Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA288783 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction. H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant seeds. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA. Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Alternatively, H2A.X may be involved in recruiting methyltransferases to those sites. Overall, our data show that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.
2023-08-07 | GSE233920 | GEO
Project description:Dynamic DNA methylation reconfiguration during seed development and germination (RNA-seq)
| PRJNA373835 | ENA
Project description:Dynamic DNA methylation reconfiguration during seed development and germination (MethylC-seq)
| PRJNA373836 | ENA
Project description:Cytosine methylation is a key epigenetic mark in many organisms, important for both transcriptional control and genome integrity. While relatively stable during somatic growth, DNA methylation is reprogrammed genome-wide during mammalian reproduction. Reprogramming is essential for zygotic totipotency, and to prevent transgenerational inheritance of epimutations. The extent of DNA methylation reprogramming in plants however remains unclear. Here, we developed sensors reporting with single-cell resolution CG and non-CG methylation in Arabidopsis. Live imaging during reproduction revealed distinct and sex-specific dynamics for both contexts. We found that CHH methylation in the egg cell depends on DRM2 and Pol V, two main actors of RNA-directed DNA methylation, but does not depend on Pol IV. Our sensors provide insight into global DNA methylation dynamics at the single cell level with high temporal resolution, and offer a powerful tool to track CG and non-CG methylation both during development and in response to environmental cues in all organisms with methylated DNA.
2017-08-01 | GSE70455 | GEO
Project description:DNA N6-adenine methylation in Arabidopsis thaliana (methylation)
| PRJNA322062 | ENA
Project description:MTHFD1 controls DNA methylation in Arabidopsis
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Project description:The objective of the study is to profile histone H3 lysine nine di-methylation (H3K9me2) in Arabidopsis thaliana and to correlate it with DNA methylation.
2008-09-11 | GSE12383 | GEO
Project description:Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation
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Project description:Ecotype-specific differences in genome methylation were assayed in Arabidopsis Col and Ler variations using genomic tiling microarrays. Comparative genome hybridization was also performed so that the contribution of ecotype-specific amplifications and deletions could be estimated and integrated into the analysis of differential DNA methylation. Keywords: methylation analysis and comparative genome hybridization
2007-05-09 | GSE7580 | GEO
Project description:DNA methylation in ddm1 seedling Arabidopsis thaliana plants
| PRJNA91037 | ENA