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GenomicsCTCF demarcates chromatin domains
Insulators are DNA elements, which prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC binding factor) is the only known major insulator binding protein in the vertebrates a...
ORGANISM(S): Homo sapiens 
2008-10-20 | E-GEOD-12889 | biostudies-arrayexpress
TranscriptomicsConserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions
The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is limited. Here we present high-resolution analyses of chromosomal organization in pluripotent and differentiated human and murine cell types determined u...
ORGANISM(S): Mus musculus 
2012-04-10 | E-GEOD-35156 | biostudies-arrayexpress
TranscriptomicsThe FUN30 Chromatin Remodeler Fft3 Protects Centromeric and Subtelomeric Domains from Euchromatin Formation
The chromosomes of eukaryotes are organized into structurally and functionally discrete domains. This implies the presence of insulator elements that separate adjacent domains, allowing them to maintain different chromatin structures. We show that the Fun30 chromatin remodeler, Fft3, is essential fo...
ORGANISM(S): Schizosaccharomyces pombe 
2011-04-02 | E-MEXP-3044 | biostudies-arrayexpress
TranscriptomicsGlobal chromatin domain organization of the Drosophila genome
In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically ...
ORGANISM(S): Drosophila melanogaster 
2008-04-07 | E-GEOD-10219 | biostudies-arrayexpress
TranscriptomicsDistinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation
The three-dimensional (3D) organization of the genome within the cell nucleus contributes to cell-specific gene expression in different cell types1. High-throughput 3CM-bM-^@M-^Sderived methods have revealed that the genome is segmented into contiguous topologically associating domains (TADs), which...
ORGANISM(S): Homo sapiens 
2014-10-06 | E-GEOD-53463 | biostudies-arrayexpress
GenomicsCharacterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
Recent epigenomic studies have predicted thousands of potential enhancers in the human genome. However, there has not been systematic characterization of target promoters for these potential enhancers. Using H3K4me2 as a mark for active enhancers, we identified genome-wide enhancer-promoter interact...
ORGANISM(S): Homo sapiens 
2012-01-24 | E-GEOD-32677 | biostudies-arrayexpress
GenomicsThe chromatin remodeler ATRX binds to atypical chromatin domains at the 3’ exons of ZNF genes to preserve H3K9me3 enrichment
Here, we report that ATRX co-localizes with the H3K9-methyl transferase SETDB1 (also known as ESET), the co-repressor TRIM28 (also known as KAP1), and the transcription factor ZNF274 at 3’ exons of Zinc Finger Genes (ZNFs) containing an atypical H3K9me3/H3K36me3 chromatin signature. Disruption of ...
ORGANISM(S): Homo sapiens 
2016-04-05 | E-GEOD-70920 | biostudies-arrayexpress
UnknownGenome-wide occupancy reveals the localization of H1T2 (H1fnt) to repeat regions and a subset of transcriptionally active chromatin domains in rat spermatids.
Not available
S-EPMC7788777 | biostudies-literature
GenomicsEDD: a program for detection of wide genomic enrichment domains robust against local variations [ChIP-Seq]
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome-wide. We disclose a novel algorithm, Enriched Domain Detect...
ORGANISM(S): Homo sapiens 
2014-04-25 | E-GEOD-54332 | biostudies-arrayexpress
GenomicsTissue-specific regulation of chromatin insulator function
Chromatin insulators organize the genome into distinct transcriptional domains and contribute to cell type-specific chromatin organization. However, factors regulating tissue-specific insulator function have not yet been discovered. Here we identify the RNA recognition motif-containing protein, Shep...
ORGANISM(S): Drosophila melanogaster 
2012-11-30 | E-GEOD-40797 | biostudies-arrayexpress
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