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Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress

Sizun Jiang1, Bradford Willox, Hufeng Zhou

  • 1Department 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.

Proceedings of the National Academy of Sciences of the United States of America
|December 18, 2013
PubMed

Insights

Epstein-Barr virus nuclear antigen 3C (EBNA3C) binds to specific DNA sites, including the p14ARF promoter, to repress CDKN2A gene expression. This repression is crucial for the growth of immortalized human B-lymphoblastoid cell lines.

Area of Science:

  • Virology
  • Molecular Biology
  • Epigenetics

Background:

  • Epstein-Barr virus nuclear antigen 3C (EBNA3C) is a key viral protein essential for the transformation of B-lymphocytes.
  • EBNA3C's role in repressing CDKN2A genes (p14ARF and p16INK4A) is critical for the immortalization of human B-lymphoblastoid cell lines (LCLs).

Purpose of the Study:

  • To investigate the binding sites and mechanisms of EBNA3C in regulating CDKN2A gene expression in LCLs.
  • To identify transcription factors and co-regulators that collaborate with EBNA3C.

Main Methods:

  • Chromatin immunoprecipitation sequencing (ChIP-sequencing) to map EBNA3C binding sites in LCL DNA.
  • Analysis of ENCODE LCL transcription factor ChIP-sequencing data to identify co-occurring factors.
  • Gene set enrichment analysis to correlate EBNA3C binding with transcriptional changes.
  • Co-immunoprecipitation assays to assess protein-protein interactions.

Main Results:

  • ChIP-sequencing identified over 13,000 EBNA3C binding sites, predominantly at active enhancers and promoters.
  • EBNA3C binding sites frequently overlapped with transcription factors like RUNX3, BATF, ATF2, IRF4, and SPI1.
  • EBNA3C binding was associated with transcriptional repression, particularly at the p14ARF promoter, involving co-recruitment of RBPJ, Sin3A, and REST.
  • Conditional inactivation of EBNA3C reduced Sin3A binding at the p14ARF promoter.

Conclusions:

  • EBNA3C utilizes specific DNA-binding sites, often enriched with factors like BATF/IRF4 and SPI1/IRF4, to regulate gene expression.
  • EBNA3C recruits repressive complexes, including RBPJ/Sin3A and REST/NRSF, to downregulate p14ARF and p16INK4A, facilitating LCL immortalization.
Keywords:
EBVlymphomaresting B lymphocytetumor suppressor

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