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Series GSE211240 Query DataSets for GSE211240
Status Public on Nov 29, 2023
Title MDA5 guards against infection by surveying cellular RNA homeostasis [I]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary MDA5 is an innate immune RNA sensor that detects a range of viruses. MDA5’s RNA agonists are not well defined. We used individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to study its ligands. Surprisingly, upon infection with SARS-CoV-2 or encephalomyocarditis virus (EMCV), MDA5 bound overwhelmingly to cellular RNAs. Many binding sites were intronic and proximal to Alu elements. MDA5-bound RNA was enriched in Poly(A) and Poly(U) motifs, some of which may form double-stranded RNA. In EMCV-infected cells, cytoplasmic levels of intron-containing unspliced transcripts were increased, suggesting dysregulation of splicing. Concomitantly, MDA5 iCLIP peaks were enriched in introns accumulating in the cytoplasm of infected cells. Moreover, rescue of splicing abrogated MDA5 activation. Finally, depletion of viral RNA from RNA extracted from infected cells did not diminish its MDA5-stimulatory potential. Taken together, MDA5 surveys RNA processing fidelity and detects splicing perturbation during infection, establishing a paradigm of innate immune ‘guarding’ for RNA sensors.
Overall design THP-1 cells (IRF3 knock out) were treated with 10 ng/ml PMA for 24 hr, and either left untreated, infected with EMCV (MOI = 2, 20 hr), or treated with human IFN beta (100 IU/ml, 6 hr) and cytoplasmic RNA was extracted to examine exon- and intron-level gene expression by RNA sequencing.
Contributor(s) Sampaio NG, Gearing LJ, Hertzog PJ, Rehwinkel J
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Submission date Aug 15, 2022
Last update date Nov 29, 2023
Contact name Jamie Gearing
Organization name Hudson Institute of Medical Research
Street address 27-31 Wright St
City Melbourne
ZIP/Postal code 3168
Country Australia
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (12)
GSM6459548 IRF3 KO THP-1 cells, uninfected, replicate 1 [1A_Unif]
GSM6459549 IRF3 KO THP-1 cells, EMCV, replicate 1 [1B_EMCV]
GSM6459550 IRF3 KO THP-1 cells, IFNb, replicate 3 [1C_IFNb]
This SubSeries is part of SuperSeries:
GSE214664 MDA5 guards against infection by surveying cellular RNA homeostasis
BioProject PRJNA869666

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Supplementary file Size Download File type/resource
GSE211240_211022_THP-1_EMCV_all_exon_counts.csv.gz 1.9 Mb (ftp)(http) CSV
GSE211240_211022_THP-1_EMCV_all_intron_counts.csv.gz 1.7 Mb (ftp)(http) CSV
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