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We will ask: how does nascent RNA synthesis from enhancers and promoters impact genome organization? Our specific hypothesis is that nascent RNA plays a central role in stabilizing transient promoter-enhancer contacts that occur within topologically-associated domains (TADs), and thus facilitates the communication between distal cis-regulatory regions. This idea is supported by recent demonstrations that nascent RNA can serve as a platform for the recruitment and retention of transcription factors and epigenetic modifiers. Accordingly, several studies have suggested roles for specific enhancer RNAs in the establishment or maintenance of three-dimensional (3D) enhancer-promoter loops and associated gene activity. However, a full appreciation for the role of nascent RNA synthesis on \ngenome structure will require a more rigorous, coordinated and comprehensive approach than has been carried out to date. We therefore propose a collaborative project within the framework of the 4D Nucleome network to address how enhancer and gene transcription impact chromosome organization.", "display_title": "ELUCIDATING THE ROLE OF NASCENT RNA IN ENHANCER-PROMOTER COMMUNICATION AND THREE-DIMENSIONAL GENOME ORGANIZATION", "name": "TCPA-2017-01", "center_title": "TCPA - Adelman", "uuid": "619535d9-ec49-4f36-9cad-a0887cf535cb", "status": "current", "@type": ["Award", "Item"], "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["karen-adelman-lab:EpiLCdiff_RNAseq_00hr"], "accession": "4DNESOTEDQUZ", "condition": "0 h", "description": "Total RNA-seq time course of EpiLC differentiation in F121-9 mESCs, 0hr time point", "date_created": "2021-01-22T00:35:29.945269+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "RNA-seq time course of EpiLC differentiation", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-08-07T22:46:36.015762+00:00"}, "public_release": "2023-06-28", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "9cff2e09-97b3-4bc7-9e3d-ae4943f1a443", "@id": "/experiments-seq/4DNEXA7YBEEP/", "display_title": "RNA-seq on F121-9-CASTx129 (Tier 2) - 4DNEXA7YBEEP", "accession": "4DNEXA7YBEEP", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "8813e3aa-b7a2-4bf9-8abe-e360b5a63fba", "@id": "/experiments-seq/4DNEX6HFLD9Z/", "display_title": "RNA-seq on F121-9-CASTx129 (Tier 2) - 4DNEX6HFLD9Z", "accession": "4DNEX6HFLD9Z", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"title": "4DNESOTEDQUZ - Processed files", "@type": ["HiglassViewConfig", "UserContent", "Item"], "lab": {"@id": "/labs/karen-adelman-lab/", "uuid": "0aae4b45-b6de-45da-84e6-738667c36f03", "status": "current", "@type": ["Lab", "Item"], "display_title": "Karen Adelman, HARVARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0aae4b45-b6de-45da-84e6-738667c36f03"]}}, "uuid": "c99c89ae-dca7-4a9c-8a01-58e5dc6f7c09", "description": "4DNESOTEDQUZ (Total RNA-seq time course of EpiLC differentiation in F121-9 mESCs, 0hr time point): 4DNFIE5QF1UL, 4DNFI3SNVNE4, 4DNFIRARQ3ZW, 4DNFI7FG5O1N", "filetype": "HiglassViewConfig", "contributing_labs": [{"uuid": "88ba2aa9-321a-43a5-af1e-75fca4236907", "status": "current", "@type": ["Lab", "Item"], "display_title": "Joanna Wysocka, STANFORD", "@id": "/labs/joanna-wysocka-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.88ba2aa9-321a-43a5-af1e-75fca4236907"]}}], "status": "released", "display_title": "4DNESOTEDQUZ - Processed files", "@id": "/higlass-view-configs/c99c89ae-dca7-4a9c-8a01-58e5dc6f7c09/", "name": "c99c89ae-dca7-4a9c-8a01-58e5dc6f7c09", "award": {"status": "current", "uuid": "619535d9-ec49-4f36-9cad-a0887cf535cb", "display_title": "ELUCIDATING THE ROLE OF NASCENT RNA IN ENHANCER-PROMOTER COMMUNICATION AND THREE-DIMENSIONAL GENOME ORGANIZATION", "@type": ["Award", "Item"], "@id": "/awards/TCPA-2017-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "project_release": "2023-06-28", "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "d3lzb2NrYUBzdGFuZm9yZC5lZHU=", "@id": "/users/1cc9469d-ff0c-4ef0-b0c7-5ed4d0966a13/", "display_title": "Joanna Wysocka"}], "@id": "/labs/joanna-wysocka-lab/", "display_title": "Joanna Wysocka, STANFORD", "uuid": "88ba2aa9-321a-43a5-af1e-75fca4236907", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.88ba2aa9-321a-43a5-af1e-75fca4236907"]}, "pi": {"error": "no view permissions"}}], "experiments_in_set": [{"display_title": "RNA-seq on F121-9-CASTx129 (Tier 2) - 4DNEXA7YBEEP", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "9cff2e09-97b3-4bc7-9e3d-ae4943f1a443", "accession": "4DNEXA7YBEEP", "files": [{"uuid": 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