Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Swc4 protects nucleosome free chromatin of telomeres, tRNA genes and rDNA loci to inhibit genome instability [ATAC-seq]

ABSTRACT: In the baker’s yeast Saccharomyces cerevisiae, Swc4, Yaf9, Arp4, and Act1 form a submodule shared by histone acetylation NuA4 complex and chromatin remodeling SWR1 complex (SWR1-C). Act1 and Arp4 are essential for cell survival. Deletion of SWC4, but not YAF9, results in severe growth defect, however, the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display mitotic defects in both faithful chromosome segregation and DNA ploidy, suggesting that the defects observed in swc4Δ cells are independent of the integrity of either NuA4 or SWR1-C. Additionally, loss of Swc4 function results in chromosomal breakage and spindle assembly check-point activation. Swc4 binds to telomeres, tRNA and rDNA regions in genome, which represent nucleosome free regions (NFRs) of chromatin. Notably, telomeres, tRNA genes and rDNA loci, in swc4Δ cells become unstable and are highly susceptible to recombination. Taking together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin from breakage to ensure genome integrity.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE202946 | GEO | 2022/05/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Swc4 protects nucleosome free chromatin of telomeres, tRNA genes and rDNA loci to inhibit genome instability [ChIP-Seq]

Project description:In the baker’s yeast Saccharomyces cerevisiae, Swc4, Yaf9, Arp4, and Act1 form a submodule shared by histone acetylation NuA4 complex and chromatin remodeling SWR1 complex (SWR1-C). Act1 and Arp4 are essential for cell survival. Deletion of SWC4, but not YAF9, results in severe growth defect, however, the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display mitotic defects in both faithful chromosome segregation and DNA ploidy, suggesting that the defects observed in swc4Δ cells are independent of the integrity of either NuA4 or SWR1-C. Additionally, loss of Swc4 function results in chromosomal breakage and spindle assembly check-point activation. Swc4 binds to telomeres, tRNA and rDNA regions in genome, which represent nucleosome free regions (NFRs) of chromatin. Notably, telomeres, tRNA genes and rDNA loci, in swc4Δ cells become unstable and are highly susceptible to recombination. Taking together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin from breakage to ensure genome integrity.

2022-10-14 | GSE215374 | GEO

Swc4 protects chromatin against genome instability and aneuploidy

Project description:In the baker’s yeast Saccharomyces cerevisiae, Swc4, Yaf9, Arp4, and Act1 form a submodule shared by histone acetylation NuA4 complex and chromatin remodeling SWR1 complex (SWR1-C). Act1 and Arp4 are essential for cell survival. Deletion of SWC4, but not YAF9, results in severe growth defect, however, the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display mitotic defects in both faithful chromosome segregation and DNA ploidy, suggesting that the defects observed in swc4Δ cells are independent of the integrity of either NuA4 or SWR1-C. Additionally, loss of Swc4 function results in chromosomal breakage, spindle assembly check-point activation and significant increase of the Rfa1 foci and γ-H2A levels. Notably, both telomeres and rDNA loci in swc4Δ cells become unstable and are highly susceptible to recombination. Mechanistically, Swc4 interacts with chromatin likely through hypoacetylated histone H4. Taking together, we conclude that the chromatin associated Swc4 protects chromatin from breakage to ensure genome integrity.

2021-11-07 | GSE188281 | GEO

Swc4 protects nucleosome-free rDNA, tDNA and telomere loci to inhibit genome instability

Project description:In the baker’s yeast Saccharomyces cerevisiae, NuA4 and SWR1-C, two multisubunit complexes, are involved in histone acetylation and chromatin remodeling, respectively. Eaf1 is the assembly platform subunit of NuA4, Swr1 is the assembly platform and catalytic subunit of SWR1-C, while Swc4, Yaf9, Arp4 and Act1 form a functional module, and is present in both NuA4 and SWR1 complexes. ACT1 and ARP4 are essential for cell survival. Deletion of SWC4, but not YAF9, EAF1 or SWR1 results in a severe growth defect, but the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display defects in DNA ploidy and chromosome segregation, suggesting that the defects observed in swc4Δ cells are independent of NuA4 or SWR1-C integrity. Swc4 is enriched in the nucleosome-free regions (NFRs) of the genome, including characteristic regions of RDN5s, tDNAs and telomeres, independently of Yaf9, Eaf1 or Swr1. In particular, rDNA, tDNA and telomere loci are more unstable and prone to recombination in the swc4Δ cells than in wild-type cells. Taken together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin of rDNA, tDNA and telomere loci to ensure genome integrity.

