title: Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines.
abstract: EBV nuclear antigen 3C (EBNA3C) is an essential transcription factor for EBV transformed lymphoblast cell line (LCL) growth. To identify EBNA3C-regulated genes in LCLs, microarrays were used to measure RNA abundances in each of three different LCLs that conditionally express EBNA3C fused to a 4-OH-Tamoxifen-dependent estrogen receptor hormone binding domain (EBNA3CHT). At least three RNAs were assayed for each EBNA3CHT LCL under nonpermissive conditions, permissive conditions, and nonpermissive conditions with wild-type EBNA3C transcomplementation. Using a two-way ANOVA model of EBNA3C levels, we identified 550 regulated genes that were at least 1.5-fold up- or down-regulated with false discovery rates < 0.01. EBNA3C-regulated genes overlapped significantly with genes regulated by EBNA2 and EBNA3A consistent with coordinated effects on cell gene transcription. Of the 550 EBNA3C-regulated genes, 106 could be placed in protein networks. A seeded Bayesian network analysis of the 80 most significant EBNA3C-regulated genes suggests that RAC1, LYN, and TNF are upstream of other EBNA3C-regulated genes. Gene set enrichment analysis found enrichment for MAP kinase signaling, cytokine-cytokine receptor interactions, JAK-STAT signaling, and cell adhesion molecules, implicating these pathways in EBNA3C effects on LCL growth or survival. EBNA3C significantly up-regulated the CXCL12 ligand and its CXCR4 receptor and increased LCL migration. CXCL12 up-regulation depended on EBNA3C's interaction with the cell transcription factor, RBPJ, which is essential for LCL growth. EBNA3C also up-regulated MYC 1.3-fold and down-regulated CDKN2A exons 2 and 3, shared by p16 and p14, 1.4-fold, with false discovery rates < 5 × 10(-4).
authors.affiliation: Department of Medicine and Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhao
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Mar
authors.forename: Seiji
authors.initials: S
authors.lastname: Maruo
authors.forename: Sungwook
authors.initials: S
authors.lastname: Lee
authors.forename: Benjamin E
authors.initials: BE
authors.lastname: Gewurz
authors.forename: Eric
authors.initials: E
authors.lastname: Johannsen
authors.forename: Kristina
authors.initials: K
authors.lastname: Holton
authors.forename: Renee
authors.initials: R
authors.lastname: Rubio
authors.forename: Kenzo
authors.initials: K
authors.lastname: Takada
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Elliott
authors.initials: E
authors.lastname: Kieff
mesh_terms: D000704:Analysis of Variance; D000956:Antigens, Viral / Q000378:metabolism*; D001499:Bayes Theorem; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019309:Epstein-Barr Virus Nuclear Antigens; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D005796:Genes / Q000235:genetics*; D006801:Humans; D051819:Immunoglobulin J Recombination Signal Sequence-Binding Protein / Q000378:metabolism; D008213:Lymphocyte Activation; D046228:Microarray Analysis; D011960:Receptors, Estrogen / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D000956:Antigens, Viral; C498774:EBNA-3C, epstein-barr virus; D019309:Epstein-Barr Virus Nuclear Antigens; D051819:Immunoglobulin J Recombination Signal Sequence-Binding Protein; C497570:RBPJ protein, human; D011960:Receptors, Estrogen; D014157:Transcription Factors