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(2024) PMID:39271748", "journal": "Communications biology", "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"], "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated Tyramide Signal Amplification (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 human embryonic stem cells (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.", "@id": "/publications/22e02dc4-37b9-4891-9084-6d85f6683252/", "uuid": "22e02dc4-37b9-4891-9084-6d85f6683252", "short_attribution": "Kumar P et al. (2024)", "title": "Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable  localization of heterochromatin in different cell types.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "journal": "Communications biology", "uuid": "22e02dc4-37b9-4891-9084-6d85f6683252", "ID": "PMID:39271748", "@type": ["Publication", "Item"], "display_title": "Kumar P et al. (2024) PMID:39271748", "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"], "title": "Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable  localization of heterochromatin in different cell types.", "abstract": "Genome differential positioning within interphase nuclei remains poorly explored.  We extended and validated Tyramide Signal Amplification (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 human embryonic stem cells (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": "2024-09-13", "@id": "/publications/22e02dc4-37b9-4891-9084-6d85f6683252/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS56GW121/", "embedded_path": "experiments_in_set.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"}}}, {"parent": "/biosamples/4DNBS74TFUQ1/", "embedded_path": "experiments_in_set.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": []}