{"lab": {"status": "current", "@id": "/labs/andrew-belmont-lab/", "title": "Andrew Belmont, ILLINOIS", "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "display_title": "Andrew Belmont, ILLINOIS", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "award": {"status": "current", "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "project": "4DN", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "description": "RT-CDF: The study of gene expression and possible role of condensates in regulating gene expression havelargely ignored known nuclear structures. 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.\"", "@type": ["Award", "Item"], "center_title": "Belmont", "name": "1U01DK127422-01", "@id": "/awards/1U01DK127422-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "status": "released", "warning": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Tiered cell line cultured after 2022-05-10 missing 4DN specified FBS vendor and lot info"]}], "status": "released", "aliases": ["belmont-lab:hct116-dbl-degron_ncv_bio2_2024_auxin"], "accession": "4DNBSE1H2XNF", "biosource": [{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], 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["alimentary tract", "alimentary system", "Entire digestive system", "gut", "gastrointestinal system"], "uuid": "111129bc-8535-4448-903e-854af460a233", "term_id": "UBERON:0001007", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "display_title": "digestive system", "term_url": "http://purl.obolibrary.org/obo/UBERON_0001007", "preferred_name": "digestive system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:HCT116T2", "4dn-dcic-lab:HCT116T2"], "accession": "4DNSRMYUIVGD", "cell_line": {"display_title": "HCT116", "preferred_name": "HCT116", "term_id": "EFO:0002824", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0002824/", "status": "released", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "term_name": "HCT116", "term_url": "http://www.ebi.ac.uk/efo/EFO_0002824", "synonyms": ["HCT-116 cell", "HCT116 cell"], 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