title: Occupancy of chromatin organizers in the Epstein-Barr virus genome.
abstract: The human CCCTC-binding factor, CTCF, regulates transcription of the double-stranded DNA genomes of herpesviruses. The architectural complex cohesin and RNA Polymerase II also contribute to this organization. We profiled the occupancy of CTCF, cohesin, and RNA Polymerase II on the episomal genome of the Epstein-Barr virus in a cell culture model of latent infection. CTCF colocalizes with cohesin but not RNA Polymerase II. CTCF and cohesin bind specific sequences throughout the genome that are found not just proximal to the regulatory elements of latent genes, but also near lytic genes. In addition to tracking with known transcripts, RNA Polymerase II appears at two unannotated positions, one of which lies within the latent origin of replication. The widespread occupancy profile of each protein reveals binding near or at a myriad of regulatory elements and suggests context-dependent functions.
authors.affiliation: Department of Cellular and Molecular Pharmacology, University of California-San Francisco, CA 94158, USA.
authors.forename: Meghan M
authors.initials: MM
authors.lastname: Holdorf
authors.forename: Samantha B
authors.initials: SB
authors.lastname: Cooper
authors.forename: Keith R
authors.initials: KR
authors.lastname: Yamamoto
authors.forename: J J L
authors.initials: JJ
authors.lastname: Miranda
mesh_terms: D001483:Base Sequence; D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism*; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D019309:Epstein-Barr Virus Nuclear Antigens / Q000235:genetics / Q000378:metabolism; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral; D004854:Herpesvirus 4, Human / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D006801:Humans; D010957:Plasmids / Q000235:genetics; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D018741:Replication Origin / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D017735:Virus Latency; D000097722:Cohesins
chemical_list: D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004279:DNA, Viral; D004268:DNA-Binding Proteins; D019309:Epstein-Barr Virus Nuclear Antigens; D012319:RNA Polymerase II; D012097:Repressor Proteins; D000097722:Cohesins; C000619697:CTCF protein, human