Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis

Hai Wu, Troy W. Whitfield, Jonathan A R Gordon, Jason R. Dobson, Phillip W L Tai, Andre J van Wijnen, Janet L. Stein, Gary S. Stein, Jane B. Lian

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

Background: Osteogenesis is a highly regulated developmental process and continues during the turnover and repair of mature bone. Runx2, the master regulator of osteoblastogenesis, directs a transcriptional program essential for bone formation through genetic and epigenetic mechanisms. While individual Runx2 gene targets have been identified, further insights into the broad spectrum of Runx2 functions required for osteogenesis are needed.Results: By performing genome-wide characterization of Runx2 binding at the three major stages of osteoblast differentiation - proliferation, matrix deposition and mineralization - we identify Runx2-dependent regulatory networks driving bone formation. Using chromatin immunoprecipitation followed by high-throughput sequencing over the course of these stages, we identify approximately 80,000 significantly enriched regions of Runx2 binding throughout the mouse genome. These binding events exhibit distinct patterns during osteogenesis, and are associated with proximal promoters and also non-promoter regions: upstream, introns, exons, transcription termination site regions, and intergenic regions. These peaks were partitioned into clusters that are associated with genes in complex biological processes that support bone formation. Using Affymetrix expression profiling of differentiating osteoblasts depleted of Runx2, we identify novel Runx2 targets including Ezh2, a critical epigenetic regulator Crabp2, a retinoic acid signaling component; Adamts4 and Tnfrsf19, two remodelers of the extracellular matrix. We demonstrate by luciferase assays that these novel biological targets are regulated by Runx2 occupancy at non-promoter regions.Conclusions: Our data establish that Runx2 interactions with chromatin across the genome reveal novel genes, pathways and transcriptional mechanisms that contribute to the regulation of osteoblastogenesis.

Original languageEnglish (US)
Article numberR52
JournalGenome Biology
Volume15
Issue number3
DOIs
StatePublished - Mar 21 2014

Fingerprint

bone formation
Osteogenesis
bone
genomics
genome
gene
osteoblasts
Genome
Osteoblasts
Epigenomics
epigenetics
matrix
chromatin
biological processes
Genes
repair
Biological Phenomena
turnover
Intergenic DNA
genes

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Medicine(all)

Cite this

Wu, H., Whitfield, T. W., Gordon, J. A. R., Dobson, J. R., Tai, P. W. L., van Wijnen, A. J., ... Lian, J. B. (2014). Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. Genome Biology, 15(3), [R52]. https://doi.org/10.1186/gb-2014-15-3-r52

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. / Wu, Hai; Whitfield, Troy W.; Gordon, Jonathan A R; Dobson, Jason R.; Tai, Phillip W L; van Wijnen, Andre J; Stein, Janet L.; Stein, Gary S.; Lian, Jane B.

In: Genome Biology, Vol. 15, No. 3, R52, 21.03.2014.

Research output: Contribution to journalArticle

Wu, H, Whitfield, TW, Gordon, JAR, Dobson, JR, Tai, PWL, van Wijnen, AJ, Stein, JL, Stein, GS & Lian, JB 2014, 'Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis', Genome Biology, vol. 15, no. 3, R52. https://doi.org/10.1186/gb-2014-15-3-r52
Wu, Hai ; Whitfield, Troy W. ; Gordon, Jonathan A R ; Dobson, Jason R. ; Tai, Phillip W L ; van Wijnen, Andre J ; Stein, Janet L. ; Stein, Gary S. ; Lian, Jane B. / Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. In: Genome Biology. 2014 ; Vol. 15, No. 3.
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AU - van Wijnen, Andre J

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