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GenomicsGadd45a promotes DNA demethylation through TDG
Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA g...
ORGANISM(S): Mus musculus 
2015-05-07 | E-GEOD-62496 | 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
TranscriptomicsRole of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RNA-seq]
With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demeth...
ORGANISM(S): Mus musculus 
2014-10-21 | E-GEOD-61329 | biostudies-arrayexpress
GenomicsRole of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RRBS]
With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demeth...
ORGANISM(S): Mus musculus 
2014-10-21 | E-GEOD-61330 | biostudies-arrayexpress
GenomicsSingle-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing
Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantita...
ORGANISM(S): Mus musculus 
2014-11-02 | E-GEOD-62631 | biostudies-arrayexpress
TranscriptomicsA promoter DNA demethylation landscape of human hematopoietic differentiation
Global mechanisms defining the gene expression programs specific for hematopoiesis are still not fully understood. Here, we show that promoter DNA demethylation is associated the activation of hematopoietic-specific genes. Using genome-wide promoter methylation arrays, we identified 694 hematopoie...
ORGANISM(S): Homo sapiens 
2011-09-14 | E-GEOD-30090 | biostudies-arrayexpress
TranscriptomicsReplication-coupled passive DNA demethylation for the erasure of genome imprints in mice
Genome-wide DNA demethylation, including the erasure of genome imprints, in primordial germ cells (PGCs), is critical as a first step for creating the totipotent epigenome in the germ line. Here, we provide evidence that contrary to the prevailing model involving active DNA demethylation, imprint er...
ORGANISM(S): Mus musculus 
2013-03-04 | E-GEOD-40412 | 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
GenomicsDNA demethylation by Tet dioxygenases controls gastrula patterning by regulating Lefty-Nodal signaling
Mammalian genomes are subjected to epigenetic modifications, including cytosine methylation by DNA methyltransferases (Dnmt) and further oxidation by Ten-eleven-translocation (Tet) family of dioxygenases. Cytosine methylation plays key roles in multiple processes such as genomic imprinting and X-chr...
ORGANISM(S): Mus musculus 
2016-10-27 | E-GEOD-76261 | biostudies-arrayexpress
TranscriptomicsHistone acetylation and DNA demethylation of T-cells result in an anaplastic large cell lymphoma-like phenotype.
A characteristic feature of anaplastic large cell lymphoma (ALCL) is the significant reduction of the T-cell expression program despite its T-cell origin, a finding very similar to the loss of B-cell identity of classical Hodgkin lymphoma (cHL). Previously we demonstrated that epigenetic mechanisms ...
ORGANISM(S): Homo sapiens 
2012-08-19 | E-GEOD-26101 | biostudies-arrayexpress
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