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Series GSE70764 Query DataSets for GSE70764
Status Public on Jul 23, 2015
Title Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary 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

Overall design Genome-wide mapping of CTCF and BORIS occupancies in both germ and cancer cells.
ChIP-seq and expression profiling by high throughput sequencing
Contributor(s) Pugacheva E, Lobanenkov V
Citation(s) 26268681
Submission date Jul 10, 2015
Last update date May 15, 2019
Contact name Elena Pugacheva
Phone 2407377366
Organization name NIH
Department NIAID
Street address Bldg.29B
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17301 Ion Torrent PGM (Homo sapiens)
Samples (27)
GSM1817654 CTCF_K562_ChIP-seq
GSM1817655 BORIS_K562_ChIP-seq
GSM1817656 Input_K562_ChIP-seq
BioProject PRJNA289515
SRA SRP060661

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Supplementary file Size Download File type/resource
GSE70764_RAW.tar 7.8 Gb (http)(custom) TAR (of BED, TXT, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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