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Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells (eCLIP)

ABSTRACT: Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells (eCLIP)

PROVIDER: PRJNA889430 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21863800_1.fastq.gz	Fastqsanger.gz
	SRR21863800_2.fastq.gz	Fastqsanger.gz
	SRR21863801_1.fastq.gz	Fastqsanger.gz
	SRR21863801_2.fastq.gz	Fastqsanger.gz
	SRR21863794_1.fastq.gz	Fastqsanger.gz

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Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells (eCLIP)

Project description:The RNA-binding protein PARP13 is a primary factor in the innate antiviral response. PARP13 can suppress translation and drive decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to perform its antiviral activities, such as activation of the pathway mediated by post-translational addition ISG15 or ISGylation. The RNA-binding domains of both PARP13 and its primary cofactor, TRIM25, are required for antiviral activity. Here we perform enhanced crosslinking immunoprecipitation (eCLIP) and RNA-seq to investigate the role of PARP13 expression and RNA binding in transcriptome regulation within human cells. We find that PARP13 regulates the transcriptome in basal and antiviral states and that the antiviral response shifts PARP13 target localization, but not its binding preferences. We demonstrate that PARP13 expression supports the expression of ISGylation-related genes, including TRIM25. Using the common targets PARP13 and TRIM25 share, we assess their spatial relationship along transcripts and show that PARP13 and TRIM25 associate in part via RNA-protein interactions. Evidence from genomic data and molecular biology experiments provide insight into the geometry of PARP13's interface with its cofactor TRIM25 and implicates PARP13 in creating and maintaining a cellular environment poised for an antiviral response.

2023-09-11 | GSE215250 | GEO

Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells

Project description:Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells

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cGAS maintains basal antiviral state

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Transcriptome regulation by PARP13 in basal and antiviral states in human cells.

Project description:The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including co-translational addition of ISG15, or ISGylation. We performed enhanced crosslinking immunoprecipitation (eCLIP) and RNA-seq in human cells to investigate PARP13's role in transcriptome regulation for both basal and antiviral states. We find that the antiviral response shifts PARP13 target localization, but not its binding preferences, and that PARP13 supports the expression of ISGylation-related genes, including PARP13's cofactor, TRIM25. PARP13 associates with TRIM25 via RNA-protein interactions, and we elucidate a transcriptome-wide periodicity of PARP13 binding around TRIM25. Taken together, our study implicates PARP13 in creating and maintaining a cellular environment poised for an antiviral response through limiting PARP13 translation, regulating access to distinct mRNA pools, and elevating ISGylation machinery expression.

| S-EPMC10943485 | biostudies-literature

Lockdown, caregiving, and antiviral gene regulation in macaques

Project description:Lockdown, caregiving, and antiviral gene regulation in macaques

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Differential Gene Expression in PARP13 Knockdown

Project description:Poly(ADP-ribose) Polymerase-13 (PARP13/ZAP/ZC3HAV1) is an antiviral factor, active against specific RNA viruses such as MLV, SINV and HIV. During infection PARP13 binds viral RNA via its 4 CCCH-type zinc finger domains and targets it for degradation by recruiting cellular mRNA decay factors such as the exosome complex and XRN1. Here we show that PARP13 binds to and regulates cellular mRNA under physiological conditions. Knock-down of PARP13 via RNAi results in the misregulation of hundreds of transcripts with an enrichment in signal peptide containing proteins. Among the most upregulated transcripts is TRILR4

2014-11-13 | GSE56667 | GEO

[eCLIP] Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

Project description:[eCLIP] Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

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The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

Project description:The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

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Evidence for an RNAi-independent role of DICER-LIKE2 in conferring growth inhibition and basal antiviral resistance

Project description:Higher plants encode four or five DICER-LIKE (DCL) enzymes responsible for the production of small non-coding RNAs which function in RNA interference (RNAi). Different RNAi pathways in plants effect transposon silencing, antiviral defense and endogenous gene regulation. DCL2 acts genetically redundantly with DCL4 to confer basal antiviral defense, but in other settings, DCL2 has the opposite function of DCL4, at least in formal genetic terms. For example, knockout of DCL4 causes growth defects that are suppressed by inactivation of DCL2. Current models maintain that the biochemical basis of both of these effects is RNAi via DCL2-dependent small interfering RNAs (siRNAs). Here, we report that neither DCL2-mediated antiviral resistance nor growth defects can be explained by silencing effects of DCL2-dependent siRNAs. Both functions are defective in genetic backgrounds that maintain high levels of DCL2-dependent siRNAs, either through specific point mutations in DCL2 or simply by reducing DCL2 dosage in plants heterozygous for dcl2 knockout alleles. Intriguingly, however, all functions of DCL2 depend on it having some level of catalytic activity. We discuss this requirement for catalytic activity, but not for the resulting siRNAs, in the light of recent findings that reveal a function of DCL2 in activation of innate immunity in response to cytoplasmic double-stranded RNA.

2024-07-26 | PXD046163 | panorama

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