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GenomicsDNaseI Digital Genomic Footprinting from ENCODE/University of Washington [Human]
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This tra...
ORGANISM(S): Homo sapiens 
2010-12-29 | E-GEOD-26328 | biostudies-arrayexpress
GenomicsDomains of genomewide gene expression dysregulation in Down syndrome [Dnase HS mapping]
Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we sh...
ORGANISM(S): Homo sapiens 
2014-04-08 | E-GEOD-55425 | biostudies-arrayexpress
TranscriptomicsMapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana
We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes with...
ORGANISM(S): Arabidopsis thaliana 
2013-12-15 | E-GEOD-53322 | biostudies-arrayexpress
TranscriptomicsConservation of mouse-human trans-regulatory circuitry despite high cis-regulatory divergence
The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we pe...
ORGANISM(S): Homo sapiens 
2014-11-19 | E-GEOD-51341 | biostudies-arrayexpress
UnknownChromatin accessibility pre-determines glucocorticoid receptor binding patterns.
Development, differentiation and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding of regulated transcriptional factors to their cognate genomic sites. The mechanism whereby a given regulatory factor selects a limited number ...
S-EPMC6386452 | biostudies-literature
UnknownContribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.

Background

Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-o...
S-EPMC3700821 | biostudies-literature
UnknownDynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism.
The glucocorticoid receptor (GR), like other eukaryotic transcription factors, regulates gene expression by interacting with chromatinized DNA response elements. Photobleaching experiments in living cells indicate that receptors transiently interact with DNA on the time scale of seconds and predict ...
S-EPMC3210475 | biostudies-literature
UnknownDiverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements.
The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. Contradicting results have been reported to date, with little consensus about the dynamics of nuclear organization and the features of the contact loci. In this stu...
S-EPMC3083086 | biostudies-literature
TranscriptomicsChromosome conformation capture-on-chip of glucocorticoid receptor-responsive loci in mouse cells
The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. Contradicting results have been reported to date, with little consensus about the dynamics of nuclear organization and the features of the contact loci. In this s...
ORGANISM(S): Mus musculus 
2011-04-21 | E-GEOD-27115 | biostudies-arrayexpress
UnknownDynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing.
Although physiological steroid levels are often pulsatile (ultradian), the genomic effects of this pulsatility are poorly understood. By utilizing glucocorticoid receptor (GR) signaling as a model system, we uncovered striking spatiotemporal relationships between receptor loading, lifetimes of the D...
S-EPMC4448681 | biostudies-literature
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