title: Core binding factor (CBF) is required for Epstein-Barr virus EBNA3 proteins to regulate target gene expression.
abstract: ChIP-seq performed on lymphoblastoid cell lines (LCLs), expressing epitope-tagged EBNA3A, EBNA3B or EBNA3C from EBV-recombinants, revealed important principles of EBNA3 binding to chromatin. When combined with global chromatin looping data, EBNA3-bound loci were found to have a singular character, each directly associating with either EBNA3-repressed or EBNA3-activated genes, but not with both. EBNA3A and EBNA3C showed significant association with repressed and activated genes. Significant direct association for EBNA3B loci could only be shown with EBNA3B-repressed genes. A comparison of EBNA3 binding sites with known transcription factor binding sites in LCL GM12878 revealed substantial co-localization of EBNA3s with RUNX3-a protein induced by EBV during B cell transformation. The beta-subunit of core binding factor (CBFβ), that heterodimerizes with RUNX3, could co-immunoprecipitate robustly EBNA3B and EBNA3C, but only weakly EBNA3A. Depletion of either RUNX3 or CBFβ with lentivirus-delivered shRNA impaired epitope-tagged EBNA3B and EBNA3C binding at multiple regulated gene loci, indicating a requirement for CBF heterodimers in EBNA3 recruitment during target-gene regulation. ShRNA-mediated depletion of CBFβ in an EBNA3C-conditional LCL confirmed the role of CBF in the regulation of EBNA3C-induced and -repressed genes. These results reveal an important role for RUNX3/CBF during B cell transformation and EBV latency that was hitherto unexplored.
authors.affiliation: Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK.
authors.forename: Kostas
authors.initials: K
authors.lastname: Paschos
authors.affiliation: Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Bazot
authors.affiliation: Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK.
authors.forename: Guiyi
authors.initials: G
authors.lastname: Ho
authors.affiliation: Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK.
authors.forename: Gillian A
authors.initials: GA
authors.lastname: Parker
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Lees
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK.
authors.forename: Geraint
authors.initials: G
authors.lastname: Barton
authors.affiliation: Molecular Virology, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Allday
mesh_terms: D001665:Binding Sites; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D050677:Core Binding Factor Alpha 3 Subunit / Q000378:metabolism / Q000502:physiology; D050658:Core Binding Factor beta Subunit / Q000378:metabolism; D050660:Core Binding Factors / Q000378:metabolism* / Q000502:physiology; D004742:Enhancer Elements, Genetic; D019309:Epstein-Barr Virus Nuclear Antigens / Q000378:metabolism*; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D002843:Chromatin; D050677:Core Binding Factor Alpha 3 Subunit; D050658:Core Binding Factor beta Subunit; D050660:Core Binding Factors; C508151:EBNA-3A antigen; C422762:EBNA-3B antigen; C498774:EBNA-3C, epstein-barr virus; D019309:Epstein-Barr Virus Nuclear Antigens; D014157:Transcription Factors