title: Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection.
abstract: HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During lytic infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of nucleosomes.
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: Jaewook
authors.initials: J
authors.lastname: Oh
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: Iryna F
authors.initials: IF
authors.lastname: Sanders
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences, Hong Kong SAR, China; Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: Eric Z
authors.initials: EZ
authors.lastname: Chen
authors.affiliation: Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: Hongzhe
authors.initials: H
authors.lastname: Li
authors.affiliation: Penn Molecular Profiling Facility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: John W
authors.initials: JW
authors.lastname: Tobias
authors.affiliation: Penn Molecular Profiling Facility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: R Benjamin
authors.initials: RB
authors.lastname: Isett
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: Sindura
authors.initials: S
authors.lastname: Penubarthi
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences, Hong Kong SAR, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Sun
authors.affiliation: Pathonomics LLC, Philadelphia, PA, 19104, United States of America.
authors.forename: Don A
authors.initials: DA
authors.lastname: Baldwin
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.
authors.forename: Nigel W
authors.initials: NW
authors.lastname: Fraser
mesh_terms: D002232:Carbocyanines / Q000737:chemistry; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000378:metabolism / Q000821:virology; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D015342:DNA Probes / Q000378:metabolism; D004279:DNA, Viral / Q000378:metabolism; D017781:Genes, Immediate-Early; D016679:Genome, Viral; D018259:Herpesvirus 1, Human / Q000235:genetics* / Q000502:physiology; D006801:Humans; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism*; D014779:Virus Replication / Q000235:genetics
chemical_list: D002232:Carbocyanines; D015342:DNA Probes; D004279:DNA, Viral; D009707:Nucleosomes; C089187:cyanine dye 3; D008836:Micrococcal Nuclease