2023-05-31 | GSE233269 | GEO

Distribution of Arp4 in G2/M phase

Project description:The actin-related proteins (ARPs) comprise a conserved protein family. Arp4p is found in large multisubunits of the INO80 and SWR1 chromatin remodeling complexes and in the NuA4 histone acetyltransferase complex. Here we show that arp4 (arp4S23AD159A) temperature-sensitive cells are defective in G2/M phase function. arp4 mutants are sensitive to the microtubule depolymering agent benomyl and arrest at G2/M phase at restrictive temperature. Arp4p is associated with centromeric and telomeric regions throughout cell cycle. Ino80p, Esa1p, and Swr1p, components of the INO80, NuA4, and SWR1 complexes, respectively, also associate with centromeres. The association of many kinetochore components including Cse4p, a component of the centromere nucleosome, Mtw1p, and Ctf3p is partially impaired in arp4 cells, suggesting that the G2/M arrest of arp4 mutant cells is due to a defect in formation of the chromosomal segregation apparatus. Keywords: ChIP-chip â¢ The goal of the experiment Genome-wide localization of Arp4 binding sites in Saccharomyces cerevisiae â¢ Experimental factors Distribution of Arp4 in WT in G2/M phase in the presence of nocodazole (Saccharomyces cerevisiae). â¢ Experimental design ChIP analysis: Hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Chromosome III, IV,V,VI S. cerevisiae: SC3456a520015F, P/N# 520015, affymetrix tiling array were used.

2010-06-11 | E-GEOD-7276 | biostudies-arrayexpress

Distribution of Arp4 in G2/M phase

2007-03-16 | GSE7276 | GEO

Gene expression data of Arabidopsis thaliana yaf9a yaf9b double mutant seedlings

Project description:Post-translational histone modifications and the dynamics of histone variant H2A.Z are key mechanisms underlying the floral transition. In yeast, SWR1-C and NuA4-C mediate the deposition of H2A.Z and the acetylation of histone H4, H2A and H2A.Z respectively. Yaf9 is a subunit shared by both chromatin remodeling complexes. The significance of the two Arabidopsis YAF9 homologs, YAF9A and YAF9B, is unknown. We performed a transcriptomic analysis of wild-type and yaf9a yaf9b double mutant seedlings in order to reveal target genes whose transcription is regulated by YAF9 proteins.

2019-02-06 | GSE126020 | GEO

Histone acetylation readers Bdf1 and Yaf9 guide targeting of SWR1 remodeler to +1 nucleosome

Project description:The histone variant H2A.Z marking permissive chromatin is preferentially deposited at promoter-proximal +1 nucleosomes by the multicomponent SWR1 chromatin remodeler. Although SWR1 targeting to nucleosome-depleted regions (NDRs) is directed by its free DNA length sensing module, how the remodeler is guided preferentially to flanking +1 nucleosomes has been enigmatic. Here, we show by live-cell, single-molecule tracking (SMT) that SWR1 subunits Bdf1 and Yaf9 harboring bromo and YEATS acetyl-histone reader domains are required for quantitative chromatin binding via distinct kinetic mechanisms: Bdf1 increases SWR1 association, Yaf9-YEATS reduces disassociation. Notably, SMT and genome-wide ChIP-exo reveals Bdf1 and Yaf9 contributions to SWR1 targeting globally and histone exchange at +1 nucleosomes. Our findings highlight the native biochemistry of histone readers and suggest a broadly applicable, two-stage mechanism wherein acetyl-histone interactions initially constrain 3D diffusion of SWR1 to increase local concentration, followed by stochastic 1D diffusion at NDRs with directional capture by acetylated +1 nucleosomes.

2024-07-29 | GSE273028 | GEO

Nucleosome free DNA- and acetyl histone-binding components recruit SWR1 to yeast promoters for H2A.Z replacement

Project description:The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. While the multi-subunit SWR1 chromatin remodeling complex is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of di-nucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA adjoining core particles, allowing discrimination of gene promoters over gene bodies. We traced the critical DNA binding component of SWR1 to the conserved Swc2/YL1 subunit, whose activity is required for both SWR1 binding and H2A.Z incorporation in vivo. Histone acetylation by NuA4 enhances SWR1 binding, but the interaction with nucleosome-free DNA is the major determinant. ‘Hierarchical cooperation’ between high affinity DNA- and low affinity histone modification-binding factors may reconcile the large disparity in affinities for chromatin substrates, and unify classical control by DNA-binding factors with post-translational histone modifications and ATP-dependent nucleosome mobility. Swr1 TAP IF of various mutants

2013-09-16 | E-GEOD-49183 | biostudies-arrayexpress

Nucleosome free DNA- and acetyl histone-binding components recruit SWR1 to yeast promoters for H2A.Z replacement

2013-09-16 | GSE49183 | GEO

NuA4 and SWR1 complex in Plasmodium falciparum

Project description:In this study, we identified an MYST-associated complex in P. falciparum, which contains 11 of 13 conserved NuA4 subunits based on their domain structures. Meanwhile, reciprocal pulldowns not only confirmed the NuA4-like complex but also identified an SWR1-like complex, a histone remodeling complex, in P. falciparum.

2024-03-18 | PXD046547 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data