Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b ...[more]
Project description:Our study reports the first genome-wide atlas of functional nodes that mediate proviral silencing in ESCs. It provides evidences for the comprehensive, interconnected and multi-layered genetic/epigenetic machineries by which ESCs maintain the repressive state of provirus and ERVs. ChIP-seq analysis of Chaf1a, Trim28, Sumo2 and Zfp809 to demonstrate the mechanism of the silencing of Endogenous retroviruses
Project description:Our study reports the first genome-wide atlas of functional nodes that mediate proviral silencing in ESCs. It provides evidences for the comprehensive, interconnected and multi-layered genetic/epigenetic machineries by which ESCs maintain the repressive state of provirus and ERVs. RNA-seq analysis to determine the regulated endogenous retroviruses by Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/ Ube2i/Sae1/Uba2/Senp6) and chromatin modifiers (Trim28/Eset/Atf7ip)
Project description:The PIWI-interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal germlines1,2. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx)3,4; however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its co-factor, Nxt1, form a complex with Panx, and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 to either RNA or DNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing. Loss of Nxf2 or Panx results in nuclear accumulation of transposon transcripts, which is for some transposons Piwi-dependent.
Project description:To test the hypothesis that the propensity for silencing of tumor suppressor genes in the respiratory epithelium of chronic smokers by promoter hypermethylation is influenced by sequence variations that modify the activity of genes and microRNAÕs that directly or indirectly influence de novo methylation and chromatin remodeling.
Project description:Here we demonstrate that epigenetic silencing of HAND2 is a key step in endometrial carcinogenesis. We performed an epigenome-wide methylation analysis of >27,000 CpG sites in endometrial cancers and controls and identified methylation of HAND2 as one of the most common hypermethylated and silenced genes in endometrial cancer. Overall design: Bisulphite converted DNA from the 87 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.
Project description:Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control. Using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements. In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others appear to influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements. The factors implicated here have previously been shown to control adjacent genes at intrachromosomal positions, suggesting dual functionality of the factors and a possible mechanism of coordinating intrachromosomal gene expression with subtelomeric silencing. These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes. These are Chip-CHIP data for myc tagged Oaf1p transcription factor from S. cerevisiae grown in the presence or absence of the fatty acid oleate. ChIP-CHIP analysis was performed to determine the genomic distribution of Oaf1p transcription factor in the BY4742 yeast strain after growth in 0.1% glucose, or in the presence of the fatty acid oleate. Three biological replicates for each growth condition (in the presence of low glucose or 5 h after a shift to medium containing oleate as a carbon source). ChIP samples were amplified by PCR, labelled and hybridized to 50-mer tiling arrays covering both strands of the entire yeast genome at a 64 bp resolution.