title: Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis.
abstract: BACKGROUND
  Since the discovery of human immunodeficiency virus (HIV-1) twenty years ago, AIDS has become one of the most studied diseases. A number of viruses have subsequently been identified to contribute to the pathogenesis of HIV and its opportunistic infections and cancers. Therefore, a multi-virus array containing eight human viruses implicated in AIDS pathogenesis was developed and its efficacy in various applications was characterized.
  
  
  RESULTS
  The amplified open reading frames (ORFs) of human immunodeficiency virus type 1, human T cell leukemia virus types 1 and 2, hepatitis C virus, Epstein-Barr virus, human herpesvirus 6A and 6B, and Kaposi's sarcoma-associated herpesvirus were spotted on glass slides and hybridized to DNA and RNA samples. Using a random priming method for labeling genomic DNA or cDNA probes, we show specific detection of genomic viral DNA from cells infected with the human herpesviruses, and effectively demonstrate the inhibitory effects of a cellular cyclin dependent kinase inhibitor on viral gene expression in HIV-1 and KSHV latently infected cells. In addition, we coupled chromatin immunoprecipitation with the virus chip (ChIP-chip) to study cellular protein and DNA binding.
  
  
  CONCLUSIONS
  An amplicon based virus chip representing eight human viruses was successfully used to identify each virus with little cross hybridization. Furthermore, the identity of both viruses was correctly determined in co-infected cells. The utility of the virus chip was demonstrated by a variety of expression studies. Additionally, this is the first demonstrated use of ChIP-chip analysis to show specific binding of proteins to viral DNA, which, importantly, did not require further amplification for detection.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland 20850, USA. eghedin@tigr.org
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.forename: Anne
authors.initials: A
authors.lastname: Pumfery
authors.forename: Cynthia
authors.initials: C
authors.lastname: de la Fuente
authors.forename: Karen
authors.initials: K
authors.lastname: Yao
authors.forename: Naomi
authors.initials: N
authors.lastname: Miller
authors.forename: Vincent
authors.initials: V
authors.lastname: Lacoste
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Steven
authors.initials: S
authors.lastname: Jacobson
authors.forename: Fatah
authors.initials: F
authors.lastname: Kashanchi
mesh_terms: D015967:Gene Expression Regulation, Viral; D006678:HIV / Q000235:genetics; D015368:Human T-lymphotropic virus 1 / Q000235:genetics; D015367:Human T-lymphotropic virus 2 / Q000235:genetics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D012190:Retroviridae / Q000235:genetics* / Q000472:pathogenicity*; D014780:Viruses / Q000235:genetics* / Q000472:pathogenicity*