Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray

Area of Science:

• Molecular Virology
• Transcriptomics
• Gene Expression Analysis

Background:

• Herpes simplex virus (HSV) type 1 expresses over 100 transcripts during infection.
• Understanding viral gene regulation and host-pathogen interactions is crucial.
• Existing methods for analyzing global gene expression patterns can be time-consuming.

Purpose of the Study:

• To develop a rapid, global method for analyzing viral and cellular gene expression during HSV-1 infection.
• To investigate the role of the viral alpha27 gene in regulating gene expression.
• To assess the impact of viral gene perturbations on host cell transcription.

Main Methods:

• Creation of custom DNA microchips with 75-mer oligonucleotides specific for HSV-1 transcripts and human stress-response genes.
• Hybridization of labeled cDNA from infected cells to the microchips for global transcription profiling.
• Analysis of transcript abundance in cells infected with wild-type and a mutant HSV-1 lacking the alpha27 gene.

Main Results:

• The DNA microchips accurately detected and quantified HSV-1 transcripts, correlating well with known mRNA accumulation kinetics.
• Infection with the alpha27 deletion mutant resulted in altered viral transcript profiles, with some immediate-early transcripts augmented.
• A significant increase in the levels of many surveyed cellular transcripts was observed in alpha27 mutant-infected cells.

Conclusions:

• DNA microchips provide a sensitive and efficient tool for global analysis of HSV-1 transcription.
• The alpha27 gene plays a critical role in the early suppression of host cellular gene expression during HSV-1 infection.
• This technology facilitates rapid investigation of viral regulatory mechanisms and their impact on the host.