Recent chromatin immunoprecipitation (ChIP) experiments in fly, mouse, and human have revealed the existence of high-occupancy target (HOT) regions or "hotspots" that show enrichment across many assayed DNA-binding proteins. Similar co-enrichment observed in yeast so far has been treated as artifactual, and has not been fully characterized.Here we reanalyze ChIP data from both array-based and sequencing-based experiments to show that in the yeast S. cerevisiae, the collective enrichment phenomen ...[more]
Project description:Genomic binding of 203 transcriptional regulatory proteins under various conditions. Hybridizations of fluorescently-labelled immunoprecipitated vs. whole-cell extract samples on S. cerevisiae intergenic arrays.
Project description:Genomes are packaged into nucleosomes whose position and modification state can profoundly influence regulation of gene expression. We have established new ChIP-based high-resolution genome-wide maps of histone acetylation and methylation that take into account changes in nucleosome occupancy at actively transcribed genes. These maps provide a more accurate picture of nucleosome occupancy and the nature of modifications associated with transcriptional activity in this eukaryotic genome. We describe the combination of modifications that occur at the average transcribed gene.
Project description:Cellular signal transduction pathways modify gene expression programs in response to changes in the environment, but the mechanisms by which they regulate populations of genes under their control are not entirely understood. We present evidence that most mitogen-activated protein kinases and protein kinase A subunits become physically associated with the genes they regulate in the yeast genome. The ability to detect this interaction of signaling kinases with target genes can be used to map more precisely and comprehensively the regulatory circuitry that eukaryotic cells use to respond to their environment.
Project description:We explore the genome-wide occupancy of 4 different chromatin regulating complexes encoded in S. cerevisiae. We provide the data for histone acetyltransferases Gcn5 and Esa1 and histone deacetylases Hst1 and Rpd3/Sin3 under rich growth condition (YPD medium). We also include the occupancy data for RNA polymerase II under the same growth condition.
Project description:Exponentially growing Sulfolobus acidocaldarius were treated with NaAc to generate replication runout and arrest in G2 phase. The cells were then resuspended in fresh acetate-free media which generates a synchronous population. Samples for investigation of gene expression change were taken during the synchronised populations progress through the cell cycle.
Project description:A gene expression study using microarray analysis was performed to elucidate the underlying mechanism leading to embryonic lethality in homozygous Commd1 null (Commd1-/-) mouse embryos. A gene expression profile of 9.5 dpc Commd1-/- embryos were generated and were compared to a gene expression profile of both 8.5 dpc and 9.5 dpc normal embryos.
Project description:Chromosomal translocations that fuse the Mixed Lineage Leukemia (MLL) gene with multiple partners typify acute leukemias of infancy as well as therapy-related leukemias. We utilized a conditional knock-in strategy to bypass the embryonic lethality caused by MLL-CBP expression and to assess the immediate effects of induced MLL-CBP expression on hematopoiesis. Within days of activating MLL-CBP, the fusion protein selectively expanded granulocyte/macrophage progenitors (GMP) and enhanced their self-renewal/proliferation. MLL-CBP altered the gene expression program of GMP, upregulating a subset of genes including Hox a9. Inhibition of Hox a9 expression by RNA interference (RNAi) demonstrated that MLL-CBP required Hox a9 for its enhanced cell expansion. Following exposure to sublethal g-irradiation or N-ethyl-N-nitrosourea (ENU), MLL-CBP mice developed myelomonocytic hyperplasia and progressed to fatal myeloproliferative disorders. These represented the spectrum of therapy-induced acute myelomonocytic leukemia (t-AMML)/chronic myelomonocytic leukemia (t-CMML)/myelodysplastic/myeloproliferative disorder (t-MD/MPD) similar to that seen in humans possessing the t(11;16). This model of MLL-CBP therapy-related myeloproliferative disease demonstrates the selectivity of this MLL-fusion for GMP cells and its ability to initiate leukemogenesis in conjunction with cooperating mutations.
Project description:In order to study the physiological consequences of a high-copper diet on hepatic gene expression, 6 mM CuCl2 was added to the drinking water for a period of 1 month. After this period, livers of seven control mice and eight copper-treated mice were isolated and were subjected to microarray analysis and copper measurements. The hepatic gene expression profile of copper-treated mice was compared to non-treated mice using a pooled reference.