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| 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
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| 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.
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| 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.
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| Contributor(s) |
Sampaio NG, Gearing LJ, Hertzog PJ, Rehwinkel J |
| Citation missing |
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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
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| Street address |
27-31 Wright St
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| City |
Melbourne |
| ZIP/Postal code |
3168 |
| Country |
Australia |
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| Platforms (1) |
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| Samples (12)
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| 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] |
| GSM6459551 |
IRF3 KO THP-1 cells, uninfected, replicate 2 [2A_Unif] |
| GSM6459552 |
IRF3 KO THP-1 cells, EMCV, replicate 2 [2B_EMCV] |
| GSM6459553 |
IRF3 KO THP-1 cells, IFNb, replicate 2 [2C_IFNb] |
| GSM6459554 |
IRF3 KO THP-1 cells, uninfected, replicate 3 [3A_Unif] |
| GSM6459555 |
IRF3 KO THP-1 cells, EMCV, replicate 3 [3B_EMCV] |
| GSM6459556 |
IRF3 KO THP-1 cells, IFNb, replicate 3 [3C_IFNb] |
| GSM6459557 |
IRF3 KO THP-1 cells, uninfected, replicate 4 [4A_Unif] |
| GSM6459558 |
IRF3 KO THP-1 cells, EMCV, replicate 4 [4B_EMCV] |
| GSM6459559 |
IRF3 KO THP-1 cells, IFNb, replicate 4 [4C_IFNb] |
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| This SubSeries is part of SuperSeries: |
| GSE214664 |
MDA5 guards against infection by surveying cellular RNA homeostasis |
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| Relations |
| BioProject |
PRJNA869666 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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