{"lab": {"status": "current", "uuid": "5cd252dd-e5b6-4f0f-8cab-99ef2bcac5a4", "correspondence": [{"contact_email": "amVkaXhvbkBzYWxrLmVkdQ==", "@id": "/users/1a8c9001-7ea5-480a-91f0-e8b030a0e7c6/", "display_title": "Jesse Dixon"}], "@type": ["Lab", "Item"], "display_title": "Jesse Dixon, SALK", "@id": "/labs/jesse-dixon-lab/", "title": "Jesse Dixon, SALK", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5cd252dd-e5b6-4f0f-8cab-99ef2bcac5a4"]}}, "award": {"name": "1U01CA260700-01", "status": "current", "@id": "/awards/1U01CA260700-01/", "display_title": "INVESTIGATING THE EFFECTS OF STRUCTURAL VARIANTS ON 3D GENOME ORGANIZATION AND GENE REGULATION IN CANCER GENOMES", "description": "OFHHD: Three-dimensional genome organization has emerged as a critical component for the proper regulation of gene expression. Recent years have seen a rapid expansion of the understanding of many of the basic features that define how genomes are organized in space inside of cells, including the identification of features such as A/B compartments, Topologically Associated Domains, and chromatin loops. Furthermore, there is evidence that mutations that alter 3D genome organization can contribute to human disease. This is most evident for a class of mutations known as structural variants, which includes translocations, inversions, tandem duplications, and deletions. When these mutations disrupt sequence features that are critical for 3D genome structure, such as the boundaries between Topologically Associating Domains, this can lead to enhancer-promoter rewiring, changes in gene expression, and phenotypic consequences. Such effects have been observed both in the context of germline structural variants that contribute to syndromic disorders of development as well as somatic structural variants that can lead to cancer. While it has become clear that structural variants can alter 3D genome organization and gene expression, more recent studies that comprehensively examined structural variants and gene expression indicate their relationship is considerably more complex. Specifically, in only a minority of instances do structural variants lead to changes in expression of neighboring genes. Therefore, why structural variants can have dramatic consequences on 3D genome structure and gene expression in some contexts but not others is currently unclear. This proposal will investigate the relationship between structural variants, 3D genome organization, and gene expression in cancer genomes with the goal of understanding where and when structural variants will actually lead to changes in gene expression that may contribute to oncogenesis. Specific aim 1 will test whether only specific sets genes are sensitive to structural variant induced changes in enhancer-promoter communication by examining changes in 3D genome structure and gene expression in haplotype resolved human tumor samples. Specific aim 2 will use CRISPR/Cas9 genome engineering to evaluate the effects of structural variant partner regions on induction of oncogene expression. Specific aim 3 will assess the role of intra-tumor heterogeneity on the effects of structural variants on 3D genome structure by using novel multi-omic methods for profiling DNA methylation and 3D genome structure simultaneously within single cells derived from patient tumor samples. Successful completion of these aims will result in a deeper understanding of the relationship between structural variation, 3D genome organization, and gene regulation in the context of cancer genomes. In the long term, this will facilitate the use of information derived from structural variants and 3D genome structure on determining patient prognosis and on identifying novel therapeutic targets in cancer.", "project": "4DN", "center_title": "OFHHD - Dixon", "uuid": "0247d660-dc33-4a2e-84a7-eb1ac2cbbaca", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Foxp3 in Treg cell development", "status": "released", "aliases": ["jesse-dixon-lab:expset_hic_TReg_Ctrl_sgRNA"], "accession": "4DNES4ZVGG33", "condition": "Treg - Crispr control", "description": "Hi-C on Treg cells with CRISPR control - genotype CD45+CD4+CD8-CD25+Foxp3-Thy1.1+", "study_group": "Disrupted or Atypical Cells", "date_created": "2023-05-02T21:14:04.858865+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_group": "Hi-C on Maturing Regulatory T-cells with Fox3p disruption", "dataset_label": "in situ Hi-C on maturing regulatory T cells (Treg)", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-08-01T06:46:23.749289+00:00"}, "public_release": "2023-10-04", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "ee211a4c-d3d5-49c5-8156-6d201be38ad4", "display_title": "in situ Hi-C on Treg - thymus - Foxp3-Thy1.1 WT with MboI - 4DNEX1ZOPLLG", "accession": "4DNEX1ZOPLLG", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEX1ZOPLLG/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "e1af7beb-f76a-4b46-bf1a-1e32957728c0", "display_title": "in situ Hi-C on Treg - thymus - Foxp3-Thy1.1 WT with MboI - 4DNEXJZUYSXF", "accession": "4DNEXJZUYSXF", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXJZUYSXF/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"status": "released", "lab": {"@type": ["Lab", "Item"], "uuid": "5cd252dd-e5b6-4f0f-8cab-99ef2bcac5a4", "display_title": "Jesse