Runt-related Transcription Factors and Gene Regulatory Mechanisms in Skeletal Development and Diseases

Abstract

Purpose of review: Runt-related transcription factors (RUNX) play critical roles in skeletal development, metabolism, and diseases. In mammals, three RUNX members, namely RUNX1, RUNX2, and RUNX3, play distinct and redundant roles, although RUNX2 is a dominant factor in skeletal development and several skeletal diseases. This review is to provide an overview of the current understanding of RUNX-mediated transcriptional regulation in different skeletal cell types.

Recent findings: Advances in chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) have revealed genome-wide RUNX-mediated gene regulatory mechanisms, including their association with cis-regulatory elements and putative target genes. Further studies with genome-wide analysis and biochemical assays have shed light on RUNX-mediated pioneering action and involvements of RUNX2 in lipid-lipid phase separation. Emerging multi-layered mechanisms of RUNX-mediated gene regulations help us better understanding of skeletal development and diseases, which also provides clues to think how genome-wide studies can help develop therapeutic strategies for skeletal diseases.

Keywords: ChIP-seq; Gene regulatory mechanisms; RUNX; Skeletal development; Skeletal diseases.

Fig. 1

Overview of ChIP-seq and ATAC-seq experiments. a In ChIP-seq experiments, chromatin DNA is first cross-linked with formaldehyde, followed by DNA shearing using either sonicator or enzymes to obtain DNA fragments of 100 to 600 bp. Then, the DNA-protein complex is immunoprecipitated by the specific antibody for a protein of interest. After protein digestions, purified DNA fragments are amplified for NGS analysis. The output data are sequences of regions that were interacted with the protein of interest. b In ATAC-seq, chromatin DNA is directly reacted with Tn5 transposase which associates with open chromatin regions. Tn5 transposase then cut open chromatin regions with tagging specific nucleotide sequences which are used for DNA amplification for NGS. The output data are sequences of Tn5 accessible regions, i.e., open chromatin regions, in the genome

Fig. 2

Emerging RUNX-mediated gene regulatory mechanisms. a Different CREs are used for RUNX binding in a cell-type- or cell-state-dependent manner. The binding regions were also not the same among RUNX factors. These variations may explain the distinct biological outcomes. b RUNX factors are likely to have pioneering functions. RUNX binds to closed chromatin regions and opens the chromatin for later activation. Chromatin modifiers physically interact with RUNX and are likely involved in its pioneering action. c RUNX is involved in liquid–liquid phase separation. Interactions between the IDRs in the N-terminus of RUNX2 and cofactors are crucial for its formation. However, whether RUNX1 and RUNX3 exert similar effects on gene regulation remains unclear. RUNX, runt-related transcription factors; CRE, cis-regulatory element; TF, transcription factor; IDR, intrinsically disordered regions