Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Helin M.musculus Identification of genes repressed by CBX8 and BMI1

ABSTRACT: The polycomb group proteins form large repressive complexes. It has recently become evident, via ChIP on chip analysis, that the polycomb complexes, PRC1 and PRC2, target a large number of genes (Boyer et al., 2006; Bracken et al., 2006; Tolhuis et al., 2006), which are involved in cell fate decisions. In order to identify genes which are truly regulated by the polycomb group proteins, CBX8 and BMI1, we expressed these two proteins in mouse embryonic fibroblasts (MEFs) by retroviral infection.

ORGANISM(S): Mus musculus

SUBMITTER: Charlotte Schjerling

PROVIDER: E-MEXP-793 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus.

Dietrich Nikolaj N Bracken Adrian P AP Trinh Emmanuelle E Schjerling Charlotte K CK Koseki Haruhiko H Rappsilber Juri J Helin Kristian K Hansen Klaus H KH

The EMBO journal 20070301 6

The Polycomb group (PcG) proteins are essential for embryogenesis, and their expression is often found deregulated in human cancer. The PcGs form two major protein complexes, called polycomb repressive complexes 1 and 2 (PRC1 and PRC2) whose function is to maintain transcriptional repression. Here, we demonstrate that the chromodomain-containing protein, CBX8, which is part of one of the PRC1 complexes, regulates proliferation of diploid human and mouse fibroblasts through direct binding to the ...[more]

PMID: 17332741

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Project description:Lassa fever virus is a zoonotic pathogen that plagues the endemic areas of West Africa. Rhesus macaques infected with a related arenavirus, LCMV-WE, serve as a model for Lassa-infection of human beings. Using a dose similar to that expected from a needle-stick, monkeys experience an early pre-viremic phase (day 1-3), a viremic phase with febrile onset (day 4-7), and, like human beings who succumb, they die within two weeks. Our goal was to monitor changes in gene expression that parallel disease progression in an effort to 1) identify genes with altered expression after infection, 2) identify genes that could discriminate between a virulent and non-virulent infection, and 3) identify genes encoding products that could serve as treatment targets for FDA-approved pharmaceuticals. Genes related to all three of these categories have been identified and some have been given preliminary validation by quantitative PCR and proteomic studies. These genes will be valuable candidates for future validation as prognostic biomarkers; We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: Rhesus macaques inoculated with a lethal dose of LCMV-WE were used to model human infection with Lassa fever virus (Lukashevich et al 2002, 2003; Rodas et al 2004). To identify molecular events that occur during the first few days of virus exposure, we monitored gene expression in peripheral blood mononuclear cell (PBMC) samples by microarray analysis. Approximately 150 samples from 23 different rhesus macaques (Table 1) were hybridized to Affymetrix U133 chips. Experiment Overall Design: Affymetrix U133 arrays cover the entire human genome with approximately 54,000 gene fragments representing approximately 22,000 genes. The use of these human arrays for macaque transcriptome analysis has been validated by other laboratories (Ace et al, 2004 Wang et al, 2004), i.e. 99.8% of the array elements for which human DNA gave a signal >1.4-fold over background were also >1.4 over background for macaque DNA (Rubins et al, 2004). LCMV-infected blood samples were compared to uninfected controls and genes with over two-fold change in expression were designated âdifferentially expressedâ (Fig. 1). Thus, out of 54,000 elements, 8410 (16%) were differentially regulated with a >2-fold change in expression [supplementary Table 1 has these genes in order of the magnitude of their differential expression]. Experiment Overall Design: Virus was detectable in these monkeys at day 4 after infection by plaque assay and by RT-PCR of blood cDNA (Djavani et al 2005). Although virus is replicating in monocytes, endothelial cells, liver, spleen, and peripheral lymphoid organs soon after inoculation (Rai et al, 1997; Lukashevich et al, 2002), virus is not detectable in the circulation for the first three days. Thus we define the early, pre-viremic stage as days 1-3, and a later viremic stage as days 4-7. Although the LCMV-Armstrong strain replicated as well in cell culture as LCMV-WE, the LCMV-Arm-infected monkeys did not experience viremia, i.e. viral nucleic acid were detected in tissues but virus loads were not high enough to be detected in the circulation. The Arm-infected monkeys resisted a lethal challenge with LCMV-WE, further confirming that they had been productively infected (Rodas et al, 2004). An overview of gene expression in monkeys shows a trend to down-regulate genes at the onset of viremia followed by a sharp increase in up-regulated genes. Those monkeys that did not experience viremia (Armstrong-infected) showed no dramatic down-regulation trend (Fig. 1). Over the entire study period of 7 days, the number of down-regulated genes in the WE-infected macaques was significantly more than the number seen in the Arm-infected monkeys (p < 0.005).

Dataset Information

Helin M.musculus Identification of genes repressed by CBX8 and BMI1

Publications

Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus.

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