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GenomicsIdentification of a novel Aire-regulating cis-regulatory element using H3K27ac ChIP-seq
Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tol...
ORGANISM(S): Mus musculus 
2015-10-23 | E-GEOD-74257 | biostudies-arrayexpress
GenomicsDifferential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus
Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance reg...
ORGANISM(S): Homo sapiens 
2016-01-07 | E-GEOD-74709 | biostudies-arrayexpress
GenomicsEnhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest
Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes. Histone modifi...
ORGANISM(S): Homo sapiens 
2015-09-11 | E-GEOD-70751 | biostudies-arrayexpress
GenomicsCis Regulatory Element Scan by Tiling-deletion and Sequencing
Cis Regulatory Element Scan by Tiling-deletion and Sequencing
PRJNA320305 | ENA
TranscriptomicsThe role of cis regulatory evolution in Zea Mays domestication
Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we asse...
ORGANISM(S): Zea mays 
2014-11-06 | E-GEOD-61810 | biostudies-arrayexpress
TranscriptomicsCis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids
Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thalian...
ORGANISM(S): Arabidopsis arenosa x Arabidopsis thaliana 
2012-05-31 | E-GEOD-29687 | biostudies-arrayexpress
GenomicsMapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts
Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantl...
ORGANISM(S): Oreochromis niloticus 
2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress
GenomicsDeciphering the cis-regulatory architecture of mammalian photoreceptors
In order to define the genomic targets of Crx, we carried out Crx chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) of eight-week-old mouse retinas using the Solexa platform. Sequence reads were mapped to the genome and 'peaks' were identified. These data were subje...
ORGANISM(S): Mus musculus 
2010-06-24 | E-GEOD-20012 | biostudies-arrayexpress
GenomicsGenome-wide identification of putative cis-regulatory elements through epigenetic profiling in zebrafish
In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome. For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-r...
ORGANISM(S): Danio rerio 
2011-02-25 | E-GEOD-20600 | biostudies-arrayexpress
GenomicsAnalysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation
Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation
PRJNA590195 | ENA
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