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Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. 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"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Micro-C on JM8.N4 (Tier 2) with MNase - 4DNEXNEHQ5BL", "external_references": [{"ref": "SRA:SRX5734618", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX5734618"}, {"ref": "GEO:GSM3735071", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3735071"}], "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES14CNC1I/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "6900ed9d-7a0e-47b8-b226-55a308be7c56", "accession": "4DNES14CNC1I", "display_title": "4DNES14CNC1I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "date_published": "2020-03-17", "ID": "PMID:32213323", "authors": ["Hsieh TS", "Cattoglio C", "Slobodyanyuk E", "Hansen AS", "Rando OJ", "Tjian R", "Darzacq X"], "title": "Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.", "journal": "Molecular cell", "status": "current", "short_attribution": "Hsieh TS et al. (2020)", "@id": "/publications/d44c7a1c-323d-41d4-bbe7-476ac10cd34f/", "abstract": "Whereas folding of genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well understood, how chromatin is folded at finer scales remains largely unexplored in mammals. Here,  we overcome some limitations of conventional 3C-based methods by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregates TAD regions into various finer-scale structures with distinct regulatory features including stripes, dots, and domains linking promoters-to-promoters (P-P) or enhancers-to-promoters (E-P) and bundle contacts between Polycomb regions. E-P stripes extending from the edge of domains predominantly link co-expressed loci,  often in the absence of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts these gene-related folding features without altering higher-order chromatin structures. Our study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin  folding and gene regulation.", "uuid": "d44c7a1c-323d-41d4-bbe7-476ac10cd34f", "display_title": "Hsieh TS et al. (2020) PMID:32213323", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"uuid": "d44c7a1c-323d-41d4-bbe7-476ac10cd34f", "authors": ["Hsieh TS", "Cattoglio C", "Slobodyanyuk E", "Hansen AS", "Rando OJ", "Tjian R", "Darzacq X"], "journal": "Molecular cell", "@type": ["Publication", "Item"], "status": "current", "display_title": "Hsieh TS et al. (2020) PMID:32213323", "date_published": "2020-03-17", "title": "Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.", "abstract": "Whereas folding of genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well understood, how chromatin is folded at finer scales remains largely unexplored in mammals. Here,  we overcome some limitations of conventional 3C-based methods by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregates TAD regions into various finer-scale structures with distinct regulatory features including stripes, dots, and domains linking promoters-to-promoters (P-P) or enhancers-to-promoters (E-P) and bundle contacts between Polycomb regions. E-P stripes extending from the edge of domains predominantly link co-expressed loci,  often in the absence of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts these gene-related folding features without altering higher-order chromatin structures. Our study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin  folding and gene regulation.", "short_attribution": "Hsieh TS et al. (2020)", "ID": "PMID:32213323", "@id": "/publications/d44c7a1c-323d-41d4-bbe7-476ac10cd34f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_summary": "Micro-C on JM8.N4 (Tier 2) with MNase", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSA6AJ5XT/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}