{"lab": {"uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "display_title": "Benoit Bruneau, UCSF", "title": "Benoit Bruneau, UCSF", "status": "current", "correspondence": [{"contact_email": "YmVub2l0LmJydW5lYXVAZ2xhZHN0b25lLnVjc2YuZWR1", "@id": "/users/c015dffd-4ca1-4070-905f-8a04b3754b2b/", "display_title": "Benoit Bruneau"}], "@id": "/labs/benoit-bruneau-lab/", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "description": "RT-CDF: A major unanswered question is how chromatin topology coordinates human development and cellular differentiation, and how genome folding is differentially regulated in human disease. It is thought that three- dimensional (3D) chromatin organization is driven by transcriptional regulators, but fundamental mechanisms of this regulation as it relates to disease-relevant human cells have not been well explored. We propose to elucidate the temporally dynamic 3D nucleome (4DN) that underlies human cardiac differentiation, its molecular underpinnings, and the impact of mutations that underly defective 4DN organization in human congenital heart disease (CHD). CHDs are the most common birth defect and arise from abnormal heart development. The genetic basis of CHD is largely mutations in genes encoding chromatin modifiers (e.g. WDR5, KMT2D) and transcription factors (TFs, e.g. TBX5, GATA4), many of which also cause adult-onset arrhythmias. The impact of CHD mutations on the 4DN has not been explored. We hypothesize that 3D genome folding is highly regulated during cardiac differentiation and is impacted by disease-causing mutations in transcriptional regulators and non-coding elements. We will use iPS cell models and machine learning to elucidate dynamic 3D chromatin organization in human cardiomyocytes and endothelial cells during normal and diseased cardiac differentiation. We propose 3 specific aims: Aim 1: Establish a kilobase-scale 4D map of genome folding in human cardiomyocytes (CM) and endothelial cell (EC) differentiation. We will use directed differentiation of human iPS cells towards the two major cell types of the developing heart: CMs and ECs, and using microC across a fine time course of differentiation we will define at kilobase scale the 3D organization of the genome, capturing the states of developmental intermediates and the final differentiated cells. This aim will generate an essential integrated 4DN template for discovery in cardiac differentiation. In Aim 2: we will Determine the regulatory and disease-related basis for cardiac 3D chromatin organization. We will perform microC in iPS cell lines with CHD-associated mutations in transcriptional regulators, differentiated into CMs and ECs. These findings will establish the degree to which CHD is caused by abnormal genome folding and chromatin states, with important relevance to other human cardiovascular diseases. Finally, Aim 3 will address High-throughput screening of millions of CHD and synthetic non- coding mutations with a deep-learning model of dynamic genome folding. We will build a deep-learning model predicting 3D chromatin contact frequencies across cardiac differentiation at kilobase-resolution. By introducing thousands of CHD patient deletions and other non-coding mutations in silico, we will prioritize variants likely to interact with transcriptional regulators to cause disease through disrupted genome folding. Several candidates will be validated in engineered iPS cells differentiated into CMs and ECs. 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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": {"status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "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. 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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": [{"genome_assembly": "GRCh38", "file_type": "contact list-combined", "file_type_detailed": "contact list-combined (pairs)", "upload_key": "5cb0f6a3-fcc1-4fa2-afb3-eeb5c09c9c1a/4DNFIGTUWJ8O.pairs.gz", "file_size": 16431136024, "display_title": "4DNFIGTUWJ8O.pairs.gz", "accession": "4DNFIGTUWJ8O", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5cb0f6a3-fcc1-4fa2-afb3-eeb5c09c9c1a/4DNFIGTUWJ8O.pairs.gz", "@id": "/files-processed/4DNFIGTUWJ8O/", "md5sum": "8b6c0e8f2da7d5578a81b1be2cbe38ae", "file_format": {"@id": "/file-formats/pairs/", "display_title": "pairs", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "5cb0f6a3-fcc1-4fa2-afb3-eeb5c09c9c1a", "href": "/files-processed/4DNFIGTUWJ8O/@@download/4DNFIGTUