FR-like EBNA1 binding repeats in the human genome

Virology. 2010 Sep 30;405(2):524-9. doi: 10.1016/j.virol.2010.06.040. Epub 2010 Jul 22.

Abstract

Epstein-Barr virus (EBV) is widely spread in the human population. EBV nuclear antigen 1 (EBNA1) is a transcription factor that activates viral genes and is necessary for viral replication and partitioning, which binds the EBV genome cooperatively. We identify similar EBNA1 repeat binding sites in the human genome using a nearest-neighbor positional weight matrix. Previously experimentally verified EBNA1 sites in the human genome are successfully recovered by our approach. Most importantly, 40 novel regions are identified in the human genome, constituted of tandemly repeated binding sites for EBNA1. Genes located in the vicinity of these regions are presented as possible targets for EBNA1-mediated regulation. Among these, four are discussed in more detail: IQCB1, IMPG1, IRF2BP2 and TPO. Incorporating the cooperative actions of EBNA1 is essential when identifying regulatory regions in the human genome and we believe the findings presented here are highly valuable for the understanding of EBV-induced phenotypic changes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autoantigens / genetics
  • Binding Sites
  • Calmodulin-Binding Proteins / genetics
  • Carrier Proteins / genetics
  • DNA / metabolism*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Epstein-Barr Virus Nuclear Antigens / genetics
  • Epstein-Barr Virus Nuclear Antigens / metabolism*
  • Extracellular Matrix Proteins / genetics
  • Eye Proteins / genetics
  • Genome, Human*
  • Genome, Viral
  • Herpesvirus 4, Human / genetics
  • Herpesvirus 4, Human / metabolism*
  • Humans
  • Iodide Peroxidase / genetics
  • Iron-Binding Proteins / genetics
  • Nuclear Proteins / genetics
  • Proteoglycans / genetics
  • Repetitive Sequences, Nucleic Acid* / genetics
  • Repetitive Sequences, Nucleic Acid* / physiology
  • Transcription Factors

Substances

  • Autoantigens
  • Calmodulin-Binding Proteins
  • Carrier Proteins
  • DNA-Binding Proteins
  • Epstein-Barr Virus Nuclear Antigens
  • Extracellular Matrix Proteins
  • Eye Proteins
  • IMPG1 protein, human
  • IQCB1 protein, human
  • IRF2BP2 protein, human
  • Iron-Binding Proteins
  • Nuclear Proteins
  • Proteoglycans
  • Transcription Factors
  • DNA
  • TPO protein, human
  • Iodide Peroxidase
  • EBV-encoded nuclear antigen 1