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This genome compartmentalization has been linked to various functions, but these links are still poorly understood. Interestingly, Lamina Associated Domains (LADs) share specific heterochromatin marks, defining chromatin domains with distinct genetic and epigenetic properties. Genomic regions associating with other nuclear compartments may similarly define distinct classes of chromatin domains. One major bottleneck towards a deeper understanding of nuclear organization has been the inability to convert microscopy views of nuclear compartments into genome-wide maps that show which loci are associated with which compartment, and how the chromosomal fiber traverses between compartments. In addition, there is an urgent need for more efficient methods to dissect the mechanisms by which large genomic regions are targeted to specific nuclear compartments. Finally, there is an urgent need for high-throughput approaches that query the functional relevance of genome compartmentalization. For this Center grant, we propose to meet these needs through the following Aims: 1. Develop a strategy that connects microscopy views to genome-wide maps that, together with modeling, reveal the localization and dynamics of genomic regions relative to all major nuclear compartments. 2. Develop methods for efficient manipulation of the genome in order to elucidate mechanisms that target loci to specific compartments. 3. Develop methods to measure, model, and validate the functional relevance of nuclear compartments. The combined results of these approaches will reveal causal relationships now hidden among entangled genomic, epigenetic, and nuclear organization features. Deliverables of this proposal include a wide range of structural and functional maps of nuclear organization, reagents for visualizing endogenous chromosome loci, a powerful pipeline for synthesis of ~100kb DNA fragments, and cell lines facilitating repeated, high-fidelity insertio of these large fragments back into selected sites in the genome. These resources will provide a powerful complement to other 4D Nucleome Consortium efforts. A key strength of this Center proposal is the experience and complementary research capabilities of its five Investigators. 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(2023)", "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated TSA-seq to map genomic regions near nucleoli and  pericentric heterochromatin in four human cell lines. Our study confirmed that  smaller chromosomes localize closer to nucleoli but further deconvolved this by  revealing a preference for chromosome arms below 36-46 Mbp in length. We  identified two lamina associated domain subsets through their differential  nuclear lamina versus nucleolar positioning in different cell lines which showed  distinctive patterns of DNA replication timing and gene expression across all  cell lines. Unexpectedly, active, nuclear speckle-associated genomic regions were  found near typically repressive nuclear compartments, which is attributable to  the close proximity of nuclear speckles and nucleoli in some cell types, and  association of centromeres with nuclear speckles in hESCs. Our study points to a  more complex and variable nuclear genome organization than suggested by current  models, as revealed by our TSA-seq methodology.", "display_title": "Kumar P et al. (2023) doi:10.1101/2023.10.29.564613", "@id": "/publications/395f743d-4d9a-49a8-9712-6bd832a66e35/", "ID": "doi:10.1101/2023.10.29.564613", "uuid": "395f743d-4d9a-49a8-9712-6bd832a66e35", "date_published": "2023-11-01", "authors": ["Kumar P", "Gholamalamdari O", "Zhang Y", "Zhang L", "Vertii A", "van Schaik T", "Peric-Hupkes D", "Sasaki T", "Gilbert DM", "van Steensel B", "Ma J", "Kaufman PD", "Belmont AS"], "status": "current", "journal": "bioRxiv : the preprint server for biology", "title": "Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin  in different cell types.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"ID": "doi:10.1101/2023.10.29.564613", "short_attribution": "Kumar P et al. (2023)", "authors": ["Kumar P", "Gholamalamdari O", "Zhang Y", "Zhang L", "Vertii A", "van Schaik T", "Peric-Hupkes D", "Sasaki T", "Gilbert DM", "van Steensel B", "Ma J", "Kaufman PD", "Belmont AS"], "@id": "/publications/395f743d-4d9a-49a8-9712-6bd832a66e35/", "status": "current", "journal": "bioRxiv : the preprint server for biology", "uuid": "395f743d-4d9a-49a8-9712-6bd832a66e35", "display_title": "Kumar P et al. (2023) doi:10.1101/2023.10.29.564613", "date_published": "2023-11-01", "@type": ["Publication", "Item"], "title": "Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin  in different cell types.", "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated TSA-seq to map genomic regions near nucleoli and  pericentric heterochromatin in four human cell lines. Our study confirmed that  smaller chromosomes localize closer to nucleoli but further deconvolved this by  revealing a preference for chromosome arms below 36-46 Mbp in length. We  identified two lamina associated domain subsets through their differential  nuclear lamina versus nucleolar positioning in different cell lines which showed  distinctive patterns of DNA replication timing and gene expression across all  cell lines. Unexpectedly, active, nuclear speckle-associated genomic regions were  found near typically repressive nuclear compartments, which is attributable to  the close proximity of nuclear speckles and nucleoli in some cell types, and  association of centromeres with nuclear speckles in hESCs. Our study points to a  more complex and variable nuclear genome organization than suggested by current  models, as revealed by our TSA-seq methodology.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "DDX18 protein", "combined": "Target: DDX18 protein"}, "experiment_summary": "TSA-seq against DDX18 protein on HCT116 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSKRLQJMM/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}]}, "validation-errors": []}