THE SPATIAL AND TEMPORAL ROLE OF EZH2 IN SKULL BONE FORMATION by JAMES W. FERGUSON Submitted in partial fulfillment of the requirements of the degree of Doctor of Philosophy Department of Biology CASE WESTERN RESERVE UNIVERSITY August 2018 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of James Ferguson candidate for the degree of Doctor of Philosophy. Committee Chair: Brian McDermott, PhD Radhika Atit, PhD Emmitt K. Jolly, PhD Stephen E. Haynesworth, PhD Veronique Lefebvre, PhD Peter Harte, PhD Date of Defense: April 18, 2018 *We also certify that written approval has been obtained for any proprietary material contained therein. Completion of this dissertation was not feat I accomplished alone. I would like to dedicate this to all the people who made this possible through both emotional and intellectual support. i Table of Contents Abstract: Chapter 1: Introduction and significance 1.1: Anatomy and development of bone: 1.1a: Structure and function of bone 1.1b: Skeletal bone formation 1.1c: Anatomy and structure of the skull bones 1.2: Cellular and molecular mechanisms of skull bone development: 1.2a: Stem cell origins of the skull bones 1.2b: Embryonic developmental timeline of cranial mesenchyme bone 1.3 Transcriptional regulation of the bone initiation program: 1.3a: MshHomeobox 1 (Msx1) and MshHomeobox 2 (Msx2) mark bone precursors 1.3b: Runt Related Transcription Factor 2 (Runx2) and Osterix (Sp7/OSX) are the key determinants of skull bone formation: 1.4: Regulation of molecular signal during of murine skull bone formation: 1.4a: Fibroblast Growth Factor signaling is preferentially active in the CNCC: 1.4b: The Bone Morphogenic Protein signaling pathway is primarily active in the PM 1.4c: Wnt/β-catenin signaling pathway is required throughout skull bone formation 1.4d: Twist Family BHLH Transcription Factor 1 (Twist1) is regulated by Wnt/β-catenin signaling and required for skull bone formation: 1.4e: Retinoic Acid signaling affects many different signaling pathways required for skull bone formation 1.4f: Epigenetic regulation of skull bone development 1.4g: The in vivo role of PRC2 in craniofacial development 1.5: Functional interaction and regulation of bone transcriptional program by BMP, FGF, Wnt/β- catenin, RA, and PRC2: 1.6: Clinical significance: Chapter 2: PRC2 is Dispensable in Vivo for β-Catenin-Mediated Repression of Chondrogenesis in Mouse Embryonic Cranial Mesenchyme Abstract: 2.1: Introduction: 2.2: Results: 2.2a: Genes dysregulated upon loss of β-catenin are enriched for the PRC2-associated H3K27me3 histone mark 2.2b: Chondrocyte fate genes are enriched for H3K27me3 in the embryonic CM 2.2c: Endogenous β-catenin and EZH2 may physically interact in the CM 2.2d: β-catenin is not required for PRC2 component expression or bulk H3K27me3 levels 2.2e: Loss of Ezh2 does not lead to ectopic cell type fate selection or chondrogenesis in the CM 2.2f: Loss of β-catenin does not significantly alter H3K27me3 enrichment genome-wide 2.2g: H3K27me3 enrichment is not depleted on ectopically expressed chondrocytic gene determinants in β-catenin mutants ii 2.3: Discussion: 2.4: Materials and methods: 2.4a: Mice and genotyping 2.4b: Cranial mesenchyme isolation 2.4c: RT-qPCR 2.4d: Immunofluorescence 2.4e: Co-immunoprecipitation 2.4f: Protein Isolation and Immunoblotting 2.4g: RNA sequencing 2.4h: ChIP-sequencing 2.4i: Cell Culture 2.4j: Statistics 2.4k: Data Availability 2.5: Acknowledgments: Chapter 3: Ezh2 is required for skull bone formation in a tissue- and developmental-stage specific manner Abstract 3.1: Introduction: 3.2: Results: 3.2a: Conditional deletion of Ezh2in cranial mesenchyme stem cells 3.2b: E8.5-CMEzh2mutants have decreased craniofacial bone volume and size 3.2c: The effect of Ezh2 on skull bone formation is developmental-stage specific 3.2d: Diminished cranial bones in E8.5-CMEzh2 mutants is not due to defects in cell survival and proliferation at E10.5 3.2e: E8.5-CMEzh2 mutants exhibit defects in the differentiation of the skull bone progenitors 3.2f: In vivo inhibition of Retinoic Acid signaling partially restores skull bones 3.3: Discussion: 3.3a: The role of Ezh2 in the lineage-restriction of cranial bone progenitors 3.3b: The genetic mechanism involved in lineage selection of the cranial bones by Ezh2 3.3c: Ectopic expression of Hox genes may lead to a reduction of skull bone in E8.5- CMEzh2 mutants 3.3d: An upregulation of Hedgehog signaling could lead to a reduction of the skull bones E8.5-CMEzh2 mutants 3.4: Materials and methods: 3.4a: Mice and genotyping 3.4b: Histology, β-Galactosidase, and Immunohistochemistry 3.4c: RT-qPCR 3.4d: Protein Isolation and immunoblotting 3.4e: MicroCT: 3.4f: Whole mount skeletal preparation: 3.4g: Cell Proliferation/Death Assay iii 3.4h: Retinoic acid inhibition 3.4i: