Genome-wide CTCF binding maps in chicken red blood cells
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE27945 | GEO | 2011/04/15
SECONDARY ACCESSION(S): PRJNA137813
REPOSITORIES: GEO
Similar Datasets
Project description:Chromatin immunoprecipitation against CTCF followed by Illumina High-throughput sequencing. Examination of CTCF binding in red blood cells at 2 stages of development
2011-04-15 | E-GEOD-27945 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation against CTCF followed by Illumina High-throughput sequencing. Examination of CTCF binding in embryonic stem cells and embryonic fibroblasts
2011-04-15 | E-GEOD-27944 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation against CTCF followed by Illumina High-throughput sequencing.
2011-04-15 | GSE27944 | GEO
Project description:CTCF is a master regulator that plays a role in genome architecture and gene expression. A key aspect of CTCF’s mechanism involves bringing together distant genetic elements for intra- and inter-chromosomal interactions. Evidence from epigenetic processes, such as X-chromosome inactivation (XCI), suggests that CTCF may carry out its functions through interacting RNAs. Using genome-wide approaches to investigate the relationship between CTCF’s RNA interactome and its epigenomic landscape, here we report that CTCF interacts with thousands of transcripts in mouse embryonic stem cells (mESC), many in close proximity to CTCF’s genomic binding sites. Biochemical analysis demonstrates that CTCF is a high-affinity RNA binding protein that contacts RNA directly and specifically. In the XCI model, CTCF binds the active and inactive X-chromosomes allele-specifically. At the X-inactivation center, Tsix RNA binds CTCF and targets CTCF to a region associated with X-chromosome pairing. Our work implicates CTCF-RNA interactions in long-range chromosomal interactions in trans and adds a new layer of complexity to CTCF regulation. The genome-wide datasets reported here will provide a useful resource for further study of CTCF-mediated epigenomic regulation. CTCF RNA interactome was identified by UV-crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq), and was compared to CTCF's epigenomic landscape as obtained by chromatin immunoprecipitation (ChIP-seq).
2015-01-09 | E-GEOD-58242 | biostudies-arrayexpress
Project description:CCCTC-binding factor (CTCF) is an architectural protein with context dependent functional outcomes. Although CTCF is conserved throughout Metazoan evolution, its functions have been only evaluated in a limited number of species. Here, we present the first analysis of CTCF binding in the zebrafish genome via chromatin immunoprecipitation followed by sequencing (ChIP-seq). To avoid the need of custom antibodies, we generated a transgenic line with an HA-tagged version of CTCF that enabled the identification of 37,625 CTCF peaks in 24 hours post-fertilization (hpf) embryos. We determined that CTCF peaks generally overlap with histone marks associated to enhancers and active promoters, and identified repeats that are enriched on CTCF binding sites. In addition, we show extended sites of CTCF binding as previously shown in mammals and lamprey, supporting the hypothesis of a CTCF “code” in vertebrates. Our results indicate a positive association between the abundance of CTCF at promoters and gene expression that could be explained by high DNA accessibility. Finally, analysis of chromosome conformation capture data confirms that histone marks associated with active chromatin are enriched at boundaries of topologically associating domains (TADs), but no general enrichment of CTCF peaks nor motifs is observed at these regions. Our zebrafish line and data generated will be important for future studies of genome organization aiming to characterize the roles of CTCF in non-mammalian vertebrates.
2020-03-30 | GSE133437 | GEO
Project description:We report high throughput profiling and co-occupancy of Trim33, Ctcf and H3K27ac in differentiating embryoid bodies derived from mouse embryonic stem cells. An average of ~37 million reads were generated for each of the described samples and input sample generating 4,426, 52,446, 30,047 peaks respectively for Trim33, CTCF and H3K27ac. Motif enrichment analyses for Trim33 ChiP-Seq data returned CTCF and BORIS (CTCF analog) motifs as best matches. Of the merged peaks, 723 were shared by Trim33, CTCF as well as H3K27ac. In addition, 1299 peaks were shared by Trim33 and CTCF, 1131 were shared by Trim33 and H3K27ac and 3321 were shared by CTCF and H3K27ac.
2019-01-01 | GSE119874 | GEO
Project description:CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in mutually exclusive manners in DNA binding and transcriptional regulation. Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells. In summary, we discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells Genome-wide mapping of CTCF and BORIS occupancies in both germ and cancer cells. ChIP-seq and expression profiling by high throughput sequencing
2015-07-23 | E-GEOD-70764 | biostudies-arrayexpress
Project description:We have used chromatin immunoprecipitation followed by high throughput sequencing to map regions of chromatin remodeler binding in Control and KDM6A knock down AML cells. We have used this data to determine KDM6A contribution to chromatin remodeler binding and thus understand its role in leukemogenesis.
2019-01-19 | GSE125310 | GEO
Project description:The study investigates CTCF/cohesin binding and chromatin looping by ChIP-seq and Micro-C. By ChIP-seq, we determined the genome-wide binding profiles of CTCF and Smc1a cohesin subunit in a knock-in mouse ES cell line (wt-CTCF; clone C59) with endogenously tagged wild type CTCF (FLAG-Halo-mCTCF) and Rad21 (mRad21-SNAPf-V5), and compared them to the same ES line expressing a mutant CTCF (ΔRBR-CTCF; clone C59D2), where we replaced a previously described RNA binding region with a short linker (GDGAGLINS) followed by a 3xHA tag (N576_D611del::3xHA). By Micro-C, we compared nucleosome-resolution chromosome folding maps of the same ES cell lines C59 and C59D2 described above, to determine the effect of deleting CTCF RNA binding region on chromatin looping.
2019-05-30 | GSE123636 | GEO
Project description:CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesinSA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human HSPC hematopoietic stem and progenitor cells (HSPC) and primary human erythroid cells from single donors. Sites of CTCF and cohesinSA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone 3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesinSA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner. These genomic data support the hypothesis that CTCF and cohesinSA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture. CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO. The cells were further cultured in the presence of EPO, and formaldehyde crosslinked chromatin was isolated after cells differentiated into R3/R4 nucleated erythroid cells. Chromatin Immunoprecipitation followed by sequencing (chIP-seq) was performed using antibodies against CTCF, Cohesin SA1 and H3K27me3, along with a total input control. Two replicates for CTCF and Cohesin SA1 were obtained.
2016-06-28 | E-GEOD-67783 | biostudies-arrayexpress