Dixon, SALK", "@id": "/labs/jesse-dixon-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5cd252dd-e5b6-4f0f-8cab-99ef2bcac5a4"]}}, "contributing_labs": [], "description": "4DNES4ZVGG33 (Hi-C on Treg cells with CRISPR control - genotype CD45+CD4+CD8-CD25+Foxp3-Thy1.1+): 4DNFI774Q3YL, 4DNFI7NZ718W, 4DNFID42SIRT, 4DNFICZSBZWK", "uuid": "e341ccd9-8478-46bb-830e-66a338e17042", "@type": ["HiglassViewConfig", "UserContent", "Item"], "award": {"status": "current", "@type": ["Award", "Item"], "display_title": "INVESTIGATING THE EFFECTS OF STRUCTURAL VARIANTS ON 3D GENOME ORGANIZATION AND GENE REGULATION IN CANCER GENOMES", "@id": "/awards/1U01CA260700-01/", "uuid": "0247d660-dc33-4a2e-84a7-eb1ac2cbbaca", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/higlass-view-configs/e341ccd9-8478-46bb-830e-66a338e17042/", "display_title": "4DNES4ZVGG33 - Processed files", "name": "e341ccd9-8478-46bb-830e-66a338e17042", "filetype": "HiglassViewConfig", "title": "4DNES4ZVGG33 - Processed files", "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": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "name": "item-page-headers.ExperimentType.insituhic", "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": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}], "processed_files": [{"file_type": "contact list-combined", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c6783097-d9bf-4f45-8d61-f9b8cdb27d9f/4DNFIF6UNRKQ.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "c6783097-d9bf-4f45-8d61-f9b8cdb27d9f/4DNFIF6UNRKQ.pairs.gz", "genome_assembly": "GRCm38", "href": "/files-processed/4DNFIF6UNRKQ/@@download/4DNFIF6UNRKQ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIF6UNRKQ", "display_title": "4DNFIF6UNRKQ.pairs.gz", "file_size": 4470079873, "file_type_detailed": "contact list-combined (pairs)", "md5sum": "fe0c272b1eabb5a38439252c876622af", "uuid": "c6783097-d9bf-4f45-8d61-f9b8cdb27d9f", "@id": "/files-processed/4DNFIF6UNRKQ/", "status": "released", "quality_metric": {"uuid": "c26ae40c-436a-4d4b-b812-a0cfff1d119c", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 232744696, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIF6UNRKQ/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/c26ae40c-436a-4d4b-b812-a0cfff1d119c/", "status": "released", "display_title": "QualityMetricPairsqc from 2023-07-08", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "232744696", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "65.389", "tooltip": "Percent of filtered reads (=152.19m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "17.394", "tooltip": "Percent of filtered reads (=40.48m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "17.217", "tooltip": "Percent of filtered reads (=40.07m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Jesse Dixon, SALK", "name": "jesse-dixon-lab", "@id": "/labs/jesse-dixon-lab/", "@type": ["Lab", "Item"], "uuid": "5cd252dd-e5b6-4f0f-8cab-99ef2bcac5a4", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5cd252dd-e5b6-4f0f-8cab-99ef2bcac5a4"]}}], "extra_files": [{"md5sum": "a7b02740dd2abd2542d267842890abe2", "file_size": 9246288, "href": "/files-processed/4DNFIF6UNRKQ/@@download/4DNFIF6UNRKQ.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "display_title": "pairs_px2", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-11-20T18:52:24.848248+00:00"}, "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on maturing regulatory T cells (Treg)", "condition": "Treg - 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This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  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Here, by  comprehensively mapping 3D chromatin organization during Treg cell  differentiation, we show that Treg-specific chromatin structures were  progressively established during its lineage specification, and highly associated  with Treg signature gene expression. Additionally, the binding sites of Foxp3, a  Treg lineage specifying transcription factor, were highly enriched at  Treg-specific chromatin loop anchors. Further comparison of the chromatin  interactions between wide-type Tregs versus Treg cells from Foxp3  knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that  Foxp3 was essential for the establishment of Treg-specific 3D chromatin  architecture, although it was not dependent on the formation of the Foxp3  domain-swapped dimer. 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Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation  of T cells specializing in suppressing excessive immune responses. Here, by  comprehensively mapping 3D chromatin organization during Treg cell  differentiation, we show that Treg-specific chromatin structures were  progressively established during its lineage specification, and highly associated  with Treg signature gene expression. Additionally, the binding sites of Foxp3, a  Treg lineage specifying transcription factor, were highly enriched at  Treg-specific chromatin loop anchors. Further comparison of the chromatin  interactions between wide-type Tregs versus Treg cells from Foxp3  knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that  Foxp3 was essential for the establishment of Treg-specific 3D chromatin  architecture, although it was not dependent on the formation of the Foxp3  domain-swapped dimer. 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