Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites

Cell. 2013 Aug 15;154(4):801-13. doi: 10.1016/j.cell.2013.07.034.

Abstract

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-establishment of TF clusters after DNA replication and chromatin condensation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Cycle Proteins / metabolism*
  • Cell Cycle*
  • Cell Line, Tumor
  • Chromatin Immunoprecipitation
  • Chromosomal Proteins, Non-Histone / metabolism*
  • Enhancer Elements, Genetic
  • Gene Expression Regulation
  • Genome-Wide Association Study
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mice
  • Nucleotide Motifs
  • Transcription Factors / metabolism*

Substances

  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • Transcription Factors
  • cohesins

Associated data

  • GEO/GSE48448
  • GEO/GSE49402