title: Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region.
abstract: BACKGROUND
  Papillomaviruses (PVs) infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR) of the virus. It is believed that there is a core of transcription factor binding sites (TFBS) common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses.
  
  
  RESULTS
  We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS.
  
  
  CONCLUSIONS
  There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide crucial information about the differential biology of cancer-associated PVs.
authors.affiliation: Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain. santi.garcia-vallve@urv.net
authors.forename: Santiago
authors.initials: S
authors.lastname: García-Vallvé
authors.forename: José R
authors.initials: JR
authors.lastname: Iglesias-Rozas
authors.forename: Angel
authors.initials: A
authors.lastname: Alonso
authors.forename: Ignacio G
authors.initials: IG
authors.lastname: Bravo
mesh_terms: D001665:Binding Sites; D019143:Evolution, Molecular; D005814:Genes, Viral; D016679:Genome, Viral; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism*; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D014764:Viral Proteins