Runx2 regulatory landscape on the skeletal cell genome

Shinsuke Ohba, Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry

Prof. Shinsuke Ohba found that Runx2, a critical determinant of skeletal cells, mediates cell fate specification by regulating chromatin landscape during skeletal development, in collaboration with Associate Prof. Hironori Hojo (The University of Tokyo), Prof. Ung-il Chung (The University of Tokyo), and Prof. Andrew McMahon (University of Southern California). This work was published in Cell Reports (Cell Press) on September 6, 2022 (


Genomic DNA, which is the “blueprint of life,” contains not only protein-encoding gene regions, but also enhancer regions that control transcription of genes (gene activity). During development, different enhancer groups become active in different cell types, leading to transcription of genes required for each cell lineage.

Transcription factor Runx2 is essential for specification of bone-forming osteoblasts and maturation of cartilage-forming chondrocytes during skeletal development. Runx2 has been shown to bind to DNA and activate genes that are related to osteoblasts and chondrocytes. However, regulatory landscape of Runx2 has not been fully clarified in skeletal cells.

Through genome-wide analyses using next-generation sequencers (ChIP-seq, RNA-seq, and ATAC-seq), the research group attempted to elucidate the whole picture of enhancer networks of chondrocytes and osteoblasts and the transcriptional program executed by Runx2. They found that Runx2 binds to cell type-specific open chromatin regions (accessible regions) in osteoblasts and chondrocytes, where Runx2 potentially cooperates with various transcriptional regulators. Additional analyses further suggest that Runx2 acts as a pioneer factor, which establishes and maintains chromatin accessibility on putative osteoblast enhancers. Lastly, by integrating genome editing technology and single-cell RNA-seq analysis, they identified an enhancer that contributes to osteogenesis. The enhancer is located 11 kb away from the transcriptional start site of Sp7, a transcriptional regulator critical for osteoblast development. They confirmed that the enhancer was specifically activated in osteoblasts in vivo. Furthermore, deletion of the enhancer resulted in decreased bone mass with decreased Sp7 expression in mice.


This study comprehensively identified the Runx2-bound enhancer regions as well as open chromatin regions in osteoblasts and chondrocytes; a series of data is available on a public database. Furthermore, the result suggests that Runx2 contributes to establishment and maintenance of the genome structure, which underlies regulatory landscape on the osteoblast genome. These results will help us understand the blueprint of skeletal cell development in terms of epigenome, and contribute to the development of therapeutic strategies for skeletal diseases including bone regenerative therapies.

Information of the article

Hironori Hojo*, Taku Saito, Xinjun He, Qiuyu Guo, Shoko Onodera, Toshifumi Azuma, Michinori Koebis, Kazuki Nakao, Atsu Aiba, Masahide Seki, Yutaka Suzuki, Hiroyuki Okada, Sakae Tanaka, Ung-il Chung, Andrew P. McMahon, Shinsuke Ohba*: Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Cell Rep 40(10):111315, 2022