Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes
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 infe...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2008-02, Vol.105 (6), p.2140-2145 |
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| container_title | Proceedings of the National Academy of Sciences - PNAS |
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| creator | Assarsson, Erika Greenbaum, Jason A Sundström, Magnus Schaffer, Lana Hammond, Jennifer A Pasquetto, Valerie Oseroff, Carla Hendrickson, R. Curtis Lefkowitz, Elliot J Tscharke, David C Sidney, John Grey, Howard M Head, Steven R Peters, Bjoern Sette, Alessandro |
| description | 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. |
| doi_str_mv | 10.1073/pnas.0711573105 |
| format | Article |
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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.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0711573105</identifier><identifier>PMID: 18245380</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Biological Sciences ; Gene expression ; Gene Expression Profiling ; Genes ; Genes, Immediate-Early ; Genes, Viral ; Genomes ; Genomics ; HeLa Cells ; Humans ; Infections ; Kinetics ; Multigene Family ; Open Reading Frames ; Orthopoxvirus ; Poxviridae - genetics ; Poxvirus ; Reverse Transcriptase Polymerase Chain Reaction ; RNA ; RNA, Messenger - genetics ; Tiling ; Transcription, Genetic ; Vaccinia virus ; Viruses</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2008-02, Vol.105 (6), p.2140-2145</ispartof><rights>Copyright 2008 The National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Feb 12, 2008</rights><rights>2008 by The National Academy of Sciences of the USA</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c616t-826ce458c109ef82f063fa61e378454337efacdda872256b0803b0098fa629c53</citedby><cites>FETCH-LOGICAL-c616t-826ce458c109ef82f063fa61e378454337efacdda872256b0803b0098fa629c53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/105/6.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25451427$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25451427$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,723,776,780,799,881,27901,27902,53766,53768,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18245380$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Assarsson, Erika</creatorcontrib><creatorcontrib>Greenbaum, Jason A</creatorcontrib><creatorcontrib>Sundström, Magnus</creatorcontrib><creatorcontrib>Schaffer, Lana</creatorcontrib><creatorcontrib>Hammond, Jennifer A</creatorcontrib><creatorcontrib>Pasquetto, Valerie</creatorcontrib><creatorcontrib>Oseroff, Carla</creatorcontrib><creatorcontrib>Hendrickson, R. Curtis</creatorcontrib><creatorcontrib>Lefkowitz, Elliot J</creatorcontrib><creatorcontrib>Tscharke, David C</creatorcontrib><creatorcontrib>Sidney, John</creatorcontrib><creatorcontrib>Grey, Howard M</creatorcontrib><creatorcontrib>Head, Steven R</creatorcontrib><creatorcontrib>Peters, Bjoern</creatorcontrib><creatorcontrib>Sette, Alessandro</creatorcontrib><title>Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>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. 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| subjects | Biological Sciences Gene expression Gene Expression Profiling Genes Genes, Immediate-Early Genes, Viral Genomes Genomics HeLa Cells Humans Infections Kinetics Multigene Family Open Reading Frames Orthopoxvirus Poxviridae - genetics Poxvirus Reverse Transcriptase Polymerase Chain Reaction RNA RNA, Messenger - genetics Tiling Transcription, Genetic Vaccinia virus Viruses |
| title | Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes |
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