GEO DataSets

(Submitter supplied) In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. more...

Organism:

Arabidopsis thaliana; Capsella rubella; Brassica rapa; Arabidopsis lyrata; Brassica oleracea; Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

10 related Platforms

44 Samples

Download data: BED, TSV

(Submitter supplied) In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H=A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. more...

Organism:

Eutrema salsugineum

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21150

41 Samples

Download data: BED, TSV, TXT

(Submitter supplied) To properly regulate the genome, cytosine methylation is established by animal DNA methyltransferase 3s (DNMT3s). While altered DNMT3 homologs, DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs), have been shown to establish methylation via the RNA directed DNA methylation (RdDM) pathway, the role of true-plant DNMT3 orthologs remains elusive. Here, we profile de novo (RPS transgene) and genomic methylation in the basal plant, Physcomitrella patens, mutated in each of its PpDNMTs. more...

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14798

10 Samples

Download data: GFF

(Submitter supplied) The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae we provide novel insights into the evolution of gbM and its underlying mechanism. The angiosperm- and eudicot-specific whole genome duplication events gave rise to what are now referred to as CMT1, 2 and 3 lineages. more...

Organism:

Psilotum; Equisetum; Synsepalum dulcificum; Araucaria; Juniperus virginiana; Pereskia grandiflora; Kalanchoe tomentosa; Aristolochia grandiflora; Lupinus angustifolius; Cyperus papyrus; Diplazium proliferum; Papuacedrus papuana; Encephalartos horridus; Thuja sutchuenensis; Gnetum gnemon; Urtica dioica; Cyathea; Aloe vera; Amentotaxus formosana; Cephalotaxus harringtonia; Selaginella kraussiana; Yucca brevifolia; Torreya taxifolia; Microsorum punctatum; Dacrycarpus compactus; Celtis occidentalis; Nepenthes bicalcarata; Amentotaxus argotaenia; Hypericum perforatum; Chamaecyparis hodginsii; Dacrydium balansae; Manoao colensoi; Cissus quadrangularis; Impatiens niamniamensis

Type:

Methylation profiling by high throughput sequencing

34 related Platforms

150 Samples

Download data: TXT

(Submitter supplied) This study investigated the regulatory mechanism of CMT3 mediated CHG methylation in A. thaliana.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21785

6 Samples

Download data: BW

(Submitter supplied) DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2 and CMT3 stably associated with H3K9me2-containing nucleosomes. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: TXT

(Submitter supplied) The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood. Mutation of the H3K27 methyltransferase genes, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, result in re-replication (repeated origin firing within the same cell cycle). Here we show that mutations that reduce DNA methylation act to suppress the re-replication phenotype of atxr5 atxr6 mutants. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL9302 GPL13222 GPL11221

43 Samples

Download data: TXT

(Submitter supplied) DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL19580

35 Samples

Download data: RESULTS, TSV

(Submitter supplied) We demonstrated that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos.Depending on whether they are located in euchromatic or heterochromatic regions of the genome, bipartite-classified TEs generate siRNAs throughout embryogenesis according to two distinct patterns. siRNAs are transcribed in embryos and required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL24270 GPL17639

69 Samples

Download data: BED, BW, TSV

(Submitter supplied) Cytosine DNA methylation regulates the expression of eukaryotic genes and transposable elements. Methylation is copied by DNA methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Trans-generational inheritance is mediated by a small group of cells that includes gametes and their progenitors. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19580 GPL13222

10 Samples

Download data: GFF

(Submitter supplied) Maintenance of CG methylation (mCG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining mCG, we found that mCG loss triggered genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms involving RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation act in a stochastic and uncoordinated fashion. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by array

Platform:

GPL198

6 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL19580 GPL21785

62 Samples

Download data: BW, GFF

(Submitter supplied) The goal of this study is to compare the methylation state of galls formed in Arabidopsis roots infected by Meloidogyne javanica at 14 days post infection compared to uninfected root segments (RC).

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

6 Samples

Download data: CSV

(Submitter supplied) The goal of this study is to compare the methylation state of galls formed in Arabidopsis roots infected by Meloidogyne javanica at 3 days post infection compared to uninfected root segments (RC).

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21785 GPL23157

6 Samples

Download data: CSV

(Submitter supplied) The goal of this study is to compare the transcriptome profilling (RNA-seq) of galls (G) formed in Arabidopsis roots infected by Meloidogyne javanica at 3 days post infection compared to uninfected root segments (RC).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platforms:

GPL10977 GPL10978

24 Samples

Download data: CEL, TXT

(Submitter supplied) CRISPR-based targeted modification of epigenetic marks is an important strategy to regulate the expression of genes and their associated phenotypes in plants and animals. The manipulation of DNA cytosine methylation is particularly attractive in plants since DNA methylation changes are often heritable in subsequent plant generations. Although plants have DNA methylation in all sequence contexts (CG, CHG, CHH, where H can be any nucleotide but G), methylation at symmetrical CG sites is the most important for gene silencing, and is also the most efficiently maintained through miotic and meiotic cell divisions. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL21785 GPL26208

60 Samples

Download data: BED, BW, TXT

(Submitter supplied) Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a novel histone modification in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: BW

(Submitter supplied) Methylation of CG dinucleotides (mCG), which regulates genome function in eukaryotes, is epigenetically propagated by Dnmt1/MET1 methyltransferases via a semiconservative mechanism. How these enzymes accomplish stable epigenetic inheritance despite imperfect fidelity remains mysterious. Here we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19580

155 Samples

Download data: GFF

(Submitter supplied) Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant species A. thaliana and A. arenosa. Here we report that reduced DNA methylation in met1-RNAi A. more...

Organism:

Arabidopsis thaliana; Arabidopsis suecica

Type:

Expression profiling by array

Platform:

GPL5680

1 Sample

Download data: GPR