Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)

Background: Infection with the Epstein-Barr virus (EBV) is associated with an increased risk of multiple sclerosis (MS). Objective: We sought genetic loci influencing EBV nuclear antigen-1 (EBNA-1) IgG titers and hypothesized that they may play a role in MS risk. Methods: We performed a genome-wide association study (GWAS) of anti-EBNA-1 IgG titers in 3599 individuals from an unselected twin family cohort, followed by a meta-analysis with data from an independent EBNA-1 GWAS. We then examined the shared polygenic risk between the EBNA-1 GWAS (effective sample size ( Neff) = 5555) and a large MS GWAS ( Neff = 15,231). Results: We identified one locus of strong association within the human leukocyte antigen (HLA) region, of which the most significantly associated genotyped single nucleotide polymorphism (SNP) was rs2516049 ( p = 4.11 × 10−9). A meta-analysis including data from another EBNA-1 GWAS in a cohort of Mexican-American families confirmed that rs2516049 remained the most significantly associated SNP ( p = 3.32 × 10−20). By examining the shared polygenic risk, we show that the genetic risk for elevated anti-EBNA-1 titers is positively correlated with the development of MS, and that elevated EBNA-1 titers are not an epiphenomena secondary to MS. In the joint meta-analysis of EBNA-1 titers and MS, loci at 1p22.1, 3p24.1, 3q13.33, and 10p15.1 reached genome-wide significance ( p < 5 × 10−8). Conclusions: Our results suggest that apart from the confirmed HLA region, the association of anti-EBNA-1 IgG titer with MS risk is also mediated through non-HLA genes, and that studies aimed at identifying genetic loci influencing EBNA immune response provides a novel opportunity to identify new and characterize existing genetic risk factors for MS.

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Epstein-Barr Virus Nuclear Antigen 3C Activates the Latent Membrane Protein 1 Promoter in the Presence of Epstein-Barr Virus Nuclear Antigen 2 through Sequences Encompassing an Spi-1/Spi-B Binding Site

Journal of Virology ◽

10.1128/jvi.74.11.5151-5160.2000 ◽

2000 ◽

Vol 74 (11) ◽

pp. 5151-5160 ◽

Cited By ~ 81

Author(s):

Bo Zhao ◽

Clare E. Sample

Keyword(s):

Dna Binding ◽

Binding Site ◽

Binding Sites ◽

Epstein Barr Virus ◽

Latent Membrane Protein ◽

Nuclear Antigen ◽

Latent Membrane Protein 1 ◽

Barr Virus ◽

Epstein Barr

ABSTRACT The Epstein-Barr virus (EBV) nuclear antigen 3C (EBNA-3C) protein is a transcriptional regulator of viral and cellular genes that is essential for EBV-mediated immortalization of B lymphocytes in vitro. EBNA-3C can inhibit transcription through an association with the cellular DNA-binding protein Jκ, a function shared by EBNA-3A and EBNA-3B. Here, we report a mechanism by which EBNA-3C can activate transcription from the EBV latent membrane protein 1 (LMP-1) promoter in conjunction with EBNA-2. Jκ DNA-binding sites were not required for this activation, and a mutant EBNA-3C protein unable to bind Jκ activated transcription as efficiently as wild-type EBNA-3C, indicating that EBNA-3C can regulate transcription through a mechanism that is independent of Jκ. Furthermore, activation of the LMP-1 promoter is a unique function of EBNA-3C, not shared by EBNA-3A and EBNA-3B. The DNA element through which EBNA-3C activates the LMP-1 promoter includes a Spi-1/Spi-B binding site, previously characterized as an important EBNA-2 response element. Although this element has considerable homology to mouse immunoglobulin light chain promoter sequences to which the mouse homologue of Spi-1 binds with its dimerization partner IRF4, we demonstrate that the IRF4-like binding sites in the LMP-1 promoter do not play a role in EBNA-3C-mediated activation. Both EBNA-2 and EBNA-3C were required for transcription mediated through a 41-bp region of the LMP-1 promoter encompassing the Spi binding site. However, EBNA-3C had no effect on transcription mediated in conjunction with the EBNA-2 activation domain fused to the GAL4 DNA-binding domain, suggesting that it does not function as an adapter between EBNA-2 and the cellular transcriptional machinery. Like EBNA-2, EBNA-3C bound directly to both Spi-1 and Spi-B in vitro. This interaction was mediated by a region of EBNA-3C encompassing a likely basic leucine zipper (bZIP) domain and the ets domain of Spi-1 or Spi-B, reminiscent of interactions between bZIP and ets domains of other transcription factors that result in their targeting to DNA. There are many examples of regulation of the hematopoietic-specific Spi transcription factors through protein-protein interactions, and a similar regulation by EBNA-3C, in conjunction with EBNA-2, is likely to be an important and unique contribution of EBNA-3C to EBV-mediated immortalization.

