RNA families in Epstein–Barr virus

Moss, William C.; Lee, Nara; Pimienta, Genaro; Steitz, Joan A.

doi:10.4161/rna.27488

Cited by 51 publications

(58 citation statements)

References 69 publications

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“…3B) (23). The large hairpin is part of an extensively structured RNA predicted throughout the long W repeat intron which was similarly suggested to be an independent sisRNA (24). In all type III or type III-like latency cell lines, we noted marked coverage across most of the intronic regions of the BamHI W repeat sequences although the levels in the Namalwa cell line were found to be low ( Fig.…”

Section: Resultsmentioning

confidence: 70%

High-Throughput RNA Sequencing-Based Virome Analysis of 50 Lymphoma Cell Lines from the Cancer Cell Line Encyclopedia Project

Cao¹,

Strong²,

Wang³

et al. 2015

J Virol

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Using high-throughput RNA sequencing data from 50 common lymphoma cell culture models from the Cancer Cell Line Encyclopedia project, we performed an unbiased global interrogation for the presence of a panel of 740 viruses and strains known to infect human and other mammalian cells. This led to the findings of previously identified infections by Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV), and human T-lymphotropic virus type 1 (HTLV-1). In addition, we also found a previously unreported infection of one cell line (DEL) with a murine leukemia virus. High expression of murine leukemia virus (MuLV) transcripts was observed in DEL cells, and we identified four transcriptionally active integration sites, one being in the TNFRSF6B gene. We also found low levels of MuLV reads in a number of other cell lines and provided evidence suggesting crosscontamination during sequencing. Analysis of HTLV-1 integrations in two cell lines, HuT 102 and MJ, identified 14 and 66 transcriptionally active integration sites with potentially activating integrations in immune regulatory genes, including interleukin-15 (IL-15), IL-6ST, STAT5B, HIVEP1, and IL-9R. Although KSHV and EBV do not typically integrate into the genome, we investigated a previously identified integration of EBV into the BACH2 locus in Raji cells. This analysis identified a BACH2 disruption mechanism involving splice donor sequestration. Through viral gene expression analysis, we detected expression of stable intronic RNAs from the EBV BamHI W repeats that may be part of long transcripts spanning the repeat region. We also observed transcripts at the EBV vIL-10 locus exclusively in the Hodgkin's lymphoma cell line, Hs 611.T, the expression of which were uncoupled from other lytic genes. Assessment of the KSHV viral transcriptome in BCP-1 cells showed expression of the viral immune regulators, K2/vIL-6, K4/vIL-8-like vCCL1, and K5/E2-ubiquitin ligase 1 that was significantly higher than expression of the latency-associated nuclear antigen. Together, this investigation sheds light into the virus composition across these lymphoma model systems and provides insights into common viral mechanistic principles. IMPORTANCEViruses cause cancer in humans. In lymphomas the Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV) and human T-lymphotropic virus type 1 are major contributors to oncogenesis. We assessed virus-host interactions using a high throughput sequencing method that facilitates the discovery of new virus-host associations and the investigation into how the viruses alter their host environment. We found a previously unknown murine leukemia virus infection in one cell line. We identified cellular genes, including cytokine regulators, that are disrupted by virus integration, and we determined mechanisms through which virus integration causes deregulation of cellular gene expression. Investigation into the KSHV transcriptome in the BCP-1 cell line revealed high-level expression of immune signaling genes. EBV transcriptome analysis sh...

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Section: Resultsmentioning

confidence: 70%

High-Throughput RNA Sequencing-Based Virome Analysis of 50 Lymphoma Cell Lines from the Cancer Cell Line Encyclopedia Project

Cao¹,

Strong²,

Wang³

et al. 2015

J Virol

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“…The observed lack of correlation between editing efficiency and ADAR expression suggests that other cellular mechanisms may be involved in the determination of RNA editing patterns. Recently, proteins that act as positive and negative regulators of ADAR2 editing activity have been identified which are thought to act by affecting ADAR2 subcellular localization and stability (Garncarz et al, 2013; Marcucci et al, 2011; Tariq et al, 2013). ADAR1 is modified by sumoylation, resulting in decreased activity in vitro (Desterro et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Reovirus-mediated induction of ADAR1 (p150) minimally alters RNA editing patterns in discrete brain regions

Hood

Morabito

Martínez

et al. 2014

Molecular and Cellular Neuroscience

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Transcripts encoding ADAR1, a double-stranded, RNA-specific adenosine deaminase involved in the adenosine-to-inosine (A-to-I) editing of mammalian RNAs, can be alternatively spliced to produce an interferon-inducible protein isoform (p150) that is up-regulated in both cell culture and in vivo model systems in response to pathogen or interferon stimulation. In contrast to other tissues, p150 is expressed at extremely low levels in the brain and it is unclear what role, if any, this isoform may play in the innate immune response of the central nervous system (CNS) or whether the extent of editing for RNA substrates critical for CNS function is affected by its induction. To investigate the expression of ADAR1 isoforms in response to viral infection and subsequent alterations in A-to-I editing profiles for endogenous ADAR targets, we used a neuro-tropic strain of reovirus to infect neonatal mice and quantify A-to-I editing in discrete brain regions using a multiplexed, high-throughput sequencing strategy. While intracranial injection of reovirus resulted in a widespread increase in the expression of ADAR1 (p150) in multiple brain regions and peripheral organs, significant changes in site-specific A-to-I conversion were quite limited, suggesting that steady-state levels of p150 expression are not a primary determinant for modulating the extent of editing for numerous ADAR targets in vivo.

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“…2D). Although Sm protein is abundant in nucleus, it does not bind EBER2, which lacks an Sm protein-binding site (Moss et al 2014). Thus, a robust RNA-PLA signal requires coexpression of the interacting protein and its target RNA, as well as the use of an antisense RNA-PLA oligonucleotide probe.…”

Section: Detection Of Complexes Between Proteins and Small Nuclear Rnasmentioning

confidence: 99%

A proximity-dependent assay for specific RNA–protein interactions in intact cells

Zhang

Xie

Shu

et al. 2016

RNA

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The proximity ligation assay (PLA) is an immune staining method that detects protein-protein interactions in fixed cells. We describe here RNA-PLA, a simple adaptation of this technology that allows the detection of specific RNA-protein interactions in fixed cells by using a DNA oligonucleotide that hybridizes to a target RNA in combination with an antibody that recognizes the protein bound to the target RNA. Stable and transient RNA-protein interactions can be readily detected by generation of a fluorescent signal in discrete compartments in intact fixed cells with high specificity. We demonstrate that this approach requires the colocalization of the binding protein and its RNA target in the same cellular compartment, use of an oligonucleotide complementary to the target RNA, and the presence of a binding site for the protein in the target RNA.

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RNA families in Epstein–Barr virus

Abstract: OverviewEpstein-Barr virus (EBV), a human γ-herpesvirus (Fig. 1), is widely dispersed (infecting as many as 95% of humans)

Cited by 51 publications

References 69 publications

High-Throughput RNA Sequencing-Based Virome Analysis of 50 Lymphoma Cell Lines from the Cancer Cell Line Encyclopedia Project

High-Throughput RNA Sequencing-Based Virome Analysis of 50 Lymphoma Cell Lines from the Cancer Cell Line Encyclopedia Project

Reovirus-mediated induction of ADAR1 (p150) minimally alters RNA editing patterns in discrete brain regions

A proximity-dependent assay for specific RNA–protein interactions in intact cells

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