Nucleosomal occupancy in a SNF2 deletion
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Lawrence Heisler
PROVIDER: E-TABM-1141 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The in vivo role of a novel domain in Swi2/Snf2 required for its function was investigated using microarray analysis. The effect of domain deletions of Swi2/Snf2 on expression changes were studied. The ?SnAC strain, along with ?snf2 and wild type strains (BY4741 and Snf2-2FLAG, PSY2), were analyzed by genome-wide expression profiling with DNA microarrays. The method has been described in Chitikila et al., Mol. Cell, 10:871-882, 2002 (PMID 12419230).
2011-09-14 | E-GEOD-30675 | biostudies-arrayexpress
Project description:Despite its streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae. One of the most striking is the regulated splicing of meiotic transcripts, part of the dramatic reprogramming of gene expression upon meiotic onset. Here we show a crucial role for the chromatin remodeler Snf2, part of the Swi/Snf complex in meiotic regulation of splicing. We find that the complex affects meiotic splicing in several ways. First, meiosis-specific expression of the splicing activator Mer1 is Swi/Snf dependent, involves precise timing of acetylation of histone H3K9 at the MER1 locus, and changes in the acetylation state of Snf2. Additionally, Swi/Snf abundance regulates meiosis-specific downregulation of ribosomal protein encoding RNAs, leading to the redistribution of spliceosomes from this abundant class of intron-containing RNAs to meiotic transcripts. This regulation is achieved by rapid downregulation of the Snf2 protein. Taken together these data reveal that the Swi/Snf complex coordinates a cascade of events to direct the regulated splicing of meiotic genes, establishing it as a master regulator of meiotic splicing in S. cerevisiae.
2017-04-20 | GSE94404 | GEO
Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern. TIP-seq recovery of transposon insertion junctions in haploid and diploid yeast
2012-01-01 | E-GEOD-33986 | biostudies-arrayexpress
Project description:Here we investigated the stability of nucleosomal modifications during pull-down affinity purification with HeLa nuclear extracts. Unmodified di-nucleosomes and di-nucleosomes decorated with H3K4me3K9acK14acK18acK23acK27ac, H4K5acK8acK12acK16acK20me2 and incorporating histone variant H2A.Z were incubated with HeLa nuclear extract or buffer alone for 4 hours at 4 degrees Celsius. The relative abundances of nucleosomal modifications were quantified using LC-MS.
2023-12-10 | PXD042823 | Pride
Project description:Cells respond to changes in environment by shifting their gene expression profile to deal with the new conditions. The cellular response to changes in metal homeostasis is an important example of this. Transition metals such as iron, zinc, and copper are essential micronutrients but other metals such as cadmium are simply toxic. The cell must maintain metal concentrations in a window that supports efficient metabolic function but must also protect against the damaging effects of high concentrations of these metals. One way a cell regulates metal homeostasis is to control genes involved in metal mobilization and storage. Much of this regulation occurs at the level of transcription and the protein most responsible for this is the conserved metal responsive transcription factor, MTF-1. Interestingly, the nature of the changes in the gene expression profile depends on the type of exposure. The cell somehow senses the kind of metal challenge and responds appropriately. We have been using the Drosophila system to try to understand the mechanism of this metal discrimination. Using genome-wide mapping of MTF-1 binding under different metal stresses, we find that, surprisingly, MTF-1 chooses different DNA binding sites depending on the specific nature of the metal insult. We also find that the type of binding site chosen is an important component of the capability to induce the metal-specific transcription activation. Chromatin immunoprecipitation coupled with Drosophila genomic tiling arrays (ChIP-chip) was used to identify genomic regions directly bound by dMTF-1 in untreated and metal (Cu and Cd) challenged S2 cells. The dMTF-1 antibody was raised against amino acids 1-113 and 406-540 of MTF-1.
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Project description:DNA methylation profiling by D-REAM
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Project description:Background: Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in P. falciparum. To better understand chromatin-mediated gene regulation, we used a high-density oligonucleotide microarray to map the position and enrichment of nucleosomes across the entire genome of P. falciparum at three time points of the intra-erythrocytic developmental cycle (IDC) in vitro. We used an unmodified histone H4 antibody for chromatin immunoprecipitation of nucleosome-bound DNA. Results: We observed generally low nucleosomal occupancy of intergenic regions and higher occupancy of protein coding regions. In contract to the overall small fluctuation of nucleosomal occupancy in most coding regions throughout the IDC, subtelomeric genes encoding surface proteins such as var and rif, as well as some core chromosomal genes such as transcription factors, showed large changes in chromatin structure. Telomeres harbored a region with the highest nucleosomal occupancy of the genome and also exhibited large changes with higher nucleosomal occupancy at schizont stages. While many of these subtelomeric genes were previously shown to be modified by H3K9 trimethylation, we also identified some housekeeping genes in core chromosome regions that showed extensive changes in chromatin structure but do not contain this modification. tRNA and basal transcription factor genes showed low nucleosomal occupancy at all times, suggesting of an open chromatin structure that might be permissive for constitutively high levels of expression. Generally, nucleosomal occupancy was not correlated with the steady-state mRNA levels. Several var genes were exceptions: the var gene with the highest expression level showed the lowest nucleosomal occupancy, and selection of parasites for var2CSA expression resulted in lower nucleosomal occupancy at the var2CSA locus. We identified nucleosome-free regions in intergenic regions that may serve as transcription start sites or transcription factor binding sites. Using the nucleosomal occupancy data as the baseline, we further mapped the genome-wide enrichment of H3K9 acetylation and detected general enrichment of this mark in intergenic regions. Conclusions: These data on nucleosome enrichment changes add to our understanding of the influence of chromatin structure on the regulation of gene expression. Histones are generally enriched in coding regions, and relatively poor in intergenic regions. Histone enrichment patterns allow for identification of new putative gene-coding regions. Most genes do not show correlation between chromatin structure and steady-state mRNA levels, indicating the dominant roles of other regulatory mechanisms. We present a genome-wide nucleosomal occupancy map, which can be used as a reference for future experiments of histone modification mapping. Three ChIP with unmodified histone H4 antibodies were performed on ring, trophozoite and schizont stage synchronized parasites. Only one experiment was performed per time point. H3K9ac antibody ChIP was performed on trophozoite stage cells. All samples were normalized to 3D7 strain genomic DNA hybridizations.
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Project description:Histone chaperones modulate the stability of histones beginning from histone synthesis, through incorporation into DNA, and during recycling during transcription and replication. Following histone removal from DNA, chaperones regulate histone storage and degradation. Here we characterize UBR7 as a histone H3.1 chaperone that modulates the supply of pre-existing post-nucleosomal histone complexes. UBR7 is a largely nuclear soluble protein. We demonstrate that UBR7 binds to post-nucleosomal H3K4me3 and H3K9me3 histones via its UBR box and PHD. UBR7 binds to the non-nucleosomal histone chaperone NASP. The pool of NASP-bound post-nucleosomal histones accumulate and chromatin is depleted of H3K4me3 nucleosomes in the absence of UBR7. We propose that the interaction of UBR7, NASP, and histones opposes the histone storage functions of NASP as UBR7 promotes reincorporation of post-nucleosomal H3 complexes.
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Project description:Genome-wide DNA methylation profiling of mouse liver analyzed by D-REAM
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