The SNF2 ATPase-independent function of the INO80 chromatin remodeler
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ABSTRACT:
PROVIDER: PRJNA681620 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13169633.fastq.gz | Fastqsanger.gz | |||
| SRR13169634.fastq.gz | Fastqsanger.gz | |||
| SRR13169635.fastq.gz | Fastqsanger.gz | |||
| SRR13169636.fastq.gz | Fastqsanger.gz | |||
| SRR13169637.fastq.gz | Fastqsanger.gz |
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Project description:In the multi-subunit INO80 chromatin-remodeling complex, all the auxiliary subunits assemble on three distinct domains of the catalytic chromatin remodeler INO80, which are N-terminal domain, HSA domain, and ATPase domain. While the ATPase and HSA domains and the auxiliary subunits assembling on the domains are known to be responsible for ATP hydrolysis and chromatin remodeling, it is largely unknown how the auxiliary subunits assembling on the INO80 N-terminal domain regulate the chromatin status. We identify both conserved and non-conserved auxiliary subunits of the INO80 complex in Arabidopsis thaliana. All the auxiliary subunits assemble on the conserved N-terminal domain, HSA domain, and ATPase domain of INO80 in Arabidopsis. While the auxiliary subunits assembling on the INO80 ATPase domain are required for the ATPase-dependent function, the INO80 N-terminal domain and the auxiliary subunits assembling on the domain can regulate gene expression and development even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. Furthermore, we find that a subclass of the COMPASS histone H3K4 methyltransferase complexes assemble on the INO80 N-terminal domain in the INO80 complex and function together with the other auxiliary subunits assembling on the INO80 N-terminal domain, thereby facilitating the ATPase-independent function. This study suggests that the conserved chromatin remodeler INO80 has an ATPase-independent role and demonstrates that the auxiliary subunits assembling on the INO80 N-terminal domain are required for the ATPase-independent role.
2021-05-25 | GSE162373 | GEO
Project description:In the multi-subunit INO80 chromatin-remodeling complex, all the auxiliary subunits assemble on three distinct domains of the catalytic chromatin remodeler INO80, which are N-terminal domain, HSA domain, and ATPase domain. While the ATPase and HSA domains and the auxiliary subunits assembling on the domains are known to be responsible for ATP hydrolysis and chromatin remodeling, it is largely unknown how the auxiliary subunits assembling on the INO80 N-terminal domain regulate the chromatin status. We identify both conserved and non-conserved auxiliary subunits of the INO80 complex in Arabidopsis thaliana. All the auxiliary subunits assemble on the conserved N-terminal domain, HSA domain, and ATPase domain of INO80 in Arabidopsis. While the auxiliary subunits assembling on the INO80 ATPase domain are required for the ATPase-dependent function, the INO80 N-terminal domain and the auxiliary subunits assembling on the domain can regulate gene expression and development even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. Furthermore, we find that a subclass of the COMPASS histone H3K4 methyltransferase complexes assemble on the INO80 N-terminal domain in the INO80 complex and function together with the other auxiliary subunits assembling on the INO80 N-terminal domain, thereby facilitating the ATPase-independent function. This study suggests that the conserved chromatin remodeler INO80 has an ATPase-independent role and demonstrates that the auxiliary subunits assembling on the INO80 N-terminal domain are required for the ATPase-independent role.
2021-05-25 | GSE162374 | GEO
Project description:The SNF2 ATPase-independent function of the INO80 chromatin remodeler [ChIP-seq]
| PRJNA681623 | ENA
Project description:The SNF2 ATPase-independent function of the INO80 chromatin remodeler [RNA-seq]
| PRJNA681622 | ENA
Project description:The mechanistics by which ATP-dependent chromatin remodelers process (epi)genetic information to generate hallmark features of chromatin are fundamental for genome regulation. Here, we advance whole-genome reconstitutions into a fully definable, recombinant approach for probing how remodelers determine nucleosome positioning. Using wild type and structure-guided mutant versions of the Saccharomyces cerevisiae 15-subunit INO80 remodeler, we show that INO80-intrinsic nucleosome positioning relies on direct DNA shape read-out. This requires especially the interplay between the INO80 nuclear actin and core modules, to a lesser extent the HMG-box Nhp10 module and not histone modifications/variants or the Rvb1/2 AAA+-ATPase activity. Extrinsically, nucleosome positioning is guided by the barrier Reb1 via Ino80 ATPase activity modulation or by mere DNA double strand breaks. Taken together, we present a defined and unbiased approach to understand remodeler-mediated nucleosome positioning and delineate how INO80 processes genomic information into nucleosome positioning.
