{"ID": "doi:10.1101/2025.10.01.679912", "lab": {"uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "status": "current", "display_title": "Andrew Belmont, ILLINOIS", "title": "Andrew Belmont, ILLINOIS", "@id": "/labs/andrew-belmont-lab/", "@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"]}}, "url": "http://biorxiv.org/lookup/doi/10.1101/2025.10.01.679912", "award": {"name": "1U01DK127422-01", "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.\"", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "@id": "/awards/1U01DK127422-01/", "@type": ["Award", "Item"], "status": "current", "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "project": "4DN", "center_title": "Belmont", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "title": "Acidic transcription factors position the genome at nuclear speckles through transcription dependent and independent mechanisms", "status": "current", "aliases": ["bel:chaturvedi_et_al_10.1101_2025.10.01.679912"], "authors": ["Chaturvedi P", "Ghosh P", "Zhang L", "Zhang M", "Zhao H", "Belmont AS"], "journal": "bioRxiv", "version": "1", "abstract": "A small fraction of the genome positions reproducibly near nuclear speckles (NS), increasing expression and/or splicing efficiency of NS-associated genes. How specific genomic regions target to NS remains unclear. Here, we demonstrate that establishment of genome-wide NS-association occurs independent of active transcription. We show that DNA sequences derived from NS-associated regions integrated as transgenes autonomously target to NS. By systematically dissecting one such genomic locus, the COL1A1-SGCA locus, we identified redundant NS-targeting cis regulatory elements, including a ~600 bp fragment with 17 binding motifs for 8 transcription factors (TFs). Four NS-targeting TFs within this fragment contain acidic activation domains (AADs) that provide both chromatin-context and transcription-dependent NS-targeting, a property that appears common among several other tested AADs. A subset of acidic activator TFs contain an additional, transcription-independent NS-targeting activity. Our findings establish diverse and partially redundant NS-targeting activities, which may facilitate dynamic gene positioning at NS periphery for context-specific transcriptional responses.", "date_created": "2025-10-06T18:51:59.135599+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-10-06T18:54:36.047152+00:00"}, "date_published": "2025-10-03", "public_release": "2025-10-06", "schema_version": "2", "project_release": "2025-10-06", "exp_sets_prod_in_pub": [{"@id": "/experiment-set-replicates/4DNESGMJ7198/", "status": "released", "display_title": "4DNESGMJ7198", "uuid": "0afd9c37-073b-47f9-a0a5-f148589a2e2d", "experimentset_type": "replicate", "accession": "4DNESGMJ7198", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experiments_in_set": [{"status": "released", "@id": "/experiments-tsaseq/4DNEXYHRZHGL/", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "display_title": "TSA-seq against Son mouse protein on NIH3T3 - 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