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Series GSE51234 Query DataSets for GSE51234
Status Public on Sep 28, 2013
Title Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites [GP5d/siRAD21 ChIP-Seq experiments]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M-phase. These results suggest that cohesin binding functions as a cellular memory that promotes re- stablishment of TF clusters after DNA replication and chromatin condensation.
Overall design Examination of TF binding by ChIP-seq in a CRC cell-line treated with non-targeting siRNA, or siRNA specific to the cohesin subunit RAD21.
Contributor(s) Enge M, Yan J
Citation(s) 23953112
Submission date Sep 27, 2013
Last update date May 15, 2019
Contact name Martin Enge
Organization name Karolinska Institute
Department Dep of Oncology-Pathology
Street address CCK, Z4
City Stockholm
ZIP/Postal code S-171 76
Country Sweden
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (28)
GSM1240813 GP5dControl_CTCF_Goat
GSM1240814 GP5dControl_H3K4me1_Rabbit
GSM1240815 GP5dControl_HNF4A_Rabbit
BioProject PRJNA221781
SRA SRP030504

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Supplementary file Size Download File type/resource
GSE51234_RAW.tar 8.7 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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