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TranscriptomicsThe SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [ChIP-chip]
In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such a...
ORGANISM(S): Arabidopsis thaliana 
2014-06-06 | E-GEOD-58030 | biostudies-arrayexpress
ProteomicsCryoEM Structures of Arabidopsis DDR Complexes Involved in RNA-directed DNA Methylation
Chemical cross-linking coupled to mass spectrometry was used to study the A. thaliana DDR complex consisting of DMS3, RMD1 and a peptide from the interaction region of DRD1. Cross-linking was performed using different cross-linking chemistries: disuccinimidyl suberate (DSS) and a combination of adip...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2019-07-15 | PXD013470 | Pride
Chemical cross-linking  dss  adh  dmtmm  structural proteomics  ddr complex 
TranscriptomicsThe SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [RNA-Seq]
In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such a...
ORGANISM(S): Arabidopsis thaliana 
2014-06-06 | E-GEOD-58029 | biostudies-arrayexpress
TranscriptomicsThe SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner
In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such a...
ORGANISM(S): Arabidopsis thaliana 
2013-08-26 | E-GEOD-39405 | biostudies-arrayexpress
GenomicsThe SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [SELEX]
In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such a...
ORGANISM(S): Arabidopsis thaliana 
2014-06-06 | E-GEOD-58034 | biostudies-arrayexpress
TranscriptomicsGenome wide profiling of H3K9me2 in Arabidopsis thaliana
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. We constructed a high-resolution genome-wide map of H3K9me2 methylation by using native chromatin immunoprecipitation coupled with HD2 whole geno...
ORGANISM(S): Arabidopsis thaliana 
2010-06-19 | E-GEOD-12383 | biostudies-arrayexpress
TranscriptomicsThe SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [mRNA-Seq]
DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: MET1, CMT3, DRM2, and CMT2. However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families an...
ORGANISM(S): Arabidopsis thaliana 
2014-11-25 | E-GEOD-62799 | biostudies-arrayexpress
GenomicsDual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in PlantsM-BM-
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 CMT...
ORGANISM(S): Arabidopsis thaliana 
2012-11-11 | E-GEOD-39097 | biostudies-arrayexpress
TranscriptomicsTranscriptome and methylome interactions in rice hybrids
This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrativ...
ORGANISM(S): Oryza sativa Indica Group 
2012-07-10 | E-GEOD-38480 | biostudies-arrayexpress
GenomicsMORC family ATPases required for heterochromatin condensation and gene silencing
Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in two Arabidopsis genes, CRT1 and CRH6, which cause de-repression of DNA-methylated genes and TEs, but no losses of DNA or histone methylatio...
ORGANISM(S): Arabidopsis thaliana 
2012-05-02 | E-GEOD-37644 | biostudies-arrayexpress
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