Epigenetic regulation of gene expression domains in pluripotent stem cells

Transcriptional and histone modification profiles were analysed in detail across several regions of the mouse genome in order to examine how tissue-specificity is determined at early stages of development and how it is maintained during cell commitment. The analysis was mainly focused on a 2 Mb gene-dense region containing 68 known closely situated genes, having very diverse expression patterns. Transcriptional profiling of this region showed that clustered tissue-restricted and housekeeping genes are associated with clearly defined monovalent or bivalent epigenetic domains. In ES cells, the actively transcribed housekeeping genes were enriched for histone H3K4me1, H3K4me2, H3K4me3, H3K9ac and binding of Pol II. Most of the silent tissue-restricted genes were marked by bivalent domains and had background levels of Pol II. In few cases, substantial levels of Pol II were found at inactive genes situated close to housekeeping genes, suggesting that transcriptional read-through could be occurring at these genes in ES cells. Epigenetic profiling of the gene-dense region in LPS-activated B cells showed that B cells have a very similar histone modification profile to ES cells. Specifically, the analysis showed that bivalent domains which were thought to be a defining characteristic of pluripotent stem cells are equally prevalent in B cells, suggesting that the epigenetic marking of silent genes is quite similar in these two very different cell types. Analysis of a large gene-poor region containing four genes encoding GABAA neurotransmitter receptor subunits showed that the this locus acquires a large bivalent domain of approximately 1.3 Mb following differentiation of ES cells into NS cells and astrocytes. The results obtained in this study demonstrate the complex and diverse nature of histone modifications at tissue-restricted genes and suggest that trans-acting factors are responsible for generating highly specific combinations of histone modifications at each individual gene at different stages of cell differentiation.EThOS - Electronic Theses Online ServiceGBUnited Kingdo