Statistics 3.5: Acknowledgements: 3.6 Conflict of interest: Chapter 4: Discussion: Discussion outline: 4.1: β-catenin and its role in the suppression of chondrogenesis 4.1a: Possible repression of chondrogenesis mediated by TWIST1 4.1b: Possible suppression of Sox9 through unliganded RARs 4.1c: Possible inhibition of chondrogensis through β-catenin-SOX9 protein-protein interactions 4.1d: Possible repression of Sox9 by direct β-catenin binding 4.2: Insights into the repressive functions of β-catenin: 4.3: The mechanisms governing the developmental stage and cell type specific role of Ezh2: 4.3a: Ezh2 is required for lineage selection of the cranial bone prior to the expression of Msx genes 4.3b: Canonical vs. non-canonical function of EZH2 4.4: Ezh2 regulates skull bone formation by inhibiting a target of the RA signaling pathway: 4.4a: Hedgehog signaling and Hox genes are potential targets of RA signaling 4.5: The correlation of H3K27me3 enrichment with mRNA expression: 4.6: Conclusion: iv List of Figures: Chapter 1: Figure 1.1: Comparative anatomy of the mouse and human skull. Figure 1.2: The migration of cranial neural crest cells from the neural tube. Figure 1.3: Spatial organization of the mesenchymal stem cell origins and bone primordia. Figure 1.4: The bone initiation program and cell fate selection of the skull bone. Figure 1.5: Temporal differences in the bone initiation program between the CNCC-CM and PM- CM Figure 1.6: Signaling mechanisms regulating the bone initiation program in the CNCC-CM and PM-CM. Figure 1.7: Canonical Wnt/β-catenin signaling: Figure 1.8: Enrichment of H3K27me3 by PRC2 leads to transcriptional repression. Chapter 2: Figure 2.1: β-catenin regulates known PRC2 targets and can physically interact with PRC2. Figure S2.1: Genomic Regions Enrichment of Annotations Tool (GREAT) analysis of differentially expressed genes upon deletion of β-catenin. Figure S2.2: Genes regulated by β-catenin are enriched for PRC2 targets in dorsal dermal fibroblasts. Figure 2.2: β-catenin activity is not required for the expression of PRC2 components and bulk H3K27me3 levels. Figure S2.3: Knockout of Ezh2 with En1Cre does not lead to a change in H3K27me3 enrichment in the CM. Figure 2.3: Knockdown of Ezh2 in the cranial mesenchyme does not lead to changes in cell type fate selection. Figure 2.4: Chemical inhibition of EZH2 methyltransferase does not lead to an up-regulation of early chondrocyte markers in CM+ectoderm. Figure 2.5: Loss of β-catenin does not significantly alter H3K27me3 enrichment genome wide or on cartilage differentiation determinants. Figure S2.4: Analysis of strong, medium, and weak H3K27me3 enrichment in the CM+ectoderm. Figure S2.5: Gene ontology analysis of strong, medium, and weak H3K27me3 enrichment. Figure S2.6: Strong, medium, and weak H3K27me3 peak groups have similar representation in genes regulated by β-catenin. Figure S2.7: H3K27me3 peaks are associated with genes actively transcribed and repressed in CM. Chapter 3: Figure 3.1: Tamoxifen induced knockout of Ezh2at E8.5 in both the mesoderm- and neural crest-derived mesenchymal stem cells is sufficient to lead to craniofacial defects. Figure S3.1: Whole mount analysis of E13.5 and E17.5 E8.5-CMEzh2 mutants. Figure 3.2: e8.5-CMEzh2leads to a reduction of CNCC-derived bones and a severe reduction in PM-derived bones. Figure S3.2: Quantification of the mandible and snout in e8.5-CMEzh2 mutants. v Figure 3.3: Ezh2 is required for skull bone formation in a developmental stage-dependent manner. Figure S3.3: Ezh2 is lost in the same tissue in the E8.5-CMEzh2 and E9.5-CMEzh2 mutant. Figure 3.4: Increased cell death in E8.5-CMEzh2 mutants is insufficient to account for loss of skull bones. Figure S3.4: Significant increase in cell death, but no change in cell proliferation, in the frontonasal process in E8.5-CMEzh2 mutants. Figure 3.5: Loss of Ezh2 at E8.5 leads to defects in bone progenitor differentiation. Figure S3.5: No change in bone marker, alkaline phosphatase (AP) inE8.5-CMEzh2 mutants and OSX in E9.5-CMEzh2mutants. Figure S3.6: E8.5-CMEzh2 mutants exhibit an ectopic expression of the Hox genes. Figure S3.7: The effects of RA signaling disruptions in the CM. Figure 3.6: Chemical inhibition of RA signaling partially rescues the in E8.5-CMEzh2 mutant phenotype and restores the PM-derived bones. Chapter 4: Figure 4.1: Proposed mechanisms by which β-catenin suppresses chondrogenesis in the cranial mesenchyme. Figure 4.2: Ezh2 is required for the lineage selection of the skull bone precursors prior to the activation of the bone initiation program. vi List of Tables: Chapter 1: Table 1.1: Signaling pathway mutants leading to skull bone defects Chapter 2: Table 2.1: Summary of publications demonstrating a biological interaction between β-catenin and PRC2.