title: Epstein-Barr Virus Nuclear Antigen 3 (EBNA3) Proteins Regulate EBNA2 Binding to Distinct RBPJ Genomic Sites.
abstract: Latent infection of B lymphocytes by Epstein-Barr virus (EBV) in vitro results in their immortalization into lymphoblastoid cell lines (LCLs); this latency program is controlled by the EBNA2 viral transcriptional activator, which targets promoters via RBPJ, a DNA binding protein in the Notch signaling pathway. Three other EBNA3 proteins (EBNA3A, EBNA3B, and EBNA3C) interact with RBPJ to regulate cell gene expression. The mechanism by which EBNAs regulate different genes via RBPJ remains unclear. Our chromatin immunoprecipitation with deep sequencing (ChIP-seq) analysis of the EBNA3 proteins analyzed in concert with prior EBNA2 and RBPJ data demonstrated that EBNA3A, EBNA3B, and EBNA3C bind to distinct, partially overlapping genomic locations. Although RBPJ interaction is critical for EBNA3A and EBNA3C growth effects, only 30 to 40% of EBNA3-bound sites colocalize with RBPJ. Using LCLs conditional for EBNA3A or EBNA3C activity, we demonstrate that EBNA2 binding at sites near EBNA3A- or EBNA3C-regulated genes is specifically regulated by the respective EBNA3. To investigate EBNA3 binding specificity, we identified sequences and transcription factors enriched at EBNA3A-, EBNA3B-, and EBNA3C-bound sites. This confirmed the prior observation that IRF4 is enriched at EBNA3A- and EBNA3C-bound sites and revealed IRF4 enrichment at EBNA3B-bound sites. Using IRF4-negative BJAB cells, we demonstrate that IRF4 is essential for EBNA3C, but not EBNA3A or EBNA3B, binding to specific sites. These results support a model in which EBNA2 and EBNA3s compete for distinct subsets of RBPJ sites to regulate cell genes and where EBNA3 subset specificity is determined by interactions with other cell transcription factors.
  
  
  OBJECTIVE
  Epstein-Barr virus (EBV) latent gene products cause human cancers and transform B lymphocytes into immortalized lymphoblastoid cell lines in vitro. EBV nuclear antigens (EBNAs) and membrane proteins constitutively activate pathways important for lymphocyte growth and survival. An important unresolved question is how four different EBNAs (EBNA2, -3A, -3B, and -3C) exert unique effects via a single transcription factor, RBPJ. Here, we report that each EBNA binds to distinct but partially overlapping sets of genomic sites. EBNA3A and EBNA3C specifically regulate EBNA2's access to different RBPJ sites, providing a mechanism by which each EBNA can regulate distinct cell genes. We show that IRF4, an essential regulator of B cell differentiation, is critical for EBNA3C binding specificity; EBNA3A and EBNA3B specificities are likely due to interactions with other cell transcription factors. EBNA3 titration of EBNA2 transcriptional function at distinct sites likely limits cell defenses that would be triggered by unchecked EBNA2 prooncogenic activity.
authors.affiliation: Department of Medicine and Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA.
authors.forename: Anqi
authors.initials: A
authors.lastname: Wang
authors.affiliation: Department of Statistics, University of Wisconsin, Madison, Wisconsin, USA.
authors.forename: Rene
authors.initials: R
authors.lastname: Welch
authors.affiliation: Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhao
authors.affiliation: Department of Statistics, University of Wisconsin, Madison, Wisconsin, USA.
authors.forename: Tram
authors.initials: T
authors.lastname: Ta
authors.affiliation: Department of Statistics, University of Wisconsin, Madison, Wisconsin, USA Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, USA.
authors.forename: Sündüz
authors.initials: S
authors.lastname: Keleş
authors.affiliation: Department of Medicine and Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, USA ejohannsen@medicine.wisc.edu.
authors.forename: Eric
authors.initials: E
authors.lastname: Johannsen
mesh_terms: D002460:Cell Line; D002472:Cell Transformation, Viral; D047369:Chromatin Immunoprecipitation; D019309:Epstein-Barr Virus Nuclear Antigens / Q000378:metabolism*; D005786:Gene Expression Regulation; D004854:Herpesvirus 4, Human / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D006801:Humans; D051819:Immunoglobulin J Recombination Signal Sequence-Binding Protein / Q000378:metabolism*; D008954:Models, Biological; D011485:Protein Binding; D014764:Viral Proteins / Q000378:metabolism*; D017735:Virus Latency
chemical_list: C402641:EBNA-2 protein, Human herpesvirus 4; C508151:EBNA-3A antigen; C422762:EBNA-3B antigen; C498774:EBNA-3C, epstein-barr virus; D019309:Epstein-Barr Virus Nuclear Antigens; D051819:Immunoglobulin J Recombination Signal Sequence-Binding Protein; C497570:RBPJ protein, human; D014764:Viral Proteins