E-GEOD-51290 - Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites [S-phase/M-phase synchronized cells]

Status
Released on 1 October 2013, last updated on 15 April 2014
Organism
Homo sapiens
Samples (12)
Protocols (4)
Description
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. 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.
Experiment type
ChIP-seq 
Contacts
Jian Yan, Martin Enge
Citation
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J. , Europe PMC 23953112
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-51290.idf.txt
Sample and data relationshipE-GEOD-51290.sdrf.txt
Processed data (1)E-GEOD-51290.processed.1.zip
Links