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The molecular dissection of TRIM25‘s RNA-binding mechanism provides key insights into its antiviral activity

ABSTRACT: The molecular dissection of TRIM25‘s RNA-binding mechanism provides key insights into its antiviral activity

PROVIDER: PRJNA1157421 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30558032.fastq.gz	Fastqsanger.gz
	SRR30558033.fastq.gz	Fastqsanger.gz
	SRR30558034.fastq.gz	Fastqsanger.gz
	SRR30558035.fastq.gz	Fastqsanger.gz
	SRR30558036.fastq.gz	Fastqsanger.gz

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The molecular dissection of TRIM25‘s RNA-binding mechanism provides key insights into its antiviral activity

Project description:TRIM25 is an RNA-binding ubiquitin E3 ligase with central but poorly understood roles in the innate immune response to RNA viruses. The link between TRIM25’s RNA binding and its role in innate immunity has not been established. Thus, we utilized a multitude of biophysical techniques to identify key RNA-binding residues of TRIM25 and developed an RNA-binding deficient mutant (TRIM25-m9). Using iCLIP2 in virus-infected and uninfected cells, we identified TRIM25’s RNA sequence and structure specificity, that it binds specifically to viral RNA, and that the interaction with RNA is critical for its antiviral activity.

2024-09-20 | GSE276465 | GEO

The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity.

Project description:TRIM25 is an RNA-binding ubiquitin E3 ligase with central but poorly understood roles in the innate immune response to RNA viruses. The link between TRIM25's RNA binding and its role in innate immunity has not been established. Thus, we utilized a multitude of biophysical techniques to identify key RNA-binding residues of TRIM25 and developed an RNA-binding deficient mutant (TRIM25-m9). Using iCLIP2 in virus-infected and uninfected cells, we identified TRIM25's RNA sequence and structure specificity, that it binds specifically to viral RNA, and that the interaction with RNA is critical for its antiviral activity.

| S-EPMC11445558 | biostudies-literature

Substrate trapping approach identifies TRIM25 ubiquitination targets involved in diverse cellular and antiviral processes

Project description:The tripartite motif (TRIM) family of E3 ubiquitin ligases is well known for its roles in antiviral restriction and innate immunity regulation, in addition to many other cellular pathways. In particular, TRIM25-mediated ubiquitination affects both carcinogenesis and antiviral response. While individual substrates have been identified for TRIM25, it remains unclear how it regulates diverse processes. Here we characterized a mutation, R54P, critical for TRIM25 catalytic activity, which we successfully utilized to “trap” substrates. We demonstrated that TRIM25 targets proteins implicated in stress granule formation (G3BP1/2), nonsense-mediated mRNA decay (UPF1), and nucleoside synthesis (NME1). R54P abolishes TRIM25 inhibition of alphaviruses independently of the host interferon response, suggesting that this antiviral effect is a direct consequence of ubiquitination. Consistent with that, we observed diminished antiviral activity upon knockdown of several TRIM25-R54P specific interactors including NME1. Our findings highlight that multiple substrates mediate the cellular and antiviral activities of TRIM25, illustrating the multi-faceted role of this ubiquitination network in diverse biological processes.

2022-08-02 | PXD034024 | Pride

TRIM25

Project description:TRIM25

| PRJNA316328 | ENA

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

The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response

Project description:In this study, we employed a combination of RIP-seq and iCLIP-seq technologies to identify long non-coding RNA associated with cytoplasmic TRIM25 and RIG-I protein in mouse macrophages cells.

2019-03-12 | GSE112175 | GEO

Somatic reprogramming of pteropus bat cells provides new insights in bat antiviral response

Project description:Somatic reprogramming of pteropus bat cells provides new insights in bat antiviral response

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The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response

Project description:The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response

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Exogenous RNA surveillance by proton-sensing TRIM25

Project description:Exogenous mRNAs require cellular machinery for delivery and translation but also encounter inhibitory factors. To investigate their regulation, we performed genome-wide CRISPR screens with in vitro-transcribed mRNAs in lipid nanoparticles (LNPs). Heparan sulfate proteoglycans and vacuolar ATPase were identified as mediators of LNP uptake and endosomal escape, respectively. TRIM25 emerged as a key suppressor inducing turnover of both linear and circular mRNAs. Endoribonucleases, N4BP1 and KHNYN, along with ZAP, act redundantly in TRIM25-dependent surveillance. TRIM25 specifically targets mRNAs delivered via endosomes, and its RNA affinity increases at acidic pH, suggesting activation by protons released from ruptured endosomes. N1-methylpseudouridine (m1Ψ) modification reduces TRIM25’s RNA binding, helping RNAs evade its suppressive effect. This study comprehensively maps cellular pathways regulating LNP-mRNAs, offering insights into RNA immunity and therapeutics.

2025-04-04 | GSE264535 | GEO

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Project description:TRIM25 E3 ubiquitin ligase is a new RNA-binding protein. We present the first high-throughput analysis of the molecular interactomes of TRIM25. We show that TRIM25 is a bona fide RNA-binding protein that interacts with numerous coding and non-coding transcripts. This suggests that TRIM25 could play a role in the regulation of RNA metabolism.

2018-07-27 | GSE104949 | GEO

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