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Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis

ABSTRACT: We used Affymetrix Arabidopsis ATH1 GeneChip to profile RNAs active in wild type columbia (glabrous) and CaMV::DME pollen and stamens. Keywords: genetic modification

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE9408 | GEO | 2007/11/01

SECONDARY ACCESSION(S): PRJNA103139

REPOSITORIES: GEO

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Transcription profiling of Arabidopsis pollen and stamen with induced DEMETER expression to identify

Project description:We used Affymetrix Arabidopsis ATH1 GeneChip to profile RNAs active in wild type columbia (glabrous) and CaMV::DME pollen and stamens. Experiment Overall Design: DME is not active in wild type pollen and stamen. DME was induced in pollen and stamen by a cauliflower mosaic virus promoter (CaMV). RNA profiles from wild type and CaMV::DME pollen and stamens were compared using Affymetrix ATH1 GeneChip.

2008-06-16 | E-GEOD-9408 | biostudies-arrayexpress

Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis.

Project description: Not available

| S-EPMC2137929 | biostudies-literature

The Catalytic Core of DEMETER Guides Active DNA Demethylation in Arabidopsis

Project description:The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization, and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, and how it is recruited to these differing chromatin landscapes is unknown. The C-terminal DME catalytic core consists of three conserved regions required for catalysis in vitro. We show that the catalytic core of DME guides active demethylation at endogenous targets, rescuing the developmental and genomic hypermethylation phenotypes of DME mutants. However, without the N-terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. We used comparative analysis to reveal that the conserved DME N-terminal domains are only present in the flowering plants, whereas the domain architecture of DME-like proteins in non-vascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in all plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N-terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.

2019-05-02 | GSE130559 | GEO

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance (BS_Seq)

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

2021-01-16 | GSE164914 | GEO

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance (RNA-Seq)

Project description:Using RNA-Seq to to analyse the gene expression pattern in Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

2021-01-16 | GSE164915 | GEO

Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape (RNA-Seq)

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

Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape (Bisulfite-Seq)

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

Transcriptomic of meiocytes.

Project description:What are the gene expressed during meiosis pathway in Arabidopsis thalina. Comparison of total RNAs from isolated meiocytes with those isolated from root tips, and those from leaves. Comparison of transcriptomes of normal stamen (ecotype columbia) with root tips and leaves. And, comparison of transcriptomes of normal stamens (ecotype L. erecta) with stamens from sporocyteless mutant (L. erecta). Keywords: organ comparison

2008-12-07 | GSE10229 | GEO

Genome-wide bisulphite sequencing of Arabidopsis thaliana embryo and endosperm

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

Male fertility in plants requires active DNA demethylation of genes that control pollen tube funcion

Project description:We show that in model plant Arabidopsis thaliana, the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) of the model plant Arabidopsis thaliana act semi-redundantly in pollen for hypomethylation of the vegetative cell, required for the activation of key genes involved in pollen tube function

2020-11-05 | GSE141154 | GEO

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