Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region

Gene. 2014 Oct 15;550(1):1-9. doi: 10.1016/j.gene.2014.05.044. Epub 2014 Jun 2.


Runx2 is a developmentally regulated gene in vertebrates and is essential for bone formation and skeletal homeostasis. The induction of runx2-P1 isoform transcripts is a hallmark of early osteoblastogenesis. Although previous in vitro studies have defined a minimal Runx2-P1 promoter sequence with well-characterized functional elements, several lines of evidence suggest that transcription of the Runx2-P1 isoform relies on elements that extend beyond the previously defined P1 promoter boundaries. In this study, we examined Runx2-P1 transcriptional regulation in a cellular in vivo context during early osteoblastogenesis of MC3T3-E1 cultures and BMSCs induced towards the bone lineage by multi-layered analysis of the Runx2-P1 gene promoter using the following methodologies: 1) sequence homology among several mammalian species, 2) DNaseI hypersensitivity coupled with massively parallel sequencing (DNase-seq), and 3) chromatin immunoprecipitation of activating histone modifications coupled with massively parallel sequencing (ChIP-seq). These epigenetic features have allowed the demarcation of boundaries that redefine the minimal Runx2-P1 promoter to include a 336-bp sequence that mediates responsiveness to osteoblast differentiation. We also find that an additional level of control is contributed by a regulatory region in the 5'-UTR of Runx2-P1.

Keywords: DNase hypersensitivity; Gene regulation; Histone modification; Osteoblast differentiation; Runx2-P1.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Cell Differentiation / genetics*
  • Cell Line
  • Cells, Cultured
  • Core Binding Factor Alpha 1 Subunit / genetics*
  • Epigenesis, Genetic*
  • Luciferases / genetics
  • Luciferases / metabolism
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Molecular Sequence Data
  • Osteoblasts / cytology
  • Osteoblasts / metabolism*
  • Osteogenesis / genetics*
  • Promoter Regions, Genetic / genetics*
  • Protein Isoforms / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Homology, Nucleic Acid
  • Transcriptional Activation


  • Core Binding Factor Alpha 1 Subunit
  • Protein Isoforms
  • Runx2 protein, mouse
  • Luciferases