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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
GenomicsComprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.
Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in a sequence specific manner. What factors regulate DNA methylation at a given site in the genome largely remains elusive. He...
ORGANISM(S): Arabidopsis thaliana 
2013-01-11 | E-GEOD-39901 | 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
GenomicsGenome-wide erasure of DNA methylation in mouse primordial germ cells is affected by Aid deficiency
Epigenetic reprogramming including demethylation of DNA occurs in mammalian primordial germ cells (PGCs) and in early embryos, and is important for the erasure of imprints and epimutations, and the return to pluripotency. The extent of this reprogramming and its molecular mechanisms are poorly under...
ORGANISM(S): Mus musculus 
2010-01-26 | E-GEOD-19960 | 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
GenomicsConservation and divergence of methylation patterning in plants and animals
Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. While DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here, we used shotgun genomic bisulfite ...
ORGANISM(S): Ciona intestinalis 
2010-04-09 | E-GEOD-21152 | biostudies-arrayexpress
TranscriptomicsRelationship between nucleosome positioning and DNA methylation: ChIP-chip
Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer1, 2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By...
ORGANISM(S): Arabidopsis thaliana 
2010-05-28 | E-GEOD-21818 | biostudies-arrayexpress
GenomicsRelationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq
Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By com...
ORGANISM(S): Homo sapiens 
2010-05-29 | E-GEOD-21821 | biostudies-arrayexpress
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