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Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

ABSTRACT: INO80, one member of ATP-ase remodeler factor, play a role on chromatin dynamic modulation. OsINO80 (LOC_Os03g22900) is identified as a homologue of INO80 in rice. To study the function of OsINO80 on H2A.Z, we analyzed the distribution of OsINO80 and H2A.Z in 14-week-old seedling of Oryza stative Japanese rice plant through ChIP assay following by high through sequencing (ChIP-seq).Integrated analysis showed that OsINO80 regulate the H2A.Z level.

ORGANISM(S): Oryza sativa

PROVIDER: GSE181808 | GEO | 2024/08/10

REPOSITORIES: GEO

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Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

Project description:INO80, one member of ATP-ase remodeler factor, play a role on chromatin dynamic modulation. OsINO80 (LOC_Os03g22900) is identified as a homologue of INO80 in rice. To study the function of OsINO80 on H2A.Z, we analyzed the distribution of OsINO80 and H2A.Z in 14-week-old seedling of Oryza stative Japanese rice plant through ChIP assay following by high through sequencing (ChIP-seq).Integrated analysis showed that OsINO80 regulate the H2A.Z level.

2024-08-10 | GSE181809 | GEO

Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

Project description:Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

| PRJNA753507 | ENA

Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

Project description:Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

| PRJNA753508 | ENA

ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

Project description:To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq.

2024-04-10 | GSE225484 | GEO

RNAseq for WT and osino80

Project description:To investigate the effect of the OsINO80, we analysed differentially expressed genes of osino80 mutant compared to WT. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and osino80 mutant.

2024-04-10 | GSE225485 | GEO

BSseq for WT and osino80

Project description:To investigate the effect of the OsINO80, we analysed DNA methylation of osino80 mutant compared to WT.

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The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis[ChIP-seq]

Project description:Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed thermomorphogenesis to facilitate plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermo-responsive genes, resulting in their activation. However, the mechanisms that regulate H2A.Z eviction and subsequent transcription activation are largely unknown. Here, we show that the ino80 chromatin-remodeling complex (ino80-C) promotes thermomorphogenesis and activates the expression of thermo-responsive and auxin-related genes. ino80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator in thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, ino80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification Histone H3 lysine 4 trimethylation (H3K4me3) and RNA Polymerase II (RNA Pol II) elongation, leading to the thermal induction of transcription. Notably, transcription elongation factors are required for the eviction of H2A.Z at PIF4 targets, suggesting the cooperation of ino80-C and transcription elongation in H2A.Z removal. Our results demonstrate that the (PIF4)-(ino80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, and establish a link between H2A.Z eviction and active transcription.

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The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis[RNA-seq]

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The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination

Project description:INO80 is an evolutionary conserved nucleosome remodelling complex that acts in transcription, replication and genome stability. It is required for resistance against genotoxic agents and involved in the repair of DNA double-strand breaks (DSB) by homologous recombination (HR). However, causes underlying the HR defect of INO80-C mutant cells have been controversially discussed. We here unite previous findings using a high-resolution system to study HR in the yeast Saccharomyces cerevisiae. We find that INO80-C has at least two distinct functions during HR, which promote DNA end resection and presynaptic filament formation, respectively. Importantly, specifically the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.

2017-05-14 | GSE95801 | GEO

The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription

Project description:To investigate the incorporation dynamics of histone variant H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. We find that Swr1 binding alone is a poor predictor of H2A.Z occupancy levels, and that normal Swr1 and Ino80 localization are actually dependent on H2A.Z. Additionally, we find that H2A.Z’s bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking -1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription.

2019-10-29 | GSE104147 | GEO

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