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BIOLOGICAL SCIENCES / MICROBIOLOGY
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes

Erika Assarsson^*, Jason A. Greenbaum^*, Magnus Sundström, Lana Schaffer, Jennifer A. Hammond, Valerie Pasquetto^*, Carla Oseroff^*, R. Curtis Hendrickson, Elliot J. Lefkowitz, David C. Tscharke^¶, John Sidney^*, Howard M. Grey^*,||, Steven R. Head, Bjoern Peters^*, and Alessandro Sette^*

*Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Department of Molecular Biology and DNA Array Core Facility, The Scripps Research Institute, La Jolla, CA 92037; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294; and ^¶School of Biochemistry and Molecular Biology, Australian National University, Canberra ACT 0200, Australia

Contributed by Howard M. Grey, December 12, 2007 (received for review November 9, 2007)

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.

gene transcription | genome tiling array | microarray | vaccinia virus

Author contributions: E.A. and J.A.G. contributed equally to this work; E.A., S.R.H., and A.S. designed research; E.A., J.A.G., M.S., and J.A.H. performed research; J.A.G., L.S., C.O., S.R.H., and B.P. contributed new reagents/analytic tools; E.A., J.A.G., V.P., R.C.H., E.J.L., J.S., H.M.G., B.P., and A.S. analyzed data; and E.A., J.A.G., D.C.T., H.M.G., and A.S. wrote the paper.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/cgi/content/full/0711573105/DC1.

^||To whom correspondence should be addressed. E-mail: hgrey{at}liai.org

© 2008 by The National Academy of Sciences of the USA

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