title: Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein.
abstract: Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form nucleosomes after release into the host cell nucleus. Here, we present hCMV genome-wide nucleosome occupancy and nascent transcript maps during infection of permissive human primary cells. We show that nucleosomes occupy nuclear viral DNA in a nonrandom and highly predictable fashion. At early times of infection, nucleosomes associate with the hCMV genome largely according to their intrinsic DNA sequence preferences, indicating that initial nucleosome formation is genetically encoded in the virus. However, as infection proceeds to the late phase, nucleosomes redistribute extensively to establish patterns mostly determined by nongenetic factors. We propose that these factors include key regulators of viral gene expression encoded at the hCMV major immediate-early (IE) locus. Indeed, mutant virus genomes deficient for IE1 expression exhibit globally increased nucleosome loads and reduced nucleosome dynamics compared with WT genomes. The temporal nucleosome occupancy differences between IE1-deficient and WT viruses correlate inversely with changes in the pattern of viral nascent and total transcript accumulation. These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function.
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Einat
authors.initials: E
authors.lastname: Zalckvar
authors.forename: Christina
authors.initials: C
authors.lastname: Paulus
authors.forename: Desiree
authors.initials: D
authors.lastname: Tillo
authors.forename: Alexandra
authors.initials: A
authors.lastname: Asbach-Nitzsche
authors.forename: Yaniv
authors.initials: Y
authors.lastname: Lubling
authors.forename: Carla
authors.initials: C
authors.lastname: Winterling
authors.forename: Nicholas
authors.initials: N
authors.lastname: Strieder
authors.forename: Katrin
authors.initials: K
authors.lastname: Mücke
authors.forename: Felicia
authors.initials: F
authors.lastname: Goodrum
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
authors.forename: Michael
authors.initials: M
authors.lastname: Nevels
mesh_terms: D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism / Q000821:virology; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D003587:Cytomegalovirus / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism / Q000821:virology; D016679:Genome, Viral / Q000235:genetics*; D054884:Host-Pathogen Interactions; D006801:Humans; D017874:Immediate-Early Proteins / Q000235:genetics* / Q000378:metabolism; D015151:Immunoblotting; D009154:Mutation; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D004279:DNA, Viral; D017874:Immediate-Early Proteins; D009707:Nucleosomes
keywords: ChIP-chip; epigenetic regulation; functional genomics; herpesvirus