Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages

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

doi:10.1016/j.celrep.2022.111315

Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages

Cell Rep. 2022 Sep 6;40(10):111315. doi: 10.1016/j.celrep.2022.111315.

Authors

Hironori Hojo¹, Taku Saito², Xinjun He³, Qiuyu Guo³, Shoko Onodera⁴, Toshifumi Azuma⁴, Michinori Koebis⁵, Kazuki Nakao⁵, Atsu Aiba⁵, Masahide Seki⁶, Yutaka Suzuki⁶, Hiroyuki Okada⁷, Sakae Tanaka², Ung-Il Chung⁸, Andrew P McMahon³, Shinsuke Ohba⁹

Affiliations

¹ Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan. Electronic address: hojo@g.ecc.u-tokyo.ac.jp.
² Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
³ Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA.
⁴ Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan.
⁵ Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
⁶ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
⁷ Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
⁸ Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan.
⁹ Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan; Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan. Electronic address: ohba.shinsuke.dent@osaka-u.ac.jp.

Abstract

The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts.

Keywords: CP: Molecular biology; Runx2; cell specification; chondrocytes; chromatin accessibility; enhancer; osteoblasts; skeletal development; transcriptional regulators.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cell Differentiation / physiology
Chromatin* / metabolism
Core Binding Factor Alpha 1 Subunit* / genetics
Core Binding Factor Alpha 1 Subunit* / metabolism
Mice
Osteoblasts* / metabolism
Osteogenesis

Substances

Chromatin
Core Binding Factor Alpha 1 Subunit
Runx2 protein, mouse

Grants and funding

P01 DK056246/DK/NIDDK NIH HHS/United States