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Series GSE49402 Query DataSets for GSE49402
Status Public on Aug 15, 2013
Title Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites
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 LoVo CRC cell-lines.
 
Contributor(s) Enge M, Yan J
Citation(s) 23953112
Submission date Jul 31, 2013
Last update date May 15, 2019
Contact name Martin Enge
E-mail(s) martin.enge@ki.se
Organization name Karolinska Institute
Department Dep of Oncology-Pathology
Street address CCK, Z4
City Stockholm
ZIP/Postal code S-171 76
Country Sweden
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (225)
GSM1208590 batch1_chrom1_LoVo_ARNT_Mouse_PassedQC
GSM1208591 batch1_chrom1_LoVo_ASCL2_Mouse_PassedQC
GSM1208592 batch1_chrom1_LoVo_ATOH1_Rabbit_PassedQC
Relations
BioProject PRJNA215231
SRA SRP028819

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49402_RAW.tar 43.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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