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This proposal is significant because we propose a novel model forthe role of nuclear organization in regulating gene expression: 1) Nuclear speckles and still unknown nuclearcompartments/bodies help organize other phase-separated condensates to modulate gene expression; 2)Nuclear speckles together with surrounding nuclear compartments/bodies and associated phase-separatedcondensates together represent active nuclear niches which may have different functional properties; 3) Smalldistances matter: gene movements of only a few hundred nm between repressive and these different activenuclear niches may differentially regulate gene expression; 4) Action-at-a distance: component flux into andout of these nuclear compartments will have global effects on gene expression; 5) These same nuclearcompartments/bodies may similarly modulate RNA processing and organize nuclear export. Here we propose to: 1) Identify multiple components of known and still unknown nuclear \u201cactiveniches\u201d; 2) Map genome-wide the positions and predicted movements of genes relative to these active nichesduring physiological transitions; 3) Visualize nuclear body/compartment dynamics and fluxes of proteinsbetween nuclear bodies in steady-state and through physiological transitions; 4) Visualize movements ofreporter transgenes, endogenous genes, and rewired chromosome loci relative to these nuclearbodies/compartments and temporally correlate changes in gene expression with their dynamic movements andcompartment associations; 5) Visualize movements of pre-mRNAs and nuclear mRNAs during RNAprocessing and export; 6) Measure fluxes of nuclear body components to and from adjacent transcribingchromatin. Additionally, we propose developing relatively low-cost, novel microscope platforms and softwarespecifically designed to facilitate these live-cell imaging goals in our laboratories as well as others. Our Aims will be to: 1. Map proteins, genes, RNAs relative to active nuclear compartment(s) usingiterative rounds of TSA-MS-Ratio, validation by light microscopy, and TSA-Seq; 2. Measure dynamics ofbodies, components of nuclear bodies using live-cell imaging; 3. Measure temporal correlation betweenchanges in gene expression and gene movement relative to nuclear bodies and visualize the export path ofexpressed transcripts; 4. Design and deliver two novel microscopes designed to facilitate Aims 1-3 at amodest cost. Successful completion of these Aims should significantly change our current understanding of therole of nuclear organization in regulating gene expression with impact across a wide range of research fields.\"", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "02512949b221f3b39a47d320109e84d6", "status": "released", "aliases": ["belmont-lab:U2OS_THRAP3_2xDTT_bio2_hg38.bw"], "filename": "U2OS_THRAP3_2xDTT_bio2_hg38.bw", "accession": "4DNFI2EKDO5E", "file_size": 1119559, "file_type": "normalized counts", "description": "20kb bin (read normalized) count track", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "display_title": "bw", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "3db0d0a2-119a-473c-8977-6380743fe449", "date_created": "2025-07-21T18:53:31.497973+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-09-05T17:46:57.700212+00:00"}, "produced_from": ["belmont-lab:U2OS_2xDTT_THRAP3_PULLDOWN_bio2_GCCAATAT_L001_R1_001.fastq", "belmont-lab:U2OS_2xDTT_THRAP3_INPUT_bio2_ACAGTGAT_L001_R1_001.fastq"], "content_md5sum": "02512949b221f3b39a47d320109e84d6", "public_release": "2025-08-27", "schema_version": "3", "static_content": [{"content": {"uuid": "abf4ff00-8c87-4f39-9a1c-7a03d7f09e8b", "contributing_labs": [], "name": "abf4ff00-8c87-4f39-9a1c-7a03d7f09e8b", "award": {"@type": ["Award", "Item"], "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "status": "current", "@id": "/awards/1U01DK127422-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "", "lab": {"uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "display_title": "Andrew Belmont, ILLINOIS", "@id": "/labs/andrew-belmont-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI2EKDO5E - 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