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Epstein–Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1422580112 ◽

2014 ◽

Vol 112 (2) ◽

pp. 554-559 ◽

Cited By ~ 31

Author(s):

Stefanie C. S. Schmidt ◽

Sizun Jiang ◽

Hufeng Zhou ◽

Bradford Willox ◽

Amy M. Holthaus ◽

...

Keyword(s):

Cell Proliferation ◽

B Cell ◽

Epstein Barr Virus ◽

Latent Infection ◽

Protein Complexes ◽

Nuclear Antigen ◽

Lymphoblastoid Cell Lines ◽

Barr Virus ◽

Genome Wide ◽

Epstein Barr

Epstein–Barr Virus (EBV) conversion of B-lymphocytes to Lymphoblastoid Cell Lines (LCLs) requires four EBV nuclear antigen (EBNA) oncoproteins: EBNA2, EBNALP, EBNA3A, and EBNA3C. EBNA2 and EBNALP associate with EBV and cell enhancers, up-regulate the EBNA promoter, MYC, and EBV Latent infection Membrane Proteins (LMPs), which up-regulate BCL2 to protect EBV-infected B-cells from MYC proliferation-induced cell death. LCL proliferation induces p16INK4A and p14ARF-mediated cell senescence. EBNA3A and EBNA3C jointly suppress p16INK4A and p14ARF, enabling continuous cell proliferation. Analyses of the EBNA3A human genome-wide ChIP-seq landscape revealed 37% of 10,000 EBNA3A sites to be at strong enhancers; 28% to be at weak enhancers; 4.4% to be at active promoters; and 6.9% to be at weak and poised promoters. EBNA3A colocalized with BATF-IRF4, ETS-IRF4, RUNX3, and other B-cell Transcription Factors (TFs). EBNA3A sites clustered into seven unique groups, with differing B-cell TFs and epigenetic marks. EBNA3A coincidence with BATF-IRF4 or RUNX3 was associated with stronger EBNA3A ChIP-Seq signals. EBNA3A was at MYC, CDKN2A/B, CCND2, CXCL9/10, and BCL2, together with RUNX3, BATF, IRF4, and SPI1. ChIP-re-ChIP revealed complexes of EBNA3A on DNA with BATF. These data strongly support a model in which EBNA3A is tethered to DNA through a BATF-containing protein complexes to enable continuous cell proliferation.

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Genome-wide analysis of Epstein-Barr virus (EBV) isolated from EBV-associated gastric carcinoma (EBVaGC)

Oncotarget ◽

10.18632/oncotarget.6751 ◽

2015 ◽

Vol 7 (4) ◽

pp. 4903-4914 ◽

Cited By ~ 29

Author(s):

Ying Liu ◽

Wenjun Yang ◽

Yaqi Pan ◽

Jiafu Ji ◽

Zheming Lu ◽

...

Keyword(s):

Gastric Carcinoma ◽

Epstein Barr Virus ◽

Genome Wide Analysis ◽

Barr Virus ◽

Genome Wide ◽

Epstein Barr

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Genome-wide Analysis of Epstein-Barr Virus (EBV) Integration and Strain in C666-1 and Raji Cells

Journal of Cancer ◽

10.7150/jca.13150 ◽

2016 ◽

Vol 7 (2) ◽

pp. 214-224 ◽

Cited By ~ 33

Author(s):

Kai Xiao ◽

Zhengyuan Yu ◽

Xiayu Li ◽

Xiaoling Li ◽

Ke Tang ◽

...

