Project description:Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler Matched MNase digests from W303 strain variants during log growth (OD600=0.4-0.6) were subject to paired-end sequencing for nucleosome mapping. For effects of the engineered fusion remodeling protein, a catalytically inactive (ATPase dead D513N) variant was included as a control.
Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast. Nucleosome occupancy was measured in the S288c derivative BY4741 and a strain lacking MSN2 and MSN4. Nucleosomes were isolated from unstressed yeast and yeast treated for 20 min with 0.4mM H2O2. Nucleosomal samples were compared in a 2-color, competitive hybridization to sheared genomic DNA.
Project description:RNA sequencing was performed on various W303 variants to determine effects of nucleosome repositioning on transcript abundance RNA sequencing was carried out in multiple backgrounds to determine effects of nucleosome repositioning in various contexts. For engineered chromatin remodeling factors, a catalytically inactive control was included.
Project description:This SuperSeries is composed of the following subset Series: GSE30897: Nucleosome occupancy in yeast BY4741and a strain lacking MSN2 and MSN4 responding to 20 min treatment with 0.4mM H2O2 GSE30898: Msn2p occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min) GSE30899: Gene expression dynamics in yeast BY4741 and a strain lacking MSN2 and MSN4 responding to 0.4mM H2O2 over time (0-60min) GSE30900: Nucleosome occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min) Refer to individual Series
Project description:We report nucleosome poisitioning under pertubation conditions such as heat shock, CHD1 deletion, and SET2 deletion Mono-nucleosome DNA was prepared from wild type strain under normal or heat shock conditions, or CHD1 or SET2 deletion strain. The mono-nucleosome DNA was mapped.
Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.
Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures. Genome-wide nucleosome occupancy maps in RSC and rsc null strains were generated by paired-end sequencing of mononucleosomal DNA. Strains carrying the Sth1 degron allele and either pGal-UBR1 (YBC3386) or ubr1 null (YBC3387) represent RSC null and RSC wildtype, respectively.
Project description:MNase-seq Experiments from Calorie Restricted and Non-Restricted Yeast from WT, ISW2DEL and ISW2K215R strains We used MNase-seq to study genome-wide nucleosome positions under Calorie Restricted and Non-restricted Saccharomyces cerevisiae