Omics · study · 2026
Functional anaylsis of IRF9 in the chicken innate antiviral immune response
Listed in NCBI GEO
The chicken immune system is distinct from many mammalian models due to its reduced immune gene repertoire yet retained ability to mount a highly effective immune response.
Description
In mammals, interferon regulatory factor 9 (IRF9) is a key transcriptional regulator of the type I interferon pathway, stimulating the expression of hundreds of antiviral genes. Although IRF9 was previously thought to be absent in chickens, recent genomic reannotation suggests the presence of a putative IRF9 ortholog.
To learn about the function of this gene in chickens, we utilized chicken embryonic fibroblast cell lines constitutively expressing clustered regularly interspaced short palindromic repeats interference (CRISPRi) to repress endogenous IRF9 gene expression. We induced an anti-viral immune response in IRF9 repressed cell lines by stimulation with double stranded RNA and analyzed the transcriptomes at 0 hours, 30 minutes, 1 hour and 6 hours post-stimulation.
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Transcriptomic analysis revealed that IRF9 repression resulted in the enrichment of pathways associated with regulating the innate anti-viral immune response, including the retinoic acid inducible gene I like (RIG-I like) receptor pathway and the Toll-like receptor pathway. Interestingly, suppressor of cytokine signaling 1 (SOCS1) and SOCS3, Major Histocompatibility Complex transactivator (CIITA) and tumor necrosis factor (TNF) receptor associated factor 2 (TRAF2) expression kinetics changed during the immune response as a result of IRF9 repression.
Our preliminary findings provide a molecular basis to elucidate the functional role of IRF9 in the innate anti-viral immune response in chickens.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE304nnn/GSE304808 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE304808 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1302777 ncbi.nlm.nih.gov/bioproject/PRJNA1302777 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Gallus gallus
- From keywords
- Life Sciences
- Inferred from text
- Cancer 65%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE304808 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[organism].NCBITaxon:9031 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |