CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

Mol Cell. 2017 Sep 21;67(6):1049-1058.e6. doi: 10.1016/j.molcel.2017.08.026.

Abstract

Recent studies indicate that even a homogeneous population of cells display heterogeneity in gene expression and response to environmental stimuli. Although promoter structure critically influences the cell-to-cell variation of gene expression in bacteria and lower eukaryotes, it remains unclear what controls the gene expression noise in mammals. Here we report that CTCF decreases cell-to-cell variation of expression by stabilizing enhancer-promoter interaction. We show that CTCF binding sites are interwoven with enhancers within topologically associated domains (TADs) and a positive correlation is found between CTCF binding and the activity of the associated enhancers. Deletion of CTCF sites compromises enhancer-promoter interactions. Using single-cell flow cytometry and single-molecule RNA-FISH assays, we demonstrate that knocking down of CTCF or deletion of a CTCF binding site results in increased cell-to-cell variation of gene expression, indicating that long-range promoter-enhancer interaction mediated by CTCF plays important roles in controlling the cell-to-cell variation of gene expression in mammalian cells.

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor
  • CD4-Positive T-Lymphocytes / metabolism*
  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Enhancer Elements, Genetic*
  • Female
  • Flow Cytometry
  • Gene Expression Regulation*
  • High-Throughput Nucleotide Sequencing
  • In Situ Hybridization, Fluorescence
  • Mice, Inbred C57BL
  • Promoter Regions, Genetic*
  • Protein Binding
  • RNA Interference
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Single-Cell Analysis
  • Transcription, Genetic
  • Transcriptional Activation
  • Transfection

Substances

  • CCCTC-Binding Factor
  • Ctcf protein, mouse
  • Repressor Proteins