{"ID": "doi:10.1101/2023.12.04.570024", "lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "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/38105994", "award": {"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/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "name": "2U01CA200059-06", "@type": ["Award", "Item"], "project": "4DN", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "center_title": "DCIC - Park", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Cell-type-specific 3D-genome organization and transcription regulation in the  brain.", "status": "replaced", "aliases": ["xiaowei-zhuang-lab:genome_wide_brain_publication"], "authors": ["Liu S", "Zheng P", "Wang CY", "Jia BB", "Zemke NR", "Ren B", "Zhuang X"], "journal": "bioRxiv : the preprint server for biology", "abstract": "3D organization of the genome plays a critical role in regulating gene  expression. However, it remains unclear how chromatin organization differs among  different cell types in the brain. Here we used genome-scale DNA and RNA imaging  to investigate 3D-genome organization in transcriptionally distinct cell types in  the primary motor cortex of the mouse brain. We uncovered a wide spectrum of  differences in the nuclear architecture and 3D-genome organization among  different cell types, ranging from the physical size of the cell nucleus to the  active-inactive chromatin compartmentalization and radial positioning of  chromatin loci within the nucleus. These cell-type-dependent variations in  nuclear architecture and chromatin organization exhibited strong correlation with  both total transcriptional activity of the cell and transcriptional regulation of  cell-type-specific marker genes. Moreover, we found that the  methylated-DNA-binding protein MeCP2 regulates transcription in a divergent  manner, depending on the nuclear radial positions of chromatin loci, through  modulating active-inactive chromatin compartmentalization.", "date_created": "2024-04-01T16:30:37.773817+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-08-12T16:42:54.960409+00:00"}, "date_published": "2023-12-05", "public_release": "2024-04-01", "schema_version": "2", "static_content": [{"content": {"@id": "/static-sections/e28c5b78-e995-4352-90fb-e5dece810e53/", "uuid": "e28c5b78-e995-4352-90fb-e5dece810e53", "content_as_html": "<div class=\"markdown-container\"><p>This biorxiv set was replaced by <a href=\"https://data.4dnucleome.org/de7e2893-e23f-4331-899f-888ee267e3a9/\" rel=\"noopener noreferrer\" target=\"_blank\">PMID:40009678</a>.</p></div>", "name": "static-header.replaced_item_130659a2-6f94-479a-97e6-3b92741c955a", "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Note: Replaced Biorxiv", "status": "released", "content": "This biorxiv set was replaced by [PMID:40009678](https://data.4dnucleome.org/de7e2893-e23f-4331-899f-888ee267e3a9/).", "display_title": "Note: Replaced Biorxiv", "award": {"status": "current", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - 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