Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival

The effects of the adenovirus Ad5 on basic host cell programs, such as cell-cycle regulation, were studied in a microarray analysis of human fibroblasts. About 2,000 genes were up- or down-regulated after Ad5 infection and Ad5 infection was shown to induce reversal of the quiescence program and recapitulation of the core serum response

Nucleolin Is Required for RNA Polymerase I Transcription In Vivo

Eukaryotic genomes are packaged with histones and accessory proteins in the form of chromatin. RNA polymerases and their accessory proteins are sufficient for transcription of naked DNA, but not of chromatin, templates in vitro. In this study, we purified and identified nucleolin as a protein that allows RNA polymerase II to transcribe nucleosomal templates in vitro. As immunofluorescence confirmed that nucleolin localizes primarily to nucleoli with RNA polymerase I, we demonstrated that nucleolin allows RNA polymerase I transcription of chromatin templates in vitro. The results of chromatin immunoprecipitation experiments established that nucleolin is associated with chromatin containing rRNA genes transcribed by RNA polymerase I but not with genes transcribed by RNA polymerase II or III. Knockdown of nucleolin by RNA interference resulted in specific inhibition of RNA polymerase I transcription. We therefore propose that an important function of nucleolin is to permit RNA polymerase I to transcribe nucleolar chromatin

The Adenoviral E1B 55-Kilodalton Protein Controls Expression of Immune Response Genes but Not p53-Dependent Transcription▿

The human adenovirus type 5 (Ad5) E1B 55-kDa protein modulates several cellular processes, including activation of the tumor suppressor p53. Binding of the E1B protein to the activation domain of p53 inhibits p53-dependent transcription. This activity has been correlated with the transforming activity of the E1B protein, but its contribution to viral replication is not well understood. To address this issue, we used microarray hybridization methods to examine cellular gene expression in normal human fibroblasts (HFFs) infected by Ad5, the E1B 55-kDa-protein-null mutant Hr6, or a mutant carrying substitutions that impair repression of p53-dependent transcription. Comparison of the changes in cellular gene expression observed in these and our previous experiments (D. L. Miller et al., Genome Biol. 8:R58, 2007) by significance analysis of microarrays indicated excellent reproducibility. Furthermore, we again observed that Ad5 infection led to efficient reversal of the p53-dependent transcriptional program. As this same response was also induced in cells infected by the two mutants, we conclude that the E1B 55-kDa protein is not necessary to block activation of p53 in Ad5-infected cells. However, groups of cellular genes that were altered in expression specifically in the absence of the E1B protein were identified by consensus k-means clustering of the hybridization data. Statistical analysis of the enrichment of genes associated with specific functions in these clusters established that the E1B 55-kDa protein is necessary for repression of genes encoding proteins that mediate antiviral and immune defenses

Changes in expression of direct p53 target genes induced by Ad5 infection

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> The 50 or so genes that are direct p53 targets in human lung fibroblasts [94] are shown clustered based on the changes in their expression observed in adenovirus type 5 (Ad5) infected human foreskin fibroblasts. The column labeled p53 summarizes the p53 induced alterations in expression of these genes, which are listed at the right. Ramps above panels indicate increases in time after infection

Changes in RNA concentrations in Ad5-infected HFFs determined by RT-PCR

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> Autoradiograms of products of reverse transcription (RT)-polymerase chain reaction (PCR) amplification of CDC6 RNA isolated from human foreskin fibroblasts (HFFs) infected for the periods indicated. The RNA samples used in experiment 1 were those also used for amplification and hybridization to microarrays, whereas experiments 2 and 3 total RNAs were from two other independent infections of quiescent HFFs. The RT-PCR signals for E2F2 and RHOQ RNAs from the three independent infections were quantified, as described in Materials and methods, zero transformed against the mean of the three zero time point samples included in each experiment, and converted to logvalues for comparison to the changes in concentration of these RNAs determined by hybridization to microarrays. Ad5, adenovirus type 5