Project description:adenovirus mediated overexpression of wild-type CtBP2 and Rossmann fold mutant CtBP2 along with control GUS in dietary induced obese mice
Project description:Using an RNA interference-based genetic screen in mouse F9 cells we identify the transcriptional corepressor CTBP2 as a coactivator critically required for retinoic acid (RA)-induced transcription. Here we perfom a whole genome transcriptome analysis in F9 cells expressing shRNA for Ctbp2 and Rxr in the absence or presence of retinoic acid (RA). A total of 2,754 genes were found to be upregulated (>2 fold) and 1518 genes were downregulated (>2 fold) in response to RA treatment in the control cells. We find that around 52% and 55% of upregulated genes are dependent on Ctbp2 and Rxr for activation respectively suggesting that Ctbp2 is a coactivator of RA signaling. Whole genome RNA-sequencing in F9 cells expressing shGFP or shCtbp2 or shRxr
Project description:Using an RNA interference-based genetic screen in mouse F9 cells we identify the transcriptional corepressor CTBP2 as a coactivator critically required for retinoic acid (RA)-induced transcription. Here we perfom a whole genome transcriptome analysis in F9 cells expressing shRNA for Ctbp2 and Rxr in the absence or presence of retinoic acid (RA). A total of 2,754 genes were found to be upregulated (>2 fold) and 1518 genes were downregulated (>2 fold) in response to RA treatment in the control cells. We find that around 52% and 55% of upregulated genes are dependent on Ctbp2 and Rxr for activation respectively suggesting that Ctbp2 is a coactivator of RA signaling.
Project description:Profiling of epigenetic and transcriptomic landscapes in normal mouse liver, phenobarbital exposed mouse livers and mouse liver tumours
Project description:We have identified the CTBP2 protein as a new ZBTB18 interactor. Here we have evaluated transcriptomic changes upon CTBP2 knockdown in the GBM cell line SNB19. Moreover, we have analyzed whether CTBP2 is required for ZBTB18-mediated gene repression.
Project description:Transcriptional Profiling of mouse liver tissues comparing normal tissues, tissues with two weeks expression of transgene, and tumors arising from transgene expression after hepatocy transplantation using the comparative hepatocyte growth assay Experimental groups: Control (hPAP marker gene); Normal Liver Expressing Transgene for Two Weeks; Liver Tumors Expressing Transgene
Project description:There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we demonstrate an effective methodology for genome-scale characterization of tumors. Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples. To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed ChIP-chip experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells. Finally, we used a âvirtual comparative genomic hybridizationâ (vCGH) method to identify copy number alterations in the tumor samples. Through comparison of RNA Polymerase II binding, chromatin structure, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number. Keywords: ChIP-chip, gene expression, CGH Source material: Liver samples from human liver cancer patients, normal human liver samples, liver cell lines and normal human hepatocytes. Experiments: ChIP-chip with abs against POLII, H3me3K27, and H3me3K9, and DNA methylation using NimbleGen 5 kb promoter arrays. RNA expression from the listed sources using Illumina Bead system. Compare normal liver to tumor liver and normal cell lines to tumor cell lines.
