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Journal of Virology, November 2000, p. 9916-9927, Vol. 74, No. 21
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Global Analysis of Herpes Simplex Virus Type 1 Transcription Using an Oligonucleotide-Based DNA Microarray†

S. W. Stingley,1 J. J. Garcia Ramirez,2 S. A. Aguilar,1 K. Simmen,3 R. M. Sandri-Goldin,1 P. Ghazal,2,* and E. K. Wagner1,*

Department of Molecular Biology and Biochemistry, University of California, Irvine,1 Departments of Immunology and Molecular Biology, The Scripps Research Institute, La Jolla,2 and The R. W. Johnson Pharmaceutical Research Institute, San Diego,3 California

Received 21 June 2000/Accepted 10 August 2000

More than 100 transcripts of various abundances and kinetic classes are expressed during phases of productive and latent infections by herpes simplex virus (HSV) type 1. To carry out rapid global analysis of variations in such patterns as a function of perturbation of viral regulatory genes and cell differentiation, we have made DNA microchips containing sets of 75-mer oligonucleotides specific for individual viral transcripts. About half of these are unique for single transcripts, while others function for overlapping ones. We have also included probes for 57 human genes known to be involved in some aspect of stress response. The chips efficiently detect all viral transcripts, and analysis of those abundant under various conditions of infection demonstrates excellent correlation with known kinetics of mRNA accumulation. Further, quantitative sensitivity is high. We have further applied global analysis of transcription to an investigation of mRNA populations in cells infected with a mutant virus in which the essential immediate-early alpha 27 (UL54) gene has been functionally deleted. Transcripts expressed at 6 h following infection with this mutant can be classified into three groups: those whose abundance is augmented (mainly immediate-early transcripts) or unaltered, those whose abundance is somewhat reduced, and those where there is a significant reduction in transcript levels. These do not conform to any particular kinetic class. Interestingly, levels of many cellular transcripts surveyed are increased. The high proportion of such transcripts suggests that the alpha 27 gene plays a major role in the early decline in cellular gene expression so characteristic of HSV infection.

* Corresponding author. Mailing address for P. Ghazal: Departments of Mol. Biol. & Immunology, The Scripps Research Institute, 10055 N. Torrey Pines Rd., La Jolla, CA 92037. Phone: (858) 784-8678. Fax: (858) 784-9272. E-mail: ghazal{at}scripps.edu. Mailing address for E. K. Wagner: Department of Molecular Biology & Biochemistry, University of California, Irvine, 19172 Jamboree Rd., Irvine, CA 92697. Phone: (949) 824-5370. Fax: (949) 824-8551. E-mail: ewagner{at}uci.edu.

dagger Publication no. 13376-IMM from the Scripps Research Institute.

Journal of Virology, November 2000, p. 9916-9927, Vol. 74, No. 21
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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