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Increasing evidence indicates that specific genomic regions each associate with these compartments. 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. 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"/experiment-set-replicates/4DNESGQFG1ZQ/", "uuid": "9525cd2c-3436-43ae-83dd-0dcf985fdbb5", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"status": "current", "display_title": "Kumar P et al. (2023) doi:10.1101/2023.10.29.564613", "short_attribution": "Kumar P et al. (2023)", "journal": "bioRxiv : the preprint server for biology", "title": "Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin  in different cell types.", "@id": "/publications/395f743d-4d9a-49a8-9712-6bd832a66e35/", "date_published": "2023-11-01", "ID": "doi:10.1101/2023.10.29.564613", "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.", "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"], "uuid": "395f743d-4d9a-49a8-9712-6bd832a66e35", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"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.", "date_published": "2023-11-01", "ID": "doi:10.1101/2023.10.29.564613", "uuid": "395f743d-4d9a-49a8-9712-6bd832a66e35", "journal": "bioRxiv : the preprint server for biology", "title": "Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin  in different cell types.", "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/", "display_title": "Kumar P et al. (2023) doi:10.1101/2023.10.29.564613", "short_attribution": "Kumar P et al. (2023)", "@type": ["Publication", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "POLR1E protein", "combined": "Target: POLR1E protein"}, "experiment_summary": "TSA-seq against POLR1E protein on HFFc6 (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS56GW121/", "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": []}