Transcriptome analysis of fibroblast cells immediate-early after human cytomegalovirus infection

Human cytomegalovirus (HCMV) has been shown to have the potential to alter cellular gene expression early after infection. However, one-gene approache s and the use of closed system gene expression technologies have identified only few cellular genes whose activity changed immediate-early. We therefo re used serial analysis of gene expression (SAGE) to investigate the transc riptional program of human fibroblasts in response to HCMV in the immediate -early phase of infection. Differential expression of various cellular gene s was monitored. Transcriptional expression changes of genes coding for rib osomal proteins reflected a general cellular response to starvation and str ess. But differential regulation of genes coding for transcription factors and proteins associated with cellular metabolism, homeostasis and cell stru cture may represent transcriptional alterations in response to HCMV infecti on. Expression kinetics by 5' nuclease fluorigenic real-time PCR of selecte d genes revealed partial protection of infected cells against initial stres s-associated alterations of gene expression and indicated fluctuations of t ranscriptional levels over time. Additionally, agreement with the quantitat ive results obtained by SAGE was observed only for genes up-regulated in HC MV-infected cells. This finding pointed to various technical and statistica l parameters that all may be critical for quantitative transcriptome studie s using global approaches, especially when exploring biological systems in a critical phase of cellular physiology. (C) 2000 Academic Press.