2020-04-30 | GSE145093 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-05-25 | GSE162375 | GEO
Project description:Neuroadaptations in the nucleus accumbens (NAc) underlie cue-induced cocaine craving that intensifies (“incubates”) during withdrawal and contributes to persistent relapse vulnerability. Long-lasting gene changes govern perpetual behavioral abnormalities but the role of epigenetic plasticity in cocaine craving during prolonged withdrawal is poorly understood. Here we show that chromatin remodeler INO80 in the NAc mediates cocaine-induced, withdrawal-dependent plasticity and incubated cocaine craving.
2019-10-29 | GSE119627 | GEO
Project description:Background: Chromatin remodeling complexes facilitate the access of enzymes that mediate transcription, replication or repair of DNA by modulating nucleosome position and/or composition. Ino80 is the DNA-dependent Snf2-like ATPase subunit of a complex whose nucleosome remodeling activity requires actin-related proteins, Arp4, Arp5 and Arp8, as well as two RuvB-like DNA helicase subunits. Budding yeast mutants deficient for Ino80 function are not only hypersensitive to reagents that induce DNA double strand breaks, but also to those that impair replication fork progression. Results: To understand why ino80 mutants are sensitive to agents that perturb DNA replication, we used chromatin immunoprecipitation to map the binding sites of the Ino80 chromatin remodeling complex on four budding yeast chromosomes. We found that Ino80 and Arp5 binding sites coincide with origins of DNA replication and tRNA genes. In addition, Ino80 was bound at 67% of the promoters of genes that are sensitive to ino80 mutation. When replication forks were arrested near origins in the presence of hydroxyurea (HU), the presence of the Ino80 complex at stalled forks and at unfired origins increased dramatically. Importantly, the resumption of DNA replication after release from a HU block was impaired in the absence of Ino80 activity. Mutant cells accumulated double-strand breaks as they attempted to restart replication. Consistently, ino80-deficient cells, although proficient for checkpoint activation, delay recovery from the checkpoint response. Conclusions: The Ino80 chromatin remodeling complex is enriched at stalled replication forks where it promotes the resumption of replication upon recovery from fork arrest. Keywords: ChIP-chip • The goal of the experiment Genome-wide localization of Ino80 on chromosome in Saccharomyces cerevisiae • Keywords DNA replication, Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI) • Experimental factor Distribution of Ino80 in random culture Distribution of Ino80 in G1 phase Distribution of Ino80 in early S phase • Experimental design ChIP analyses: W303 background cells expressing Myc-tagged Ino80 were used for the ChIP using anti-Myc monoclonal antibody (9E11). ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI) was used. • Quality control steps taken Confirmation of several loci by quantitative real time PCR.
2008-04-10 | E-GEOD-9420 | biostudies-arrayexpress
Project description:INO80 complex is an ATPase-dependent chormatin remodeling complex, which regulates various DNA metabolic processes such as DNA replication and repair. Additionally, INO80 complex also contributes to the regulation of gene expression in sterss response and development. In order to investigate the function of INO80 complex in rhabdomyosarcoma, we examined the knockdown of subunits of INO80 complex Actr5, Ies6, and Ino80 in human rhabdomyosarcoma RD cells. As a result, it was found that INO80 complex is involved in the sarcomagenicity and the disregulation of myogenic properties of rhabdomyosarcoma cells.
2022-04-01 | GSE169681 | GEO
Project description:Background: Chromatin remodeling complexes facilitate the access of enzymes that mediate transcription, replication or repair of DNA by modulating nucleosome position and/or composition. Ino80 is the DNA-dependent Snf2-like ATPase subunit of a complex whose nucleosome remodeling activity requires actin-related proteins, Arp4, Arp5 and Arp8, as well as two RuvB-like DNA helicase subunits. Budding yeast mutants deficient for Ino80 function are not only hypersensitive to reagents that induce DNA double strand breaks, but also to those that impair replication fork progression. Results: To understand why ino80 mutants are sensitive to agents that perturb DNA replication, we used chromatin immunoprecipitation to map the binding sites of the Ino80 chromatin remodeling complex on four budding yeast chromosomes. We found that Ino80 and Arp5 binding sites coincide with origins of DNA replication and tRNA genes. In addition, Ino80 was bound at 67% of the promoters of genes that are sensitive to ino80 mutation. When replication forks were arrested near origins in the presence of hydroxyurea (HU), the presence of the Ino80 complex at stalled forks and at unfired origins increased dramatically. Importantly, the resumption of DNA replication after release from a HU block was impaired in the absence of Ino80 activity. Mutant cells accumulated double-strand breaks as they attempted to restart replication. Consistently, ino80-deficient cells, although proficient for checkpoint activation, delay recovery from the checkpoint response. Conclusions: The Ino80 chromatin remodeling complex is enriched at stalled replication forks where it promotes the resumption of replication upon recovery from fork arrest. Keywords: ChIP-chip
2008-04-10 | GSE9420 | GEO