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Interferon inhibits a model RNA virus via a limited set of inducible effector genes

ABSTRACT: Interferon inhibits a model RNA virus via a limited set of inducible effector genes

PROVIDER: PRJNA975286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24679700_1.fastq.gz	Fastqsanger.gz
	SRR24679700_2.fastq.gz	Fastqsanger.gz
	SRR24679701_1.fastq.gz	Fastqsanger.gz
	SRR24679701_2.fastq.gz	Fastqsanger.gz
	SRR24679702_1.fastq.gz	Fastqsanger.gz

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Interferon inhibits a model RNA virus via a limited set of inducible effector genes [GW_CRISPR_Screen]

Project description:Interferon inhibits a model RNA virus via a limited set of inducible effector genes [GW_CRISPR_Screen]

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Interferon inhibits a model RNA virus via a limited set of inducible effector genes [ISG_CRISPR_Screen]

Project description:Interferon inhibits a model RNA virus via a limited set of inducible effector genes [ISG_CRISPR_Screen]

| PRJNA975291 | ENA

Interferon inhibits a model RNA virus via a limited set of inducible effector genes [RNA-seq]

Project description:Interferon inhibits a model RNA virus via a limited set of inducible effector genes [RNA-seq]

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Interferon inhibits a model RNA virus via a limited set of inducible effector genes.

Project description:Interferons control viral infection by inducing the expression of antiviral effector proteins encoded by interferon-stimulated genes (ISGs). The field has mostly focused on identifying individual antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is not known how many ISGs are required to protect cells from a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, we used CRISPR-based loss-of-function screens to identify a markedly limited set of ISGs that confer interferon-mediated suppression of a model alphavirus, Venezuelan equine encephalitis virus (VEEV). We show via combinatorial gene targeting that three antiviral effectors-ZAP, IFIT3, and IFIT1-together constitute the majority of interferon-mediated restriction of VEEV, while accounting for < 0.5% of the interferon-induced transcriptome. Together, our data suggest a refined model of the antiviral interferon response in which a small subset of "dominant" ISGs may confer the bulk of the inhibition of a given virus.

| S-EPMC10481653 | biostudies-literature

Interferon inhibits a model RNA virus via a limited set of inducible effector genes

Project description:Interferons control viral infection by inducing the expression of antiviral effector proteins encoded by interferon-stimulated genes (ISGs). The field has mostly focused on identifying individual antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is not known how many ISGs are required to protect cells from a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, we used CRISPR-based loss-of-function screens to identify a markedly limited set of ISGs that confer interferon-mediated suppression of a model alphavirus, Venezuelan equine encephalitis virus (VEEV). We show via combinatorial gene targeting that three antiviral effectors - ZAP, IFIT3, and IFIT1 - together constitute the majority of interferon-mediated restriction of VEEV, while accounting for less than 0.5% of the interferon-induced transcriptome. Together, our data suggests a refined model of the antiviral interferon response in which a small subset of "dominant" ISGs may confer the bulk of the inhibition of a given virus.

| S-SCDT-10_15252-EMBR_202356901 | biostudies-other

Interferon inhibits a model RNA virus via a limited set of inducible effector genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-05-26 | GSE233197 | GEO

Interferon inhibits a model RNA virus via a limited set of inducible effector genes [ISG_CRISPR_Screen]

Project description:Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). An ISG-targeted CRISPR screen using IFN beta-treated U-2 OS cells was performed to determine which ISGs were required in order for host cells to suppress Venezuelan equine encephalitis virus (VEEV) infection.

2023-05-26 | GSE233196 | GEO

Interferon inhibits a model RNA virus via a limited set of inducible effector genes [GW_CRISPR_Screen]

Project description:Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). A genome-wide CRISPR screen using IFN beta-treated U-2 OS cells was performed to determine which ISGs were required in order for host cells to suppress Venezuelan equine encephalitis virus (VEEV) infection.

2023-05-26 | GSE233195 | GEO

Interferon inhibits a model RNA virus via a limited set of inducible effector genes [RNA-seq]

Project description:To investigate the transcripts induced by the cytokine interferon (IFN) β in U-2 OS cells, we treated U-2 OS cells with IFNβ 20U/mL for 6 and 24 hours and performed RNA-Seq to determine differentially expressed genes.

2023-05-26 | GSE233003 | GEO

Interferon-inducible effector mechanisms in cell-autonomous immunity.

Project description:Interferons (IFNs) induce the expression of hundreds of genes as part of an elaborate antimicrobial programme designed to combat infection in all nucleated cells - a process termed cell-autonomous immunity. As described in this Review, recent genomic and subgenomic analyses have begun to assign functional properties to novel IFN-inducible effector proteins that restrict bacteria, protozoa and viruses in different subcellular compartments and at different stages of the pathogen life cycle. Several newly described host defence factors also participate in canonical oxidative and autophagic pathways by spatially coordinating their activities to enhance microbial killing. Together, these IFN-induced effector networks help to confer vertebrate host resistance to a vast and complex microbial world.

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