1. Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions
- Author
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Shinsuke Ohba, Danny Chan, Zhijia Tan, Ben Niu, Andrew P. McMahon, Ralf Jauch, Xinjun He, Kwok Yeung Tsang, Kathryn S.E. Cheah, Cheng Wang, Yong-Heng Huang, Michael Q. Zhang, and Ian G. Melhado
- Subjects
0301 basic medicine ,Cancer Research ,Cellular differentiation ,Gene Expression ,Transactivation ,Database and Informatics Methods ,Mice ,0302 clinical medicine ,Cell Signaling ,Animal Cells ,Transcriptional regulation ,Medicine and Health Sciences ,Gene Regulatory Networks ,Growth Plate ,Genetics (clinical) ,Connective Tissue Cells ,Regulation of gene expression ,Bone growth ,integumentary system ,MEF2 Transcription Factors ,Physics ,Transcriptional Control ,Cell Differentiation ,SOX9 Transcription Factor ,musculoskeletal system ,Cell biology ,Physical sciences ,AP-1 transcription factor ,Chemistry ,medicine.anatomical_structure ,Connective Tissue ,embryonic structures ,Hepatocyte Nuclear Factor 3-beta ,Female ,Anatomy ,Cellular Types ,Sequence Analysis ,Chondrogenesis ,Research Article ,Signal Transduction ,Mef2 ,Transcriptional Activation ,endocrine system ,animal structures ,lcsh:QH426-470 ,Bioinformatics ,Chemical physics ,Biology ,Research and Analysis Methods ,Models, Biological ,Zinc Finger Protein GLI1 ,Chondrocyte ,03 medical and health sciences ,Chondrocytes ,Sequence Motif Analysis ,medicine ,Genetics ,Animals ,Gene Regulation ,Bone ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Bone Development ,SOX9-GLI-FOXA phasic transcriptional network ,Biology and Life Sciences ,Core Binding Factor alpha Subunits ,Dimers (Chemical physics) ,Cell Biology ,Mice, Inbred C57BL ,lcsh:Genetics ,030104 developmental biology ,Biological Tissue ,Cartilage ,Hedgehog Signaling ,Mice, Inbred CBA ,030217 neurology & neurosurgery - Abstract
The growth plate mediates bone growth where SOX9 and GLI factors control chondrocyte proliferation, differentiation and entry into hypertrophy. FOXA factors regulate hypertrophic chondrocyte maturation. How these factors integrate into a Gene Regulatory Network (GRN) controlling these differentiation transitions is incompletely understood. We adopted a genome-wide whole tissue approach to establish a Growth Plate Differential Gene Expression Library (GP-DGEL) for fractionated proliferating, pre-hypertrophic, early and late hypertrophic chondrocytes, as an overarching resource for discovery of pathways and disease candidates. De novo motif discovery revealed the enrichment of SOX9 and GLI binding sites in the genes preferentially expressed in proliferating and prehypertrophic chondrocytes, suggesting the potential cooperation between SOX9 and GLI proteins. We integrated the analyses of the transcriptome, SOX9, GLI1 and GLI3 ChIP-seq datasets, with functional validation by transactivation assays and mouse mutants. We identified new SOX9 targets and showed SOX9-GLI directly and cooperatively regulate many genes such as Trps1, Sox9, Sox5, Sox6, Col2a1, Ptch1, Gli1 and Gli2. Further, FOXA2 competes with SOX9 for the transactivation of target genes. The data support a model of SOX9-GLI-FOXA phasic GRN in chondrocyte development. Together, SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon hypertrophy, FOXA competes with SOX9, and control toward terminal differentiation passes to FOXA, RUNX, AP1 and MEF2 factors., Author summary In the development of the mammalian growth plate, while several transcription factors are individually well known for their key roles in regulating phases of chondrocyte differentiation, there is little information on how they interact and cooperate with each other. We took an unbiased genome wide approach to identify the transcription factors and signaling pathways that play dominant roles in the chondrocyte differentiation cascade. We developed a searchable library of differentially expressed genes, GP-DGEL, which has fine spatial resolution and global transcriptomic coverage for discovery of processes, pathways and disease candidates. Our work identifies a novel regulatory mechanism that integrates the action of three transcription factors, SOX9, GLI and FOXA. SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon entry into prehypertrophy, FOXA competes with SOX9, and control of hypertrophy passes to FOXA, RUNX, AP1 and MEF2 factors.
- Published
- 2018