{"ID": "PMID:41407856", "lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "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/41407856", "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "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.", "@id": "/awards/2U01CA200059-06/", "center_title": "DCIC - Park", "project": "4DN", "name": "2U01CA200059-06", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@type": ["Award", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "An integrated view of the structure and function of the human 4D nucleome.", "status": "current", "aliases": ["4dn-dcic-lab:2025_4DN_marker_JA_pmid41407856"], "authors": ["Dekker J", "Oksuz BA", "Zhang Y", "Wang Y", "Minsk MK", "Kuang S", "Yang L", "Gibcus JH", "Krietenstein N", "Rando OJ", "Xu J", "Janssens DH", "Henikoff S", "Kukalev A", "Andrea W", "Winick-Ng W", "Kempfer R", "Pombo A", "Yu M", "Kumar P", "Zhang L", "Belmont AS", "Sasaki T", "van Schaik T", "Brueckner L", "Peric-Hupkes D", "van Steensel B", "Wang P", "Chai H", "Kim M", "Ruan Y", "Zhang R", "Quinodoz SA", "Bhat P", "Guttman M", "Zhao W", "Chien S", "Liu Y", "Venev SV", "Plewczynski D", "Azcarate II", "Szabo D", "Thieme CJ", "Szczepinska T", "Chilinski M", "Sengupta K", "Conte M", "Esposito A", "Abraham A", "Zhang R", "Wang Y", "Wen X", "Wu Q", "Yang Y", "Liu J", "Boninsegna L", "Yildirim A", "Zhan Y", "Chiariello AM", "Bianco S", "Lee L", "Hu M", "Li Y", "Barnett RJ", "Cook AL", "Emerson DJ", "Marchal C", "Zhao P", "Park PJ", "Alver BH", "Schroeder AJ", "Navelkar R", "Bakker C", "Ronchetti W", "Ehmsen S", "Veit AD", "Gehlenborg N", "Wang T", "Li D", "Wang X", "Nicodemi M", "Ren B", "Zhong S", "Phillips-Cremins JE", "Gilbert DM", "Pollard KS", "Alber F", "Ma J", "Noble WS", "Yue F"], "journal": "Nature", "abstract": "The dynamic three-dimensional (3D) organization of the human genome (the 4D  nucleome) is linked to genome function. Here we describe efforts by the 4D  Nucleome Project(1) to map and analyse the 4D nucleome in widely used H1 human  embryonic stem cells and immortalized fibroblasts (HFFc6). We produced and  integrated diverse genomic datasets of the 4D nucleome, each contributing unique  observations, which enabled us to assemble extensive catalogues of more than  140,000 looping interactions per cell type, to generate detailed classifications  and annotations of chromosomal domain types and their subnuclear positions, and  to obtain single-cell 3D models of the nuclear environment of all genes including  their long-range interactions with distal elements. Through extensive  benchmarking, we describe the unique strengths of different genomic assays for  studying the 4D nucleome, providing guidelines for future studies.  Three-dimensional models of population-based and individual cell-to-cell  variation in genome structure showed connections between chromosome folding,  nuclear organization, chromatin looping, gene transcription and DNA replication.  Finally, we demonstrate the use of computational methods to predict genome  folding from DNA sequence, which will facilitate the discovery of potential  effects of genetic variants, including variants associated with disease, on  genome structure and function.", "categories": ["key publication"], "date_created": "2025-12-18T14:21:41.933175+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-12-18T14:43:29.375608+00:00"}, "date_published": "2025-12-17", "public_release": "2025-12-18", "schema_version": "2", "static_content": [{"content": {"error": "no view permissions"}, "location": "header"}], "project_release": "2025-12-18", "@id": "/publications/566a4020-eb39-4471-98f2-2db7c00adcfd/", "@type": ["Publication", "Item"], "uuid": "566a4020-eb39-4471-98f2-2db7c00adcfd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Dekker J et al. (2025) PMID:41407856", "external_references": [], "short_attribution": "Dekker J et al. (2025)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}