Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA141253 | ENA |
REPOSITORIES: ENA
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Project description:The DEMETER (DME) DNA glycosylase mediates genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-demethylation are small, AT-rich transposons and boundaries of large heterochromatic transposons, but how DME interacts with chromatin is unclear. To investigate the interaction between DME and chromatin, we analyzed DNA methylation in Arabidopsis seeds and pollen deficient in the chromatin remodeler FAcilitates Chromatin Transactions (FACT) complex. We find that FACT co-localizes with nuclear DME, and is required for DME activity in chromatin domains with high nucleosome occupancy and histone modifications associated with heterochromatin, which comprise over half of DME target loci. We also demonstrate that heterochromatin-associated linker histone H1 mediates the requirement for FACT at a subset of DME-target loci. However, FACT is not required for DME demethylation of targets in euchromatic regions. Thus, chromatin structure determines the degree to which FACT facilitates access of DME to its targets.
2018-04-17 | GSE105000 | GEO
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:rs10-02_ros_dme - genes regulated by ros and dme - Genes regulated by ros/dme? - Seeds of Col x ROS-/-/DME+/- 3 and 6 days after pollination (DAP) were harvested. Seeds of the cross Col x Col (3 and 6 DAP) were used as a control.
2011-06-02 | GSE29626 | GEO
Project description:rs10-02_ros_dme - genes regulated by ros and dme - Genes regulated by ros/dme? - Seeds of Col x ROS-/-/DME+/- 3 and 6 days after pollination (DAP) were harvested. Seeds of the cross Col x Col (3 and 6 DAP) were used as a control. 4 dye-swap - gene knock out
2011-06-01 | E-GEOD-29626 | biostudies-arrayexpress
Project description:The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these target loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which how H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that unlike in the vegetative cell, both canonical histone H1 variants are present in the central cell. Our endosperm methylome analysis revealed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-containing nucleosomes are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation.
2022-11-11 | GSE217277 | GEO
Project description:TheArabidopsisDEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these target loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which how H1 influences DME demethylation and gene imprinting in theArabidopsisendosperm has not been investigated. Here, we showed that unlike in the vegetative cell, both canonical histone H1 variants are present in the central cell. Our endosperm methylome analysis revealed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-containing nucleosomes are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation.
2022-11-11 | GSE217278 | GEO
Project description:Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethylation to imprinted gene expression. Our data furthermore suggest an absence of de novo DNA methylation in the early endosperm, providing an explanation how DME-mediated hypomethylation of the maternal genome is maintained after fertilization. Lastly, we show that paternal-specific H3K27me3- marked regions are located at pericentromeric regions, suggesting that H3K27me3 and DNA methylation are not necessarily exclusive marks at pericentromeric regions in the endosperm.
2016-04-26 | GSE66585 | GEO
Project description:Genome-wide Identification of APETALA1 Regulated Genes during Early Flower Development in Arabidopsis
| PRJNA255919 | ENA
Project description:dgpp-DGPP regulated genes. Identification of diacylglycerol pyrophosphate regulated genes in ABA signaling.
| PRJNA112559 | ENA