Virus Dataset Detail

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Dataset Information
Accession GSE167075
Status 2021/4/27
Title m6A modification in SARS-CoV-2 virus regulates host cell innate immune response
Organism Homo sapiens;Chlorocebus aethiops;Severe acute respiratory syndrome coronavirus 2
Experiment type Expression profiling by high throughput sequencing;Methylation profiling by high throughput sequencing
Summary It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlying molecular mechanism. RNA modification landscape of SARS-CoV-2 and its functional relevance to host cell innate immune response remain unknown. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigated m6A modification of SARS-CoV-2 gene in regulating host cell innate immune response. Our data showed that SARS-CoV-2 virus has m6A modification enriched in 3' region of the viral genome. We also found that host cell m6A methyltransferase METTL3 depletion reduced viral load in infected cells, decreased m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increased RIG-1 binding and subsequently enhanced downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in severe COVID-19 patients. These findings will aid to understand the COVID-19 pathogenesis and help in designing future studies of regulating innate immunity for COVID-19 treatment.
Samples
GSM ID Sample info Characteristics Description
GSM5092424 cov2-shNTC-1 cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (shNTC); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus shM3_vs_NTC(human).xlsx
GSM5092425 cov2-shNTC-2 cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (shNTC); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus shM3_vs_NTC(human).xlsx
GSM5092426 cov2-shNTC-3 cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (shNTC); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus shM3_vs_NTC(human).xlsx
GSM5092427 cov2-shM3-1 cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus shM3_vs_NTC(human).xlsx
GSM5092428 cov2-shM3-2 cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus shM3_vs_NTC(human).xlsx
GSM5092429 cov2-shM3-3 cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus shM3_vs_NTC(human).xlsx
GSM5092430 Cov2-Input cell line:Kidney epithelial Vero E6 cells from an African green monkey; infection:SARS-CoV-2 virus; passages:P1; viral strain:Betacoronavirus; merip antibody:none -
GSM5092431 Cov2-MeRIP cell line:Kidney epithelial Vero E6 cells from an African green monkey; infection:SARS-CoV-2 virus; passages:P1; viral strain:Betacoronavirus; merip antibody:anti-m6A polyclonal antibody (ab151230, abcam) -
GSM5092432 Cov2-Ctrl_Input cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (Ctrl); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:none -
GSM5092433 Cov2-M3_Input cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:none -
GSM5092434 Cov2-Ctrl_IP cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (Ctrl); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:anti-m6A polyclonal antibody (ab151230, abcam) -
GSM5092435 Cov2-M3_IP cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:anti-m6A polyclonal antibody (ab151230, abcam) -
GSM5092436 Cov2-Ctrl_m_Input cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (Ctrl); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:none -
GSM5092437 Cov2-M3_m_Input cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:none -
GSM5092438 Cov2-Ctrl_m_IP cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:control (Ctrl); infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:anti-m6A polyclonal antibody (ab151230, abcam) -
GSM5092439 Cov2-M3_m_IP cell line:Human colorectal adenocarcinoma Caco-2 cells; genotype:METTL3 KD; infection:SARS-CoV-2 virus; passages:P2; viral strain:Betacoronavirus; merip antibody:anti-m6A polyclonal antibody (ab151230, abcam) -
Platform GPL29320  GPL29742  : Illumina NovaSeq 6000 (Homo sapiens; Severe acute respiratory syndrome coronavirus 2);Illumina NovaSeq 6000 (Chlorocebus aethiops; Severe acute respiratory syndrome coronavirus 2)
Literature 33961823  
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xCell Plot
* p<0.05 ** p<0.01