UMass Chan Medical School Faculty Publications


Genomic occupancy of HLH, AP1 and Runx2 motifs within a nuclease sensitive site of the Runx2 gene

UMMS Affiliation

Department of Cell and Developmental Biology

Publication Date


Document Type



Animals; Cell Line; Chromatin; Core Binding Factor Alpha 1 Subunit; Deoxyribonuclease I; Gene Expression Regulation; Helix-Loop-Helix Motifs; Histones; Mesoderm; Mice; Osteoblasts; Point Mutation; Promoter Regions, Genetic; Protein Interaction Domains and Motifs; Transcription Factor AP-1


Cell and Developmental Biology | Genetics and Genomics | Molecular Genetics


Epigenetic mechanisms mediating expression of the Runt-related transcription factor Runx2 are critical for controlling its osteogenic activity during skeletal development. Here, we characterized bona fide regulatory elements within 120 kbp of the endogenous bone-related Runx2 promoter (P1) in osteoblasts by genomic DNase I footprinting and chromatin immuno-precipitations (ChIPs). We identified a ~10 kbp genomic domain spanning the P1 promoter that interacts with acetylated histones H3 and H4 reflecting an open chromatin conformation in MC3T3 osteoblasts. This large chromatin domain contains a single major DNaseI hypersensitive (DHS) region that defines a 0.4 kbp "basal core" promoter. This region encompasses two endogenous genomic protein/DNA interaction sites (i.e., footprints at Activating Protein 1 [AP1], E-box and Runx motifs). Helix-Loop-Helix (HLH)/E-box occupancy and presence of the DHS region persists in several mesenchymal cell types, but AP1 site occupancy occurs only during S phase when Runx2 expression is minimal. Point-mutation of the HLH/E box dramatically reduces basal promoter activity. Our results indicate that the Runx2 P1 promoter utilizes two stable principal protein/DNA interaction domains associated with AP1 and HLH factors. These sites function together with dynamic and developmentally responsive sites in a major DHS region to support epigenetic control of bone-specific transcription when osteoblasts transition into a quiescent or differentiated state.

DOI of Published Version



J Cell Physiol. 2013 Feb;228(2):313-21. doi: 10.1002/jcp.22109. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Journal of cellular physiology

PubMed ID