title: FR-like EBNA1 binding repeats in the human genome.
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.
authors.affiliation: Department of Computational Biology, Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden. afd@kth.se
authors.forename: Aymeric Fouquier
authors.initials: AF
authors.lastname: d'Hérouël
authors.forename: Anna
authors.initials: A
authors.lastname: Birgersdotter
authors.forename: Maria
authors.initials: M
authors.lastname: Werner
mesh_terms: D001324:Autoantigens / Q000235:genetics; D001665:Binding Sites; D002148:Calmodulin-Binding Proteins / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D019309:Epstein-Barr Virus Nuclear Antigens / Q000235:genetics / Q000378:metabolism*; D016326:Extracellular Matrix Proteins / Q000235:genetics; D005136:Eye Proteins / Q000235:genetics; D015894:Genome, Human; D016679:Genome, Viral; D004854:Herpesvirus 4, Human / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D007453:Iodide Peroxidase / Q000235:genetics; D033862:Iron-Binding Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D011509:Proteoglycans / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics / Q000502:physiology; D014157:Transcription Factors
chemical_list: D001324:Autoantigens; D002148:Calmodulin-Binding Proteins; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D019309:Epstein-Barr Virus Nuclear Antigens; D016326:Extracellular Matrix Proteins; D005136:Eye Proteins; C486428:IMPG1 protein, human; C498171:IQCB1 protein, human; C475082:IRF2BP2 protein, human; D033862:Iron-Binding Proteins; D009687:Nuclear Proteins; D011509:Proteoglycans; D014157:Transcription Factors; D004247:DNA; C056658:TPO protein, human; D007453:Iodide Peroxidase; C417029:EBV-encoded nuclear antigen 1