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Mansperger, Katrin (2007): Analysis of Developmental Epistasis by Chromatin Immunoprecipitation in Xenopus laevis. Dissertation, LMU München: Faculty of Biology
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Abstract

The development of an organism from the fertilized zygote to a multicellular organism is a unidirectional process. It occurs in a spatially and temporally tightly controlled fashion. To understand how the genetic information is interpreted and how the cellular identity is inherited, are major challenges towards the understanding of developmental processes. Epigenetic marks like histone modifications, changes of the protein composition binding to DNA or the remodeling of nucleosomes have been shown to be important for the establishment of tissue-specific transcription profiles. Chromatin immunoprecipitation (ChIP) is a method to investigate the association of proteins to specific genomic loci. In this study, I have established two protocols for ChIP analyses of Xenopus laevis embryos: the In Situ ChIP and the Douncer ChIP. In addition, I have generated several antibodies in collaboration with Dr. Elisabeth Kremmer (GSF München) for ChIP analyses, which were directed against the muscle determination factor MyoD and the Wnt/β-catenin signaling components Lef/Tcf transcription factors Lef1 and Tcf1. While optimizing of the ChIP protocols, I have analyzed successfully the binding of various transcription factors, chromatin remodeling enzymes and histone modifications on genomic loci of key developmental regulators. With the In Situ ChIP, I have shown that the serum response factor SRF interacts predominantly with the actively transcribed myoD gene. Together with other data, this result helps to define a specific role of SRF protein in the stable maintenance of myoD transcription, which is essential for proper muscle differentiation. With the Douncer ChIP protocol, a time course study has been performed in order to understand, when and which histone modification marks appear during muscle cell determination and differentiation on the myoD locus. The temporal and spatial distribution of the analyzed histone modification marks was correlated for the most part with the expected patterns. Furthermore, I have demonstrated that direct binding of the chromatin remodeler CHD4/Mi2-β to the 5' part of the sip1 gene in gastrula stage embryos. This interaction represents a crucial regulatory module, which determines the position along the animal-vegetal axis of the embryo, where the border between the mesodermal and neuroectodermal germ layer will be formed. These examples represent on of the very few successful ChIP applications for the endogenous proteins in young Xenopus embryos, and I hope that my protocols will turn out useful for future investigations of regulatory interactions in this vertebrate model organism.