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Series GSE5559 Query DataSets for GSE5559
Status Public on Jan 01, 2007
Title Analysis of the vertebrate insulator protein CTCF binding sites in the human genome
Project Pilot ENCODE
Organism(s) Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Insulators are an important class of transcriptional regulatory sequences that affect gene expression by preventing the spread of heterochromatin and restricting how transcriptional enhancers select their target genes. The vertebrate insulators function by interacting with the CCCTC-binding factor (CTCF), an evolutionarily conserved DNA binding protein. Knowledge of the CTCF binding sites in the human genome is crucial for identifying potential insulators and understanding the role of these elements in regulating genome expression in the human cells. Here, we report the identification and characterization of a large number of CTCF binding sites in the human genome. Using chromatin immunoprecipitation combined with high-resolution genome-tiling arrays, we have determined the locations of CTCF throughout the non-repetitive human DNA sequences, identifying 13,804 binding sites in the genome of human fibroblasts. Computational analysis of these sequences revealed a single dominant CTCF consensus motif that is shared by a vast majority of the CTCF binding sites and is highly conserved in other vertebrate genomes. The CTCF binding segments the human genome into 5,969 domains, which contain an average of 2.5 genes each. Many large gene families, such as the olfactory receptor genes, are bounded by the CTCF sites, implicating a role of CTCF in the regulation or evolution of these genes. We demonstrate that CTCF binding can occur in a cell type dependent manner, and that binding of CTCF between two neighboring genes coincides with a loss of coordinated expression, consistent with their role as insulators. Our results provide a general resource and framework for analyzing the role of CTCF and insulator elements in the regulation of nearly every gene in the human genome.
Keywords: ChIP-chip
 
Overall design Chromatin immunoprecipitation was performed using monoclonal antibodies against CTCF and formaldehyde crosslinked chromatin from primary human fibroblast, IMR90 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides. These oligonucleotides are evenly positioned every 100 basepairs (bp) to cover the non-repeat sequence of the entire human genome.
Web Link http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
 
Contributor(s) Kim TH, Abdullayev Z, Ching KA, Smith A, Loukinov D, Green RD, Zhang MQ, Lobanenkov V, Ren B
Citation(s)
Submission date Aug 17, 2006
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Department Department of Cellular and Molecular Medicine
Lab Laboratory of Gene Regulation
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platforms (40)
GPL1454 RenLab ENCODE PCR tiling array
GPL4132 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 01 of 38
GPL4137 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 02 of 38
Samples (42)
GSM129154 CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 01 of 38
GSM129189 CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 02 of 38
GSM129190 CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 03 of 38

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