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GenomicsPlants regenerated from tissue culture contain stable epigenome changes in rice
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plan...
ORGANISM(S): Oryza sativa Japonica Group 
2013-03-26 | E-GEOD-42410 | biostudies-arrayexpress
TranscriptomicsLoss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes in Arabidopsis, and relocation of H3K27 trimethylation to transposons [array]
Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, whil...
ORGANISM(S): Arabidopsis thaliana 
2016-06-22 | E-GEOD-83606 | biostudies-arrayexpress
GenomicsThe SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Arabidopsis thaliana 
2014-11-25 | E-GEOD-62801 | biostudies-arrayexpress
GenomicsThe Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis
Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown. Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in conde...
ORGANISM(S): Arabidopsis thaliana 
2014-07-05 | E-GEOD-50942 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana
Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, H3, H4, H2A and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3.1 and H3.3 variants in the genome of the plant Arabidopsis thali...
ORGANISM(S): Arabidopsis thaliana 
2012-03-05 | E-GEOD-34840 | biostudies-arrayexpress
TranscriptomicsLoss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes in Arabidopsis, and relocation of H3K27 trimethylation to transposons [RNA-seq]
Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, whil...
ORGANISM(S): Arabidopsis thaliana 
2016-06-22 | E-GEOD-83607 | biostudies-arrayexpress
GenomicsNon-CG methylation patterns shape the epigenetic landscape in Arabidopsis
DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation...
ORGANISM(S): Arabidopsis thaliana 
2013-12-15 | E-GEOD-51304 | biostudies-arrayexpress
TranscriptomicsLoss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes in Arabidopsis, and relocation of H3K27 trimethylation to transposons.
Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, whil...
ORGANISM(S): Arabidopsis thaliana 
2013-03-02 | E-GEOD-37075 | biostudies-arrayexpress
TranscriptomicsMapping origins of replication in Arabidopsis thaliana
Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially i...
ORGANISM(S): Arabidopsis thaliana 
2011-02-06 | E-GEOD-21828 | biostudies-arrayexpress
TranscriptomicsMapping origins of replication in Arabidopsis thaliana: Examination of BrdU labeled DNA and unlabeled DNA in one cell type
Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially i...
ORGANISM(S): Arabidopsis thaliana 
2011-11-06 | E-GEOD-21781 | biostudies-arrayexpress
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