Epigenetic chromatin states during embryonic development and adult homeostasis of the mammalian gut
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Abstract
The mammalian small intestine is a complex 3D-structure comprised of various specialized, proliferative and fully differentiated cell types. Although highly specialized in adults, all cellular lineages originate from a monolayered epithelial tube in the early embryo, which consists of a presumably homogenous population. As the fastest proliferating tissue, the murine small intestine is an established model to study embryonic development and adult homeostasis. These processes are mainly regulated in two ways: intracellular signaling, such as the proliferative Wnt-pathway in combination with Notch- Hedgehog- and BMP-signaling, and epigenetic mechanisms, on which this thesis focuses. Here, I assessed the epigenetic marks H3K27Ac, H3K27me3, H3K4me3, H2A.Z and DNA-methylation, which are involved in the regulation of gene activity, providing a cell type and a development specific expression pattern.
The main goal of the projects described in this thesis was to elucidate epigenetic mark deposition and their interaction on the genome-wide scale and to assess their functional impact on gene activity at single genetic loci. Furthermore, single cell in situ analysis was employed to visualize tissue heterogeneity of gene expression and epigenetic patterning. Both approaches were used to deepen our understanding of epigenetic mechanisms involved in development and homeostasis as well as in cancer pathogenesis.
Active and repressive epigenetic marks’ genomic distribution was analyzed throughout the intestinal development from embryonic to the fully differentiated adult cell types. In combination with RNA-seq data, these ChIP-seq and MBD-seq experiments provided a comprehensive dataset, which allows for the investigation of epigenetic marks’ interactions along the intestinal cell development timecourse. Hereby, H2A.Z, a histone variant previously annotated to active genes, was found to be positioned on responsive rather than on active promoters. Moreover, H2A.Z was found to be decoupled from gene activity regulation in fully differentiated cells. The well-known active promoter and enhancer mark H3K27Ac was additionally found to mark poised enhancers, long before the corresponding gene’s expression. This novel premarking effect, in combination with the available timecourse gene expression data, could be used for improved genome-wide enhancer prediction and target gene identification.
Numerous potential developmental marker genes were identified through developmental clustering. Single locus analysis of these genes revealed strong heterogeneity of gene expression and epigenetic levels in adult intestinal tissue. Strikingly, similar gene expression patterns were also observed at embryonic stages, which previously were believed to be uniform. This heterogeneity might be the key to adult tissue homeostasis and functionality as well as to the early cell fate commitment and structural patterning in the embryonic epithelium.