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TranscriptomicsHistone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements...
ORGANISM(S): Arabidopsis thaliana 
2008-10-02 | E-GEOD-12212 | biostudies-arrayexpress
TranscriptomicsDeposition of histone variant H2A.Z within gene bodies regulates responsive genes
The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start si...
ORGANISM(S): Arabidopsis thaliana 
2012-12-13 | E-GEOD-39045 | biostudies-arrayexpress
GenomicsActive DNA demethylation in plant companion cells reinforces transposon methylation in gametes
The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation prior to fertilization, but the targeting preferences and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase acco...
ORGANISM(S): Arabidopsis thaliana 
2012-09-21 | E-GEOD-38935 | biostudies-arrayexpress
TranscriptomicsGenome-wide evolutionary analysis of eukaryotic DNA methylation
Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite se...
ORGANISM(S): Bombyx mori 
2010-04-15 | E-GEOD-19824 | biostudies-arrayexpress
TranscriptomicsImprinted expression of genes and small RNA is triggered by localized demethylation of the maternal genome in rice endosperm
We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes a...
ORGANISM(S): Oryza sativa 
2013-05-01 | E-GEOD-44898 | biostudies-arrayexpress
GenomicsGenome-wide demethylation of Arabidopsis endosperm
Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known.  Here we show that virtually the entire endosperm gen...
ORGANISM(S): Arabidopsis thaliana 
2009-06-16 | E-GEOD-15922 | biostudies-arrayexpress
GenomicsLocal DNA hypomethylation activates genes in rice endosperm
Cytosine methylation silences transposable elements in plants, vertebrates and fungi, but also regulates gene expression1. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C or T) and CHH, with CHH methylation targeted by the RNA in...
ORGANISM(S): Oryza sativa 
2010-11-01 | E-GEOD-22591 | biostudies-arrayexpress
GenomicsDDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis
Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from...
ORGANISM(S): Arabidopsis thaliana 
2013-04-17 | E-GEOD-41302 | biostudies-arrayexpress
TranscriptomicsExtensive imprinted gene expression in Arabidopsis endosperm
Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embry...
ORGANISM(S): Arabidopsis thaliana 
2011-03-10 | E-GEOD-24644 | biostudies-arrayexpress
GenomicsDnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes
Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG met...
ORGANISM(S): Fragilariopsis cylindrus 
2014-03-13 | E-GEOD-46692 | biostudies-arrayexpress
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