The RUNX2 cistrome in osteoblasts: characterization, down-regulation following differentiation, and relationship to gene expression

J Biol Chem. 2014 Jun 6;289(23):16016-31. doi: 10.1074/jbc.M114.552216. Epub 2014 Apr 24.


RUNX2 is a transcription factor that is first expressed in early osteoblast-lineage cells and represents a primary determinant of osteoblastogenesis. While numerous target genes are regulated by RUNX2, little is known of sites on the genome occupied by RUNX2 or of the gene networks that are controlled by these sites. To explore this, we conducted a genome-wide analysis of the RUNX2 cistrome in both pre-osteoblastic MC3T3-E1 cells (POB) and their mature osteoblast progeny (OB), characterized the two cistromes and assessed their relationship to changes in gene expression. We found that although RUNX2 was widely bound to the genome in POB cells, this binding profile was reduced upon differentiation to OBs. Numerous sites were lost upon differentiation, new sites were also gained; many sites remained common to both cell states. Additional features were identified as well including location relative to potential target genes, abundance with respect to single genes, the frequent presence of a consensus TGTGGT RUNX2 binding motif, co-occupancy by C/EBPβ and the presence of a typical epigenetic histone enhancer signature. This signature was changed quantitatively following differentiation. While RUNX2 binding sites were associated extensively with adjacent genes, the distal nature of the majority of these sites prevented assessment of whether they represented direct targets of RUNX2 action. Changes in gene expression, however, revealed an abundance of genes that contained RUNX2 binding sites and were regulated in concert. These studies establish a basis for further analysis of the role of RUNX2 activity and its function during osteoblast lineage maturation.

Keywords: CCAAT-enhancer-binding Protein (C/EBP); Cell Differentiation; ChIP-seq; Chromatin Histone Modification; Chromatin Immunoprecipitation (ChiP); Cistrome; Osteoblast; RUNX2.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 3T3 Cells
  • Animals
  • CCAAT-Enhancer-Binding Protein-beta / metabolism
  • Cell Differentiation*
  • Chromatin Immunoprecipitation
  • Core Binding Factor Alpha 1 Subunit / metabolism
  • Core Binding Factor Alpha 1 Subunit / physiology*
  • Down-Regulation*
  • Gene Expression*
  • Mice
  • Osteoblasts / cytology*
  • Osteoblasts / metabolism
  • Protein Binding


  • CCAAT-Enhancer-Binding Protein-beta
  • Core Binding Factor Alpha 1 Subunit
  • Runx2 protein, mouse