Nucleosome positioning in Yeast expressing active or inactive murine DNMTs
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ABSTRACT: Effect of induced Methylation on Nucleosome positioning in yeast. Mnase digested DNA from a control strain, a strain expressing the 4 murine DNMTs or a strain expressing catalytically inactive murine DNMTs were extracted and sequenced on a hiseq 2000
Project description:Effect of induced Methylation on Nucleosome positioning in yeast. Mnase digested DNA from a control strain and a strain expressing the 4 murine DNMTs were extracted and sequenced on a hiseq 2000
Project description:Effect of induced Methylation on Gene expression in yeast. Total RNA from a control strain and a strain expressing the 4 murine DNMTs were extracted and sequenced in a hiseq 4000
Project description:Localisation of CpG methylation in yeast expressing murine DNMTS Genomic DNA was purified from a control strain and a strain expressing murine DNMTs, treated with Bisulfite and sequenced on a hiseq 2000
Project description:Effect of induced Methylation on 3D genome organisation in yeast. Hi-C experiment were performed on yeast expressing or not the 4 murine DNMTs (DNMT1, 3a, 3b and 3L).
Project description:Localisation of CpG methylation in yeast expressing murine DNMTS Genomic DNA was purified from a control strain and a strain expressing murine DNMTs
Project description:The oomycete pathogen Phytophthora sojae causes root rot of soybean. During infection, the pathogen is thought to deliver dozens, if not hundreds, of effector proteins into the host to manipulate intracellular systems. Although these pathogen proteins often exhibit similar N-terminal delivery domains, the remaining effector region is rarely homologous to known protein domains, making it difficult to predict its biochemical function during infection. As a complement to studies in the natural host, Saccharomyces cerevisiae has been successfully used as a model system to explore the biochemical function of individual pathogen effectors. The presumption is that many effectors target conserved eukaryotic pathways in the host and consequently the expression of effectors in yeast will confer corresponding phenotypes. Indeed, putative effector functions identified using yeast functional genomic approaches have subsequently been validated in the natural host. Over-expression of the Phytophthora sojae effector Avh172 (PsAvh172) inhibits the growth of Saccharomyces cerevisiae, suggesting that the effector targets a biological pathway conserved with plants. In this study, the transcriptomes of yeast expressing PsAvh172 or an empty vector were compared to examine the global transcriptional response, in hopes of discerning the effectors biochemical target.
Project description:We studied the transcriptional profile in response to acute PtdIns-4,5P2 depletion induced by heterologous expression of a plasma membrane-directed version of mammalian PI3K catalytic subunit (p110M-NM-1-CAAX). Three biological samples were analyzed for samples expressing for 4 hours p110M-NM-1-CAAX (PI3K) versus the kinase dead mutant p110M-NM-1-CAAX K802R (KD), and one microarray experiment was carried out for each sample.
Project description:We show that ligation-competent Okazaki fragments in Saccharomyces cerevisiae are sized according to the chromatin repeat. Using deep sequencing, we demonstrate that ligation junctions preferentially occur around nucleosome midpoints rather than in internucleosomal linker regions. Disrupting chromatin assembly or lagging strand polymerase processivity impacts both the size and the distribution of Okazaki fragments, suggesting a role for nascent chromatin, assembled immediately after the passage of the replication fork, in the termination of lagging strand synthesis. Our studies represent the first high-resolution analysis of eukaryotic Okazaki fragments in vivo, and establish a mechanistic link between the fundamental processes of DNA replication and chromatin assembly. 4 samples: replicate samples of wild-type and pol32 knockout