KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

Nat Cell Biol. 2019 Oct;21(10):1179-1190. doi: 10.1038/s41556-019-0390-6. Epub 2019 Sep 23.


Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors, as is exemplified by reprogramming somatic cells to pluripotent stem cells through the expression of OCT4, KLF4, SOX2 and cMYC. How transcription factors orchestrate the complex molecular changes around their target gene loci remains incompletely understood. Here, using KLF4 as a paradigm, we provide a transcription-factor-centric view of chromatin reorganization and its association with three-dimensional enhancer rewiring and transcriptional changes during the reprogramming of mouse embryonic fibroblasts to pluripotent stem cells. Inducible depletion of KLF factors in PSCs caused a genome-wide decrease in enhancer connectivity, whereas disruption of individual KLF4 binding sites within pluripotent-stem-cell-specific enhancers was sufficient to impair enhancer-promoter contacts and reduce the expression of associated genes. Our study provides an integrative view of the complex activities of a lineage-specifying transcription factor and offers novel insights into the nature of the molecular events that follow transcription factor binding.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cells, Cultured
  • Cellular Reprogramming / genetics*
  • Chromatin Assembly and Disassembly / genetics*
  • Enhancer Elements, Genetic*
  • Female
  • HEK293 Cells
  • Humans
  • Kruppel-Like Transcription Factors / metabolism*
  • Male
  • Mice
  • Mouse Embryonic Stem Cells / metabolism*
  • Pluripotent Stem Cells / metabolism


  • GKLF protein
  • Kruppel-Like Transcription Factors