H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation

Mol Cell. 2015 Nov 19;60(4):584-96. doi: 10.1016/j.molcel.2015.10.025.


Bivalent H3K4me3 and H3K27me3 chromatin domains in embryonic stem cells keep active developmental regulatory genes expressed at very low levels and poised for activation. Here, we show an alternative and previously unknown bivalent modified histone signature in lineage-committed mesenchymal stem cells and preadipocytes that pairs H3K4me3 with H3K9me3 to maintain adipogenic master regulatory genes (Cebpa and Pparg) expressed at low levels yet poised for activation when differentiation is required. We show lineage-specific gene-body DNA methylation recruits H3K9 methyltransferase SETDB1, which methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establish the bivalent domain. At the Cebpa locus, this prevents transcription factor C/EBPβ binding, histone acetylation, and further H3K4me3 deposition and is associated with pausing of RNA polymerase II, which limits Cebpa gene expression and adipogenesis.

Keywords: DNA methylation; H3K27me3; H3K4me3; H3K9me3; Histone methylation; RNA polymerase II; adipogenesis; bivalent chromatin domains; epigenome; gene-body methylation; lineage commitment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3T3 Cells
  • Adipocytes / cytology*
  • Adipocytes / physiology
  • Animals
  • CCAAT-Enhancer-Binding Proteins / metabolism*
  • Cell Differentiation
  • Cell Lineage
  • Cells, Cultured
  • Chromatin / metabolism
  • DNA Methylation*
  • Histone-Lysine N-Methyltransferase / metabolism
  • Histones / chemistry
  • Histones / genetics*
  • Mesenchymal Stem Cells / cytology
  • Mesenchymal Stem Cells / physiology
  • Mice
  • PPAR gamma / metabolism*
  • Protein Structure, Tertiary


  • CCAAT-Enhancer-Binding Proteins
  • CEBPA protein, mouse
  • Chromatin
  • Histones
  • PPAR gamma
  • Histone-Lysine N-Methyltransferase
  • SETDB1 protein, mouse

Associated data

  • GEO/GSE73434