Genome-wide CTCF binding maps in chicken red blood cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
SUBMITTER: David Martin
PROVIDER: E-GEOD-27945 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Drosophila melanogaster CTCF, CTCF, is differentially expressed in 13 experiment(s);
| FBgn0035769 | ExpressionAtlas
Project description:Drosophila melanogaster CTCF, CTCF, is expressed in 3 baseline experiment(s);
| FBgn0035769 | ExpressionAtlas
Project description: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 and has been shown to bind many enhancer-blocking elements. However, it is not clear whether it plays a role in chromatin domain barriers between active and repressive domains. Here, we used ChIP-Seq to map the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3. Although we find an extensive overlapping of CTCF binding sites across the three cell types, its association with the domain boundaries is cell type-specific. We further show that the nucleosomes flanking CTCF binding sites are well positioned and associated with histone H2AK5 acetylation (H2AK5ac). Interestingly, we found a complementary pattern between the repressive H3K27me3 and the active H2AK5ac regions, which are separated by CTCF. Our findings indicate that CTCF may play important roles in the barrier activity of insulators and provide a resource for further investigation of the CTCF function in organizing chromatin in the human genome. Examination of the role of CTCF in chromatin domain barrier function In addition to the ChIP-seq analysis, two replicates of HeLa expression data were studied.
2008-10-20 | E-GEOD-12889 | biostudies-arrayexpress
Project description:The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. Here we systematically integrated multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, CRISPR-Cas9 survival dropout screening, time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewired genome-wide chromatin accessibility. Increased accessible chromatin regions were largely located adjacent to CTCF-binding sites at promoter regions and insulator sites and were associated with enhanced transcription of nearby genes. In addition, we used CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners in regulating downstream gene expression. We successfully identified 40 candidates, including multiple established partners (i.e., MYC) supported by all layers of evidence. Interestingly, many CTCF co-regulators (e.g., YY1, ZBTB7A) that have evident alterations of respective downstream gene expression do not show changes at their expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. This study highlights CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation
2021-07-04 | PXD026484 | Pride
Project description:Rattus norvegicus Ctcf, CCCTC-binding factor [Source:RGD Symbol;Acc:621344], is differentially expressed in 12 experiment(s);
| ENSRNOG00000017674 | ExpressionAtlas
Project description:Rattus norvegicus Ctcf, CCCTC-binding factor [Source:RGD Symbol;Acc:621344], is expressed in 7 baseline experiment(s);
| ENSRNOG00000017674 | ExpressionAtlas
Project description:Monodelphis domestica CTCF, CCCTC-binding factor [Source:NCBI gene;Acc:100616788], is expressed in 2 baseline experiment(s);
| ENSMODG00000005757 | ExpressionAtlas
Project description:Chromatin immunoprecipitation against CTCF followed by Illumina High-throughput sequencing.
2011-04-15 | GSE27945 | GEO
Project description:Macaca mulatta CTCF, CCCTC-binding factor [Source:VGNC Symbol;Acc:VGNC:99504], is expressed in 3 baseline experiment(s);
| ENSMMUG00000009798 | ExpressionAtlas
Project description:Homo sapiens CTCF, CCCTC-binding factor [Source:HGNC Symbol;Acc:HGNC:13723], is differentially expressed in 165 experiment(s);
| ENSG00000102974 | ExpressionAtlas