Keyword(s):

Epstein Barr Virus ◽

Raji Cells ◽

Genome Wide Analysis ◽

Barr Virus ◽

Genome Wide ◽

Epstein Barr

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The Replicator of the Epstein-Barr Virus Latent Cycle Origin of DNA Replication, oriP, Is Composed of Multiple Functional Elements

Journal of Virology ◽

10.1128/jvi.75.22.10582-10592.2001 ◽

2001 ◽

Vol 75 (22) ◽

pp. 10582-10592 ◽

Cited By ~ 23

Author(s):

Michelle D. Koons ◽

Sarah Van Scoy ◽

Janet Hearing

Keyword(s):

Binding Sites ◽

Epstein Barr Virus ◽

Protein S ◽

Virus Genome ◽

Nuclear Antigen ◽

Cell Protein ◽

Present Evidence ◽

Replication Assay ◽

Barr Virus ◽

Epstein Barr

ABSTRACT Replication of the Epstein-Barr virus genome initiates at one of several sites in latently infected, dividing cells. One of these replication origins is close to the viral DNA maintenance element, and, together, this replication origin and the maintenance element are referred to as oriP. The replicator oforiP contains four binding sites for Epstein-Barr virus nuclear antigen 1 (EBNA-1), the sole viral protein required for the replication and maintenance of oriP plasmids. We showed previously that these EBNA-1 sites function in pairs and that mutational inactivation of one pair does not eliminate replicator function. In this study we characterized the contribution of each EBNA-1 site within the replicator and flanking sequences through the use of an internally controlled replication assay. We present evidence that shows that all four EBNA-1 sites are required for anoriP plasmid to be replicated in every cell cycle. Results from these experiments also show that the paired EBNA-1 binding sites are not functionally equivalent and that the low affinity of sites 2 and 3 compared to that of sites 1 and 4 is not essential for replicator function. Our results suggest that a host cell protein(s) binds sequences flanking the EBNA-1 sites and that interactions between EBNA-1 and this protein(s) are critical for replicator function. Finally, we present evidence that shows that the minimal replicator oforiP consists of EBNA-1 sites 3 and 4 and two copies of a 14-bp repeat that is present in inverse orientation flanking these EBNA-1 sites. EBNA-1 sites 1 and 2, together with an element(s) within nucleotides 9138 to 9516, are ancillary elements required for full replicator activity.

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Interaction of the lymphocyte-derived Epstein-Barr virus nuclear antigen EBNA-1 with its DNA-binding sites.

Journal of Virology ◽

10.1128/jvi.63.1.101-110.1989 ◽

1989 ◽

Vol 63 (1) ◽

pp. 101-110 ◽

Cited By ~ 45

Author(s):

C H Jones ◽

S D Hayward ◽

D R Rawlins

Keyword(s):

Dna Binding ◽

Binding Sites ◽

Epstein Barr Virus ◽

Nuclear Antigen ◽

Barr Virus ◽

Dna Binding Sites ◽

Epstein Barr

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Identifying Sites Bound by Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) in the Human Genome: Defining a Position-Weighted Matrix To Predict Sites Bound by EBNA1 in Viral Genomes

Journal of Virology ◽

10.1128/jvi.01974-08 ◽

2009 ◽

Vol 83 (7) ◽

pp. 2930-2940 ◽

Cited By ~ 45

Author(s):

Lindsay R. Dresang ◽

David T. Vereide ◽

Bill Sugden

Keyword(s):

Dna Binding ◽

Human Genome ◽

Binding Sites ◽

Epstein Barr Virus ◽

Consensus Sequence ◽

Nuclear Antigen ◽

Barr Virus ◽

Dna Binding Sites ◽

Weighted Matrix ◽

Epstein Barr

ABSTRACT We identified binding sites for Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) in the human genome using chromatin immunoprecipitation and microarrays. The sequences for these newly identified sites were used to generate a position-weighted matrix (PWM) for EBNA1's DNA-binding sites. This PWM helped identify additional DNA-binding sites for EBNA1 in the genomes of EBV, Kaposi's sarcoma-associated herpesvirus, and cercopithecine herpesvirus 15 (CeHV-15) (also called herpesvirus papio 15). In particular, a homologue of the Rep* locus in EBV was predicted in the genome of CeHV-15, which is notable because Rep* of EBV was not predicted by the previously developed consensus sequence for EBNA1's binding DNA. The Rep* of CeHV-15 functions as an origin of DNA synthesis in the EBV-positive cell line Raji; this finding thus builds on a set of DNA-binding sites for EBNA1 predicted in silico.

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