Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of Atino80-5 mutant in comparison with wild type.

ABSTRACT: INO80 is a conserved chromatin remodeler through evolution. We identified a novel ino80 mutant allele, Atino80-5, in Arabidopsis thaliana, and performed the transcriptome analysis of this mutant in comparison with wild type (WT).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE60306 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA258000

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The SNF2 ATPase-independent function of the INO80 chromatin remodeler [ChIP-seq]

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

The SNF2 ATPase-independent function of the INO80 chromatin remodeler [RNA-seq]

2021-05-25 | GSE162373 | GEO

Expression data from inflorescence (unopened flower buds) of Arabidopsis thaliana - comparison between Ler and ask1 mutant

Project description:ARABIDOPSIS SKP1-LIKE1 (ASK1) protein is involved in regulating flower development. We have compared ask1 mutant floral transcriptome with wild-type Ler to identify the role of ASK1-containing E3 ubiquitin ligases in regulating flower transcriptome. In this dataset, we include the expression data obtained from Arabidopsis thaliana Ler and ask1 mutant flower buds. We identified 42 genes and 74 genes that are down-regulated and up-regulated, respectively.

2013-02-01 | GSE42841 | GEO

leaf transcriptome comparison between wt and urt1 (salk_087647) -Transcriptome comparison between WT and a mutant impaired in RNA uridylation.

Project description:rs11-10_urt1 - leaf transcriptome comparison between wt and urt1 (salk_087647) - Identification of mRNA targets of the terminal uridylyltransferase URT1 (AT2G45620) in Arabidopsis thaliana. - Identification of the RNA targets of the terminal uridylyl transferase URT1 (AT2G45620). Mature rosettte leaf transcriptomes were compared between WT and a urt1 knock-out mutant (SALK_087647).

2012-07-13 | GSE38902 | GEO

Mnase-Seq study of Arabidopsis thaliana mutant chr5

Project description:Comparative study of nuclesome occupancy in Arabidopsis thaliana mutant chr5 and wild type strain.

2019-05-23 | GSE99639 | GEO

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

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

Proteomic analysis of histone modifications present on nucleosomes bound by INO80 complex

Project description:The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChIP-MS approach to quantitatively profile modifications present on nucleosomes co-purified with INO80 from MNAse-digested HeLa chromatin.

2023-12-10 | PXD042210 | Pride

Quantitative ChIP-MS analysis of histone modifications present on H3K4me1- and H3K4me3-enriched mono-nucleosomes purified from crosslinked IMR-90 cells

2023-12-12 | PXD042224 | Pride

WGBS of Arabidopsis thaliana rll6 mutant

Project description:WGBS of Arabidopsis thaliana rll6 mutant

| PRJNA859377 | ENA

Transcriptome of Arabidopsis thaliana mem1-1 mutant

Project description:Transcriptome of Arabidopsis thaliana mem1-1 mutant and Col-0 under normal and 200ppm MMS treatment conditions, respectively

2021-08-04 | GSE181302 | GEO