Transcriptional analysis of Marek's disease virus (MDV) genes in MDV-transformed lymphoblastoid cell lines without MDV-activated cells

The identification of functional motifs in temporal gene expression analysis

The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR) and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur) binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

Marek's disease virus down-regulates surface expression of MHC (B Complex) Class I (BF) glycoproteins during active but not latent infection of chicken cells

Infection of chicken cells with three Marek's disease virus (MDV) serotypes interferes with expression of the major histocompatibility complex (MHC or B complex) class I (BF) glycoproteins. BF surface expression is blocked after infection of OU2 cells with MDV serotypes 1, 2, and 3. MDV-induced T-cell tumors suffer a nearly complete loss of cell surface BF upon virus reactivation with 5-bromo-2'-deoxyuridine (BUdR). The recombinant virus (RB1BUS2gfpDelta) transforming the MDCC-UA04 cell line expresses green fluorescent protein (GFP) during the immediate early phase of viral gene expression. Of the UA04 cells induced to express the immediate early GFP, approximately 60% have reduced levels of BF expression. All of the reactivated UA04 and MSB1 tumor cells expressing the major early viral protein pp38 display reduced levels of BF. Thus, BF down-regulation begins in the immediate early phase and is complete by the early phase of viral gene expression. The intracellular pool of BF is not appreciably affected, indicating that the likely mechanism is a block in BF transport and not the result of transcriptional or translational regulation.