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

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

PROVIDER: PRJNA974702 | 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

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

| PRJNA975286 | ENA

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]

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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 [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 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

Regulation by the RNA-binding protein Unkempt at its effector interface

Project description:How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of ‘dual-purpose’ peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface.

2024-04-11 | PXD050601 | Pride

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