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RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [MNase-Seq]

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE65593 | GEO | 2015/04/01

SECONDARY ACCESSION(S): PRJNA275207

REPOSITORIES: GEO

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RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [MNase-Seq]

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.

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RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-seq]

2015-04-01 | GSE65592 | GEO

RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [HybMap microarray]

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RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-chip]

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RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [nucleosome occupancy]

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RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-seq]

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. Genomic localization of RSC, ISW1a, and SWI/SNF complexes were measured by chromatin immunoprecipitation followed by Illumina paired-end sequencing. Four strains were analyzed, including Rsc8-9xMyc (YBC2882), Sth1-2xFlag (YBC601 p3018), Ioc3-13xMyc (YBC2883), and Snf2-13xMyc (YBC3010). Each sample consists of one chromatin immunoprecipitate and one input chromatin control.

2015-04-01 | E-GEOD-65592 | biostudies-arrayexpress

RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [nucleosome occupancy]

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 wild-type, mutant RSC, and mutant ISW1 strains were generated by hybridization of mononucleosomal DNA to microarrays. Strains carrying Sth1 degron and either pGal-UBR1 (YBC2191) or ubr1 null (YBC2192) represent RSC null and RSC wildtype, respectively. Strains carrying Sth1 degron isw1 null and either pGal-UBR1 (YBC2467) or ubr1 null (YBC2468) represent RSC null isw1 null and RSC wildtype isw1 null, respectively. Mononucleosomes were isolated from three independent biological replicates from each genotype. Please note that each sample consists of three replicates (i.e. three raw data files) and the sample data table contains combined quantile normalized data of the replicates.

2015-04-01 | E-GEOD-65590 | biostudies-arrayexpress

RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [HybMap microarray]

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. Total RNA expression was determined by the HybMap protocol, hybridization of total RNA to genomic tiling microarray followed by detection with an anti-RNA-DNA-hybrid antibody. Total RNA was isolated from three independent biological replicates of each strain, including wild type (YBC1894), rsc2ts (YBC1111), isw1 null (YBC1416), ioc3 null (YBC2693), isw1 null rsc2ts (YBC3227), and ioc3 null rsc2ts (YBC3228). Please note that each sample consists of three replicates (i.e. three raw data files) and the sample data table contains combined quantile normalized data of the replicates.

2015-04-01 | E-GEOD-65591 | biostudies-arrayexpress

RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-chip]

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. Genomic localization of RSC and ISW1a complexes were measured by chromatin immunoprecipitation followed by genome-wide microarray hybridization. Two independent biological replicates of two strains, Rsc8-9xMyc (YBC2882) and Ioc3-13xMyc (YBC2883), each grown in two different media, rich glucose media (YPD) or minimal synthetic glucose (SD) media. Each sample consists of one chromatin immunoprecipitate and one input chromatin control. Please note that each sample consists of two replicates (i.e. two raw data files) and the sample data table contains combined quantile normalized data of the replicates.

2015-04-01 | E-GEOD-65589 | biostudies-arrayexpress

Stepwise reconstitution of genomic nucleosome organization with pure proteins

Project description:Nucleosome arrays begin at nucleosome-free promoter regions (NFRs) and regulate gene expression. Reconstituting such organization throughout a genome with purified proteins is a critical challenge in establishing biochemical mechanisms for chromosome assembly. Here we establish a four-step hierarchical building plan for yeast genomic nucleosome organization using only purified components: genomic DNA, histones, site-specific organizing factors Abf1 and Reb1, and the chromatin remodelers RSC, ISW2, INO80, and ISW1a. First, RSC makes NFRs by translating promoter poly(dA:dT) tracts into directional nucleosome removal. Second, +1 nucleosomes are positioned by INO80 at most genes potentially involving DNA shape, or by ISW2 using gene-specific Abf1 and Reb1. Third, INO80 or ISW2 create arrays with wide spacing. Fourth, ISW1a tightens the spacing and creates properly positioned arrays. We conclude that entire genomes use a simple set of rules and proteins, without transcription, to build a common chromatin architecture. In this study, nucleosomes were assembled using Salt Gradient Dialysis (SGD) on yeast genomic DNA library. Assembled nucleosomes were either left untreated (labelled as "SGD", control), treated with whole cell extract (WCE), mutant extracts (rsc3ts WCE, isw1 isw2 chd1 WCE), purified remodelers; singly or in combinations (RSC, ISW1a, ISW1b, ISW2, INO80, CHD1, SWI/SNF), combinations of mutant extracts and chromatin remodelers or combination of General Regulatory Factors (Abf1, Reb1) and chromatin remodelers. The resulting nucleosome positions were mapped genome-wide using MNase-(anti-H3-ChIP)-Seq.

2016-08-14 | E-GEOD-72106 | biostudies-arrayexpress

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