RNA levels in a cell are determined by the relative rates of RNA synthesis and decay. State-of-the-art transcriptional analyses only employ total cellular RNA. Therefore, changes in RNA levels cannot be attributed to RNA synthesis or decay, and temporal resolution is poor. Recently, it was reported that newly transcribed RNA can be biosynthetically labeled for 1-2 h using thiolated nucleosides, purified from total cellular RNA and subjected to microarray analysis. However, in order to study signaling events at molecular level, analysis of changes occurring within minutes is required. We developed an improved approach to separate total cellular RNA into newly transcribed and preexisting RNA following 10-15 min of metabolic labeling. Employing new computational tools for array normalization and half-life determination we simultaneously study short-term RNA synthesis and decay as well as their impact on cellular transcript levels. As an example we studied the response of fibroblasts to type I and II interferons (IFN). Analysis of RNA transcribed within 15-30 min at different times during the first three hours of interferon-receptor activation resulted in a >10-fold increase in microarray sensitivity and provided a comprehensive profile of the kinetics of IFN-mediated changes in gene expression. We identify a previously undisclosed highly connected network of short-lived transcripts selectively down-regulated by IFNg in between 30 and 60 min after IFN treatment showing strong associations with cell cycle and apoptosis, indicating novel mechanisms by which IFNg affects these pathways.

CD8+ T lymphocytes play an important role in the control of intracellular pathogens during both acute and persistent infections. This is particularly true in the case of persistent herpesviruses such as human CMV, which are typified by large virus-specific CD8+ T cell populations during viral latency. To understand the origin of these populations and the factors shaping them over time, we investigated the CD8+ T cell response after murine CMV (MCMV) infection. The kinetics of the acute response were characterized by rapid expansion of activated T cells, followed by a contraction phase. Thereafter, we observed a striking pattern, where MCMV-specific memory CD8+ T cells steadily accumulated over time, with 20% of all CD8+ T cells at 1 year specific for one MCMV epitope. Accumulation of MCMV-specific CD8+ T lymphocytes was seen in all organs tested and was associated with continuous activation of specific CD8+ T lymphocytes, primarily within lymph nodes. The pattern of accumulation was observed in only two of five epitopes tested, and was accompanied by a gradual restriction in usage of the variable region of the TCR β-chain over time. This novel pattern of a virus-specific CD8+ T cell response suggests that continuous or repetitive exposure to Ag can slowly mold memory T cell populations over time. This may be relevant for understanding the evolution of the large human CMV-specific CD8+ T cell populations seen in humans.

A strategy for cloning and mutagenesis of an infectious herpesvirus genome is described. The mouse cytomegalovirus genome was cloned and maintained as a 230 kb bacterial artificial chromosome (BAC) in E. coli. Transfection of the BAC plasmid into eukaryotic cells led to a productive virus infection. The feasibility to introduce targeted mutations into the BAC cloned virus genome was shown by mutation of the immediate-early 1 gene and generation of a mutant virus. Thus, the complete construction of a mutant herpesvirus genome can now be carried out in a controlled manner prior to the reconstitution of infectious progeny. The described approach should be generally applicable to the mutagenesis of genomes of other large DNA viruses.Cytomegalovirus (CMV) is an important human pathogen with a high prevalence in the human population that causes severe and even fatal disease in immunologically immature or immunocompromised patients (1). Because human and mouse CMV (MCMV) show a series of similarities in biology and pathogenesis (2) infection of the mouse with MCMV has become an extensively used in vivo model to study the pathogenesis of CMV infection. The 235-kb genomes of both human and mouse CMV are the largest genomes of mammalian DNA viruses. Sequence analysis of the human and mouse CMV genomes revealed a similar genetic organization and a coding capacity for presumably more than 220 polypeptides (3-5). However, information on the function of the majority of CMV gene products is still rather limited. This is in sharp contrast to the alphaherpesviruses, where the study of a wealth of viral mutants contributed significantly to the understanding of viral gene functions (reviewed in ref. 6). There is a lack of CMV mutants because due to the large genome size and slow replication kinetics construction of CMV recombinants turned out to be difficult.The technique of insertional mutagenesis has been developed for disruption and deletion of CMV genes (7,8). Because the frequency of homologous recombination in eukaryotic cells is low the technique is quite ineffective. In addition adventitious deletions and the formation of illegitimate recombinant viruses have frequently been observed (refs. 7 and 9; I.C., unpublished data). Although selection procedures have improved the original technique (9-11) generation of CMV mutants remains a laborious, time-consuming, and often unsuccessful task. Recently, the technique for construction of recombinant herpesviruses from cloned overlapping fragments (12) has been extended to CMV (13). This is a major improvement in that the technique generates only recombinant virus and obviates selection against nonrecombinant wild type (wt) virus. Still, the resultant mutant is the product of several recombination events in eukaryotic cells that are difficult to control. Correct reconstitution of the viral genome can only be verified after growth and isolation of the mutant virus.Here we describe an approach for production of CMV mutants. Construction of the mutant genome is completely inde...

No abstract