{"ID": "PMID:38712201", "aka": "http://biorxiv.org/lookup/doi/10.1101/2024.04.23.590809", "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/38712201", "award": {"center_title": "DCIC - Park", "project": "4DN", "@id": "/awards/2U01CA200059-06/", "status": "current", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@type": ["Award", "Item"], "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "name": "2U01CA200059-06", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function.", "status": "current", "aliases": ["4dn-dcic-lab:belmont_compartment_locales_pmid_38712201_pp"], "authors": ["Gholamalamdari O", "van Schaik T", "Wang Y", "Kumar P", "Zhang L", "Zhang Y", "Gonzalez GAH", "Vouzas AE", "Zhao PA", "Gilbert DM", "Ma J", "van Steensel B", "Belmont AS"], "journal": "bioRxiv : the preprint server for biology", "abstract": "Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.", "categories": ["basic biology"], "date_created": "2024-05-16T18:14:25.724471+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-04-10T17:16:14.238181+00:00"}, "date_published": "2025-02-26", "public_release": "2024-05-16", "schema_version": "2", "static_content": [{"content": {"options": {"filetype": "jsx", "collapsible": false, "default_open": true, "convert_ext_links": true}, "content_as_html": "