title: Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A.
abstract: Epstein-Barr virus nuclear antigen 3C (EBNA3C) repression of CDKN2A p14(ARF) and p16(INK4A) is essential for immortal human B-lymphoblastoid cell line (LCL) growth. EBNA3C ChIP-sequencing identified >13,000 EBNA3C sites in LCL DNA. Most EBNA3C sites were associated with active transcription; 64% were strong H3K4me1- and H3K27ac-marked enhancers and 16% were active promoters marked by H3K4me3 and H3K9ac. Using ENCODE LCL transcription factor ChIP-sequencing data, EBNA3C sites coincided (±250 bp) with RUNX3 (64%), BATF (55%), ATF2 (51%), IRF4 (41%), MEF2A (35%), PAX5 (34%), SPI1 (29%), BCL11a (28%), SP1 (26%), TCF12 (23%), NF-κB (23%), POU2F2 (23%), and RBPJ (16%). EBNA3C sites separated into five distinct clusters: (i) Sin3A, (ii) EBNA2/RBPJ, (iii) SPI1, and (iv) strong or (v) weak BATF/IRF4. EBNA3C signals were positively affected by RUNX3, BATF/IRF4 (AICE) and SPI1/IRF4 (EICE) cooccupancy. Gene set enrichment analyses correlated EBNA3C/Sin3A promoter sites with transcription down-regulation (P < 1.6 × 10(-4)). EBNA3C signals were strongest at BATF/IRF4 and SPI1/IRF4 composite sites. EBNA3C bound strongly to the p14(ARF) promoter through SPI1/IRF4/BATF/RUNX3, establishing RBPJ-, Sin3A-, and REST-mediated repression. EBNA3C immune precipitated with Sin3A and conditional EBNA3C inactivation significantly decreased Sin3A binding at the p14(ARF) promoter (P < 0.05). These data support a model in which EBNA3C binds strongly to BATF/IRF4/SPI1/RUNX3 sites to enhance transcription and recruits RBPJ/Sin3A- and REST/NRSF-repressive complexes to repress p14(ARF) and p16(INK4A) expression.
authors.affiliation: Department of Medicine, Brigham and Women's Hospital, Program in Virology, Department of Microbiology and Immunobiology, and Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115.
authors.forename: Sizun
authors.initials: S
authors.lastname: Jiang
authors.forename: Bradford
authors.initials: B
authors.lastname: Willox
authors.forename: Hufeng
authors.initials: H
authors.lastname: Zhou
authors.forename: Amy M
authors.initials: AM
authors.lastname: Holthaus
authors.forename: Anqi
authors.initials: A
authors.lastname: Wang
authors.forename: Tommy T
authors.initials: TT
authors.lastname: Shi
authors.forename: Seiji
authors.initials: S
authors.lastname: Maruo
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.forename: Eric C
authors.initials: EC
authors.lastname: Johannsen
authors.forename: Elliott
authors.initials: E
authors.lastname: Kieff
authors.forename: Bo
authors.initials: B
authors.lastname: Zhao
mesh_terms: D020816:Amino Acid Motifs; D000956:Antigens, Viral / Q000737:chemistry*; D001402:B-Lymphocytes / Q000166:cytology / Q000821:virology*; D050976:Basic-Leucine Zipper Transcription Factors / Q000737:chemistry*; D001665:Binding Sites; D049109:Cell Proliferation; D047369:Chromatin Immunoprecipitation; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000378:metabolism*; D019309:Epstein-Barr Virus Nuclear Antigens; D005786:Gene Expression Regulation; D015972:Gene Expression Regulation, Neoplastic; D004854:Herpesvirus 4, Human / Q000378:metabolism; D006657:Histones / Q000737:chemistry; D006801:Humans; D050835:Interferon Regulatory Factors / Q000737:chemistry*; D008223:Lymphoma / Q000378:metabolism; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000737:chemistry*; D011994:Recombinant Proteins / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism*; D056264:Sin3 Histone Deacetylase and Corepressor Complex; D015534:Trans-Activators / Q000737:chemistry*; D025803:Tumor Suppressor Protein p14ARF / Q000378:metabolism; D000099232:Proto-Oncogene Protein Spi-1; D000099218:Interferon Regulatory Factor-4
chemical_list: D000956:Antigens, Viral; D050976:Basic-Leucine Zipper Transcription Factors; D019941:Cyclin-Dependent Kinase Inhibitor p16; D019309:Epstein-Barr Virus Nuclear Antigens; D006657:Histones; D050835:Interferon Regulatory Factors; D011518:Proto-Oncogene Proteins; D011994:Recombinant Proteins; D012097:Repressor Proteins; D056264:Sin3 Histone Deacetylase and Corepressor Complex; D015534:Trans-Activators; D025803:Tumor Suppressor Protein p14ARF; D000099232:Proto-Oncogene Protein Spi-1; D000099218:Interferon Regulatory Factor-4; C099359:BATF protein, human; C498774:EBNA-3C, epstein-barr virus; C099683:SIN3A transcription factor
keywords: EBV; lymphoma; resting B lymphocyte; tumor suppressor