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Here we propose to create the University of Washington Center for Nuclear Organization and Function, bringing together an interdisciplinary team of investigators whose diverse areas of expertise - technology development, computational modeling, and mouse and human biology - make them ideally suited to this challenge. Our overall hypothesis is that characterizing and understanding changes in genome architecture over time (the 4D nucleome) will lead to fundamental insights into human biology and disease. We will address this hypothesis by developing a combination of experimental and computational methods development, coupled with their systematic biological validation and application to development- and disease-relevant systems. On the experimental side, we will further optimize our recently developed DNase Hi- C assay, including combinatorial methods for single cells, ultimately aiming to concurrently assay nuclear architecture and gene expression within each of many single cells. On the computational side, we will extend our existing 3D modeling algorithms to account for diploidy, cell-to-cell variabilit, the hierarchical nature of genome architecture, and to explicitly model architectural changes over cell cycle and cell differentiation time scales. We will then employ several complementary computational methods to link our 4D nucleome models to existing, 1D genomics data sets. The outputs of these new experimental and computational technologies will be subjected to orthogonal validation in several well-understood model systems: human cell lines, in vivo tissues from interspecific F1 hybrid mice, mouse embryonic stem cells (ESCs) and skeletal myoblasts. We will also test specific predictions of the models in response to targeted (genome editing) or large-scale (chromosome silencing) perturbations. After initial validation and in parallel with further methods development, we will apply our new tools to the analysis of three biological systems: we will characterize the dynamics of nuclear architecture during the directed differentiation of na\u00efve human ESCs into cardiomyocytes and endothelial cells; we will test the hypothesis that cardiomyopathy-inducing mutations in the nuclear scaffolding protein, lamin A, are associated with derangements in cardiomyocyte nuclear architecture; and we will determine the changes in human cardiomyocyte nuclear architecture induced by trisomy 21. The proposed center will produce new experimental protocols for ascertaining 4D nucleome architecture, two new software toolkits for modeling the 4D nucleome and linking features of the nucleome to other types of genomic data, a variety of publicly available, large-scale 4D nucleome data sets in mouse and human systems, and fundamental insights into human biology and disease. 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(2015) doi:10.1186/s13059-015-0728-8", "status": "current", "@type": ["Publication", "Item"], "abstract": "BACKGROUND: In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently  developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. RESULTS: We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary region. Comparison with the recently reported two-superdomain structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the  boundary region is conserved and located near the Dxz4/DXZ4 locus. In mouse, the  boundary region also contains a minisatellite, Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation compared with the active alleles and with genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. CONCLUSIONS: By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization  of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.", "@id": "/publications/8aeb7ef2-26e2-4458-99df-64d57e97cde8/", "authors": ["Deng X", "Ma W", "Ramani V", "Hill A", "Yang F", "Ay F", "Berletch JB", "Blau CA", "Shendure J", "Duan Z", "Noble WS", "Disteche CM"], "ID": "doi:10.1186/s13059-015-0728-8", "uuid": "8aeb7ef2-26e2-4458-99df-64d57e97cde8", "journal": "Genome biology", "date_published": "2015-08-07", "short_attribution": "Deng X et al. (2015)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2018-04-13", "abstract": "The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts, separated by a hinge region. Using Hi-C in edited mouse cells with allelic deletions or inversions within the hinge, here we show that the conserved Dxz4 locus is necessary to maintain this bipartite structure. Dxz4 orientation controls the distribution of  contacts on the Xi, as shown by a massive reversal in long-range contacts after Dxz4 inversion. Despite an increase in CTCF binding and chromatin accessibility on the Xi in Dxz4-edited cells, only minor changes in TAD structure and gene expression were detected, in accordance with multiple epigenetic mechanisms ensuring X silencing. We propose that Dxz4 represents a structural platform for frequent long-range contacts with multiple loci in a direction dictated by the orientation of its bank of CTCF motifs, which may work as a ratchet to form the distinctive bipartite structure of the condensed Xi.", "journal": "Nature communications", "status": "current", "short_attribution": "Bonora G et al. (2018)", "display_title": "Bonora G et al. (2018) PMID:29654302", "title": "Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.", "uuid": "9c94ba12-dfc9-40a7-b37e-018e919c3528", "ID": "PMID:29654302", "@type": ["Publication", "Item"], "authors": ["Bonora G", "Deng X", "Fang H", "Ramani V", "Qiu R", "Berletch JB", "Filippova GN", "Duan Z", "Shendure J", "Noble WS", "Disteche CM"], "@id": "/publications/9c94ba12-dfc9-40a7-b37e-018e919c3528/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "DNaseI", "combined": "Enzyme: DNaseI"}, "experiment_summary": "DNase Hi-C on Patski with DNaseI", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSYUR8K9A/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}