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Understanding the basis of transcriptional regulation during development and in pathologies is one of the fundamental challenges of modern biology. The expression of most genes is controlled by the interplay of activating and repressive transcription factors acting at DNA regulatory elements. Enhancers represent the largest class of distal regulatory elements, which can be spread across large regions of the genome. According to the prevailing model, multiple enhancer elements activate their target genes by making direct physical contacts with their promoters. Both enhancers and promoters are defined not only by a specific DNA sequence but also by a particular chromatin signature. The fundamental element of the chromatin, the nucleosome core, is a multi-subunit structure consisting of four histone types. Each histone has the potential to be differentially altered by a number of covalent modifications. Modifications of core histones influence the gene expression program. Acetylation of lysine residues within histone tails increases the accessibility of the chromatin template to the transcriptional machinery. Tri-methylation of histone H3 at lysine 9 (H3K9me3) is essential for the formation of silent heterochromatin. On the other hand, tri-methylation of histone H3 at lysine 27 (H3K27me3) is required for the repression of genes, encoding for transcription factors, receptors and signalling molecules, which are involved in developmental patterning and differentiation of multicellular organisms. Consistently, the distribution of H3K27me3 positive nucleosomes strongly correlates with transcriptional silencing of the target genes. In contrast, high levels of histone acetylation and tri-methylation of histone H3 at lysine 4 (H3K4me3) were detected in promoter regions of active genes. Furthermore, distinct chromatin signatures were associated with enhancers. Specifically, H3K4me1 positive nucleosomes were found at putative poised enhancers whereas the combination of both H3K27Ac and H3K4me1 marks was associated with active enhancer elements in various cell types.
We investigate the biological significance of histone modifications covering enhancer and promoter sequences in the developing mouse small intestine as well as in the adult gut. The small intestine epithelium homeostasis requires rapid and continuous regeneration and differentiation of specific cell types from intestinal stem cells. The adult intestinal stem cells give rise to the first few generations of stem cell daughters, transit-amplifying cells, which in turn, undergoing a limited number of cell divisions, provide a vast progeny of terminally differentiated cell types: absorptive enterocytes and secretory Paneth, goblet, entero-endocrine and tuft cells. We have generated genome-wide transcriptome and chromatin state maps from the embryonic intestinal epithelium, adult intestinal stem cells, enterocytes and Paneth cells. We have uncovered the significance of chromatin modifications during (1) formation of the adult intestinal stem cell from their embryonic progenitors, (2) their maintenance and (3) as the adult intestinal stem cells differentiate along either absorptive or secretory lineages. We have defined sets of genes that are co-regulated by a combination of certain histone modifications at each stage of the intestinal stem cells lifespan. We have identified a large number of potential regulatory elements, including distal, proximal as well as intergenic enhancers. Some of these regulatory elements are common for all cells of the endodermal lineage whereas the others are specific for each cell type within the small intestinal epithelium. Our findings elucidated how the adult intestinal stem cells sustain their stemness. The results of this study increased our understanding of epigenetic mechanisms that control intestinal homeostasis. Furthermore, they provide important knowledge for development of potential therapeutic interventions for treatment of cancer, inflammatory and metabolic disorders.

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