Studies on the role of transcription factor Dpf3 in epigenetic control of heart and skeletal muscle development

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1 Studies on the role of transcription factor Dpf3 in epigenetic control of heart and skeletal muscle development Untersuchung des Einflusses des Transkriptionsfaktors Dpf3 auf die epigenetische Regulation der Herz- und Skelettmuskelentwicklung DISSERTATION zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Diplom-Biologe Martin Lange aus Brilon durchgeführt am Max-Planck-Institut für Molekulare Genetik eingereicht im Fachbereich Biologie, Chemie, Pharmazie der Freien Universität Berlin Juni 2008

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3 1. Gutachter: Prof. Dr. T. Schmülling, Institut für Angewandte Genetik, Freie Universität Berlin Albrecht-Thaer-Weg 6, D Berlin 2. Gutachter: Prof. Dr. H. Lehrach, Max-Planck-Institut für molekulare Genetik, Ihnestr.73, D Berlin Disputation am

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5 Introduction 1 Introduction Dpf3, the third member of the d4 protein family Heart development Human congenital heart disease Skeletal muscle development The sarcomere Muscle disease in humans Epigenetic regulation of gene expression Chromatin remodeling Histone shuffling Histone modifications Epigenetic regulation of heart and skeletal muscle development Purpose & Aims Materials and Methods Chemicals, reagents and equipment Consumables and Machines Software Kits Bioinformatic analyses Cell lines C2C12 Cells HL-1 Cells HEK293T cells H9c2 cells Molecular Biology techniques DNA gel electrophoresis Enzymatic DNA digestion Ethanol precipitation of DNA DNA ligation Genomic DNA isolation Isolation of RNA Reverse transcription of RNA cdna synthesis Polymerase chain reaction (PCR) Site-directed mutagenesis Inverse PCR TOPO cloning Plasmid transformation into bacteria Reportergene assays Electromobility shift assays Quantitative real-time PCR Microarray analysis of dpf3 morphant zebrafish embryos Animal studies Generation of transgenic mice X-gal staining of mouse embryos Embedding and sectioning of mouse embryos Counter-staining of histological sections after X-gal staining Morpholino antisense-oligonucleotide knockdown in zebrafish embryos mrna rescue of zebrafish embryos in situ hybridization Protein biochemistry Recombinant protein expression and purification

6 Introduction GST pulldown assays Histone Peptide Binding Assays Results Embryonic expression profiles of Dpf3 splice variants The role of dpf3 in zebrafish embryonic development Cloning of full-length zebrafish dpf In situ hybridization of dpf3 in zebrafish embryos Knockdown of dpf3 by morpholino antisense-oligonucleotide injection of zebrafish embryos Microarray gene expression analysis of dpf3 morphant embryos Gene ontology analysis of differentially expressed genes from zebrafish genomewide expression arrays DPF3 is a novel component of the BAF chromatin remodeling complex Interaction of DPF3 proteins with components of the BAF complex The PHD fingers of DPF3b interact with modified histone tails The role of DPF3 in developmental signaling pathways DPF3 promoter analysis DPF3 minimal promoter analysis in transgenic mice DPF3 minimal promoter: COUP-TF binding site deletion DPF3 minimal promoter: Nkx2.5 binding element (NKE) deletion A fate-map of DPF3 minimal promoter activity: Cre transgenics DPF3 enhancer DPF3 downstream targets: Analysis of signaling pathways The evolution of the d4 protein family Discussion Expression profiles of Dpf3 splice variants The role of dpf3 in zebrafish embryonic development DPF3 is a novel subunit of the BAF chromatin remodeling complex The Plant-Homeodomains of DPF3b recognize modified histone lysine residues ChIP-chip analysis of Dpf3 downstream targets Dpf3 binding sites co-localize with acetylated and methylated histone tails The role of DPF3 in developmental signaling pathways Evolution of the d4 protein family Summary Zusammenfassung References Appendix Appendix B: Abbreviations Appendix C: sirnas Appendix D: Lists of Primers Human primers Mouse primers Zebrafish primers Appendix E: Zebrafish Expression arrays Array quality control Data analysis Publications Acknowledgements