title: Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes.
abstract: Vaccinia virus is the prototypic orthopoxvirus and was the vaccine used to eradicate smallpox, yet the expression profiles of many of its genes remain unknown. Using a genome tiling array approach, we simultaneously measured the expression levels of all 223 annotated vaccinia virus genes during infection and determined their kinetics. For 95% of these genes, significant transcript levels were detected. Most remarkably, classification of the genes by their expression profiles revealed 35 genes exhibiting immediate-early expression. Although a similar kinetic class has been described for other virus families, to our knowledge, this is the first demonstration of its existence in orthopoxviruses. Despite expression levels higher than for genes in the other three kinetic classes, the functions of more than half of these remain unknown. Additionally, genes within each kinetic class were spatially grouped together in the genome. This genome-wide picture of transcription alters our understanding of how orthopoxviruses regulate gene expression.
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Erika
authors.initials: E
authors.lastname: Assarsson
authors.forename: Jason A
authors.initials: JA
authors.lastname: Greenbaum
authors.forename: Magnus
authors.initials: M
authors.lastname: Sundström
authors.forename: Lana
authors.initials: L
authors.lastname: Schaffer
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Hammond
authors.forename: Valerie
authors.initials: V
authors.lastname: Pasquetto
authors.forename: Carla
authors.initials: C
authors.lastname: Oseroff
authors.forename: R Curtis
authors.initials: RC
authors.lastname: Hendrickson
authors.forename: Elliot J
authors.initials: EJ
authors.lastname: Lefkowitz
authors.forename: David C
authors.initials: DC
authors.lastname: Tscharke
authors.forename: John
authors.initials: J
authors.lastname: Sidney
authors.forename: Howard M
authors.initials: HM
authors.lastname: Grey
authors.forename: Steven R
authors.initials: SR
authors.lastname: Head
authors.forename: Bjoern
authors.initials: B
authors.lastname: Peters
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette
mesh_terms: D020869:Gene Expression Profiling; D017781:Genes, Immediate-Early; D005814:Genes, Viral; D006367:HeLa Cells; D006801:Humans; D007700:Kinetics; D005810:Multigene Family; D016366:Open Reading Frames; D011212:Poxviridae / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger