The zinc finger antiviral protein ZAP destabilises viral transcripts and restricts human cytomegalovirus

Gonzalez-Perez, Ana Cristina; Stempel, Markus; Wyler, Emanuel; Urban, Christian; Piras, Antonio; Hennig, Thomas; Heim, Albert; Landthaler, Markus; Pichlmair, Andreas; Erhard, Florian; Dölken, Lars; Brinkmann, Melanie M.

doi:10.1101/2020.09.15.297804

Cited by 3 publications

(3 citation statements)

References 85 publications

(110 reference statements)

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“…In epithelial cell lines, ATXN2L regulates stress granules and processing bodies (48). ZC3HAV1 destabilizes IFNB and IFNL3 mRNAs in hepatocytes and human cytomegalovirus RNA in fibroblasts and inhibits programmed ribosomal frameshifting of the SARS-CoV-2 virus (49)(50)(51).…”

Section: Discussionmentioning

confidence: 99%

Time-dependent regulation of cytokine production by RNA binding proteins defines T cell effector function

Popović

Guislain

Engels

et al. 2021

Preprint

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SummaryEffective T cell responses against target cells require controlled production of the key pro-inflammatory cytokines IFN-γ, TNF and IL-2. Post-transcriptional events determine the magnitude and duration of cytokine production in T cells, a process that is largely regulated by RNA binding proteins (RBPs). Here we studied the identity and mode of action of RBPs interacting with cytokine mRNAs. With an RNA aptamer-based capture assay from human T cell lysates, we identified >130 RBPs interacting with the full length 3’untranslated regions of IFNG, TNF and IL2. The RBP landscape altered upon T cell activation. Furthermore, RBPs display temporal activity profiles to control cytokine production. Whereas HuR promotes early cytokine production, the peak production levels and response duration is controlled by ZFP36L1, ATXN2L and ZC3HAV1. Importantly, ZFP36L1 deletion boosts T cell responses against tumors in vivo, revealing the potential of the RBP map to identify critical modulators of T cell responses.

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Section: Discussionmentioning

confidence: 99%

Time-dependent regulation of cytokine production by RNA binding proteins defines T cell effector function

Popović

Guislain

Engels

et al. 2021

Preprint

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“…Samples were harvested by resuspension in Trizol (Thermo Fisher Scientific). RNA extraction, library preparation, total RNA sequencing and data processing were performed as previously described (Gonzalez-Perez et al, 2021). Splice junctions were identified using Geneious Prime software.…”

Section: Methodsmentioning

confidence: 99%

“…Transcriptomic and proteomic studies have provided a comprehensive picture of the viral gene expression program (Gatherer et al, 2011;Gonzalez-Perez et al, 2021;Marcinowski et al, 2012;Stern-Ginossar et al, 2012;Tirosh et al, 2015;Weekes et al, 2014). This has been complemented by global assessment of virus-virus and virus-host protein interactions (Hernández Durán et al, 2019;Nobre et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Engineering, Decoding and Systems-Level Characterization of Chimpanzee Cytomegalovirus

Phan

Bogdanow

Wyler

et al. 2021

Preprint

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The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome (BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the transcriptome and proteome of infected cells and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of CCMV gene expression and found that viral proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMV's cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.

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SHIFTR enables the unbiased and multiplexed identification of proteins bound to specific RNA regions in live cells

Aydin,

Gabel,

Zielinski

et al. 2023

Preprint

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RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNaseH-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures close to zero background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions ofcis-regulatory elements located at the 5ʹ and 3ʹ- terminal regions of the authentic SARS-CoV-2 RNA genome in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.

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The zinc finger antiviral protein ZAP destabilises viral transcripts and restricts human cytomegalovirus

Cited by 3 publications

References 85 publications

Time-dependent regulation of cytokine production by RNA binding proteins defines T cell effector function

Time-dependent regulation of cytokine production by RNA binding proteins defines T cell effector function

Engineering, Decoding and Systems-Level Characterization of Chimpanzee Cytomegalovirus

SHIFTR enables the unbiased and multiplexed identification of proteins bound to specific RNA regions in live cells

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