DNA microarrays of the complex human cytomegalovirus genome

Profiling kinetic class with drug sensitivity of viral gene expression

James Chambers, Ana Angulo, Dhammika Amaratunga, Hongqing Guo, Ying Jiang, Jackson S. Wan, Anton Bittner, Klaus Frueh, Michael R. Jackson, Per A. Peterson, Mark G. Erlander, Peter Ghazal

Research output: Contribution to journalArticle

220 Citations (Scopus)

Abstract

We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate- early (α), early (β), early-late (γ1), and late (γ2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5' noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for β, γ1, and γ2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.

Original languageEnglish (US)
Pages (from-to)5757-5766
Number of pages10
JournalJournal of Virology
Volume73
Issue number7
StatePublished - 1999
Externally publishedYes

Fingerprint

Human herpesvirus 5
Viral Genes
Viral DNA
Human Genome
Oligonucleotide Array Sequence Analysis
Cytomegalovirus
Open Reading Frames
open reading frames
Gene Expression
kinetics
drugs
gene expression
genome
Viral Genome
oligonucleotides
Pharmaceutical Preparations
Foreskin
Ganciclovir
Herpesviridae
viral proteins

ASJC Scopus subject areas

  • Immunology

Cite this

Chambers, J., Angulo, A., Amaratunga, D., Guo, H., Jiang, Y., Wan, J. S., ... Ghazal, P. (1999). DNA microarrays of the complex human cytomegalovirus genome: Profiling kinetic class with drug sensitivity of viral gene expression. Journal of Virology, 73(7), 5757-5766.

DNA microarrays of the complex human cytomegalovirus genome : Profiling kinetic class with drug sensitivity of viral gene expression. / Chambers, James; Angulo, Ana; Amaratunga, Dhammika; Guo, Hongqing; Jiang, Ying; Wan, Jackson S.; Bittner, Anton; Frueh, Klaus; Jackson, Michael R.; Peterson, Per A.; Erlander, Mark G.; Ghazal, Peter.

In: Journal of Virology, Vol. 73, No. 7, 1999, p. 5757-5766.

Research output: Contribution to journalArticle

Chambers, J, Angulo, A, Amaratunga, D, Guo, H, Jiang, Y, Wan, JS, Bittner, A, Frueh, K, Jackson, MR, Peterson, PA, Erlander, MG & Ghazal, P 1999, 'DNA microarrays of the complex human cytomegalovirus genome: Profiling kinetic class with drug sensitivity of viral gene expression', Journal of Virology, vol. 73, no. 7, pp. 5757-5766.
Chambers, James ; Angulo, Ana ; Amaratunga, Dhammika ; Guo, Hongqing ; Jiang, Ying ; Wan, Jackson S. ; Bittner, Anton ; Frueh, Klaus ; Jackson, Michael R. ; Peterson, Per A. ; Erlander, Mark G. ; Ghazal, Peter. / DNA microarrays of the complex human cytomegalovirus genome : Profiling kinetic class with drug sensitivity of viral gene expression. In: Journal of Virology. 1999 ; Vol. 73, No. 7. pp. 5757-5766.
@article{1a449bfa82ed4c75b41dc00cba992e31,
title = "DNA microarrays of the complex human cytomegalovirus genome: Profiling kinetic class with drug sensitivity of viral gene expression",
abstract = "We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate- early (α), early (β), early-late (γ1), and late (γ2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5' noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for β, γ1, and γ2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.",
author = "James Chambers and Ana Angulo and Dhammika Amaratunga and Hongqing Guo and Ying Jiang and Wan, {Jackson S.} and Anton Bittner and Klaus Frueh and Jackson, {Michael R.} and Peterson, {Per A.} and Erlander, {Mark G.} and Peter Ghazal",
year = "1999",
language = "English (US)",
volume = "73",
pages = "5757--5766",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "7",

}

TY - JOUR

T1 - DNA microarrays of the complex human cytomegalovirus genome

T2 - Profiling kinetic class with drug sensitivity of viral gene expression

AU - Chambers, James

AU - Angulo, Ana

AU - Amaratunga, Dhammika

AU - Guo, Hongqing

AU - Jiang, Ying

AU - Wan, Jackson S.

AU - Bittner, Anton

AU - Frueh, Klaus

AU - Jackson, Michael R.

AU - Peterson, Per A.

AU - Erlander, Mark G.

AU - Ghazal, Peter

PY - 1999

Y1 - 1999

N2 - We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate- early (α), early (β), early-late (γ1), and late (γ2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5' noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for β, γ1, and γ2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.

AB - We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate- early (α), early (β), early-late (γ1), and late (γ2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5' noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for β, γ1, and γ2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.

UR - http://www.scopus.com/inward/record.url?scp=0033064855&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0033064855&partnerID=8YFLogxK

M3 - Article

VL - 73

SP - 5757

EP - 5766

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 7

ER -