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Title: RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [nucleosome occupancy]      
dateReleased:
04-01-2015
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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-65590
refinement:
raw
alternateIdentifiers:
65590
keywords:
functional genomics
dateModified:
04-04-2015
availability:
available
types:
gene expression
name:
Saccharomyces cerevisiae
ID:
A-GEOD-4130
name:
Agilent-014741 Yeast Whole Genome ChIP-on-Chip Microarray 244K (G4491A)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-65590/E-GEOD-65590.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-65590/E-GEOD-65590.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65590
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress