM: 101084138
Informations de publication
Date de publication:
Oct 2020
Oct 2020
Historique:
received:
29
03
2020
revised:
16
05
2020
accepted:
27
05
2020
pubmed:
1
6
2020
medline:
3
10
2020
entrez:
1
6
2020
Statut:
ppublish
Résumé
SARS-CoV-2 is a new virus responsible for an outbreak of respiratory illness known as COVID-19, which has spread to several countries around the world and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In silico analysis of the transcription start sites, promoter regions, transcription factors and their binding sites, gene ontology, CpG islands for SARS-CoV-2 viral genome are a first step to understand the regulation mechanisms of gene expression and its association with genetic variations in the genomes. For this purpose, we first computationally surveyed all SARS-CoV-2 virus genes with the open reading frames from NCBI database and found eleven sequences to accomplish the mentioned features by using bioinformatics tools. Our analysis revealed that all (100%) of the SARS-CoV-2 virus genes have more than one TSS. By taking all TSSs with the highest predictive score we determined promoter regions and identified five common candidate motifs (MVI, MVII, MVIII, MVIV and MVV) of which MVI was found to be shared by all promoter regions of SARS-CoV-2 virus genes with the least E-value (3.8e-056, statistically highly significant). In our further analysis of MVI we showed MVI serve as binding sites for a single transcription factor (TF) family, EXPREG, involved in the regulatory mode of these genes. From EXPREG family four TFs that belongs to Cyclic AMP (cAMP) receptor protein (CRP) and Catabolite control protein A (CcpA) group mostly serve as transcriptional activator whereas two TFs that belong to LexA group always serve as transcriptional repressor in different kinds of cellular processes and molecular functions. Therefore, we unfolded SARS-CoV-2 viral genome to shed light on its gene expression regulation that could help to design and evaluate diagnostic tests, to track and trace the ongoing outbreak and to identify potential intervention options.
Identifiants
pubmed: 32473977
pii: S1567-1348(20)30217-3
doi: 10.1016/j.meegid.2020.104386
pmc: PMC7256514
pii:
doi:
Substances chimiques
Transcription Factors
0
Viral Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
104386Informations de copyright
Copyright © 2020 Elsevier B.V. All rights reserved.
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