The Epstein-Barr Virus Regulome in Lymphoblastoid Cells

Sizun Jiang; Hufeng Zhou; Jun Liang; Catherine Gerdt; Chong Wang; Liangru Ke; Stefanie C S Schmidt; Yohei Narita; Yijie Ma; Shuangqi Wang; Tyler Colson; Benjamin Gewurz; Guoliang Li; Elliott Kieff; Bo Zhao

doi:10.1016/j.chom.2017.09.001

The Epstein-Barr Virus Regulome in Lymphoblastoid Cells

Cell Host Microbe. 2017 Oct 11;22(4):561-573.e4. doi: 10.1016/j.chom.2017.09.001.

Authors

Affiliations

¹ Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
² Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
³ Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen Cancer Center, Sun Yat-Sen University, Guangzhou 510060, China.
⁴ National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
⁵ Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: [email protected].
⁶ Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address: [email protected].

Abstract

Epstein-Barr virus (EBV) transforms B cells to continuously proliferating lymphoblastoid cell lines (LCLs), which represent an experimental model for EBV-associated cancers. EBV nuclear antigens (EBNAs) and LMP1 are EBV transcriptional regulators that are essential for LCL establishment, proliferation, and survival. Starting with the 3D genome organization map of LCL, we constructed a comprehensive EBV regulome encompassing 1,992 viral/cellular genes and enhancers. Approximately 30% of genes essential for LCL growth were linked to EBV enhancers. Deleting EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets included MCL1, IRF4, and EBF. MYC ESE looping to the transcriptional stat site of MYC was dependent on EBNAs. Deleting MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study provides a comprehensive view of the spatial organization of chromatin during EBV-driven cellular transformation.

Keywords: CDKN2A/B; ChIA-PET; EBV regulome; EBV super-enhancers; Epstein-Barr virus; MYC.

MeSH terms

B-Lymphocytes / virology*
Cell Line
Chromatin / virology*
Cyclin-Dependent Kinase Inhibitor p15 / genetics
Cyclin-Dependent Kinase Inhibitor p15 / metabolism
Cyclin-Dependent Kinase Inhibitor p16
Cyclin-Dependent Kinase Inhibitor p18 / genetics
Cyclin-Dependent Kinase Inhibitor p18 / metabolism
Epstein-Barr Virus Nuclear Antigens / genetics
Epstein-Barr Virus Nuclear Antigens / metabolism
Herpesvirus 4, Human / genetics*
Host-Pathogen Interactions*
Humans
Interferon Regulatory Factors / genetics
Interferon Regulatory Factors / metabolism
Myeloid Cell Leukemia Sequence 1 Protein / genetics
Myeloid Cell Leukemia Sequence 1 Protein / metabolism
Primary Cell Culture
Proto-Oncogene Proteins c-myc / genetics
Proto-Oncogene Proteins c-myc / metabolism
Trans-Activators / genetics
Trans-Activators / metabolism
Viral Matrix Proteins / genetics
Viral Matrix Proteins / metabolism

Substances

CDKN2A protein, human
CDKN2B protein, human
Chromatin
Cyclin-Dependent Kinase Inhibitor p15
Cyclin-Dependent Kinase Inhibitor p16
Cyclin-Dependent Kinase Inhibitor p18
EBF1 protein, human
EBV-associated membrane antigen, Epstein-Barr virus
Epstein-Barr Virus Nuclear Antigens
Interferon Regulatory Factors
MCL1 protein, human
MYC protein, human
Myeloid Cell Leukemia Sequence 1 Protein
Proto-Oncogene Proteins c-myc
Trans-Activators
Viral Matrix Proteins
interferon regulatory factor-4

Abstract

MeSH terms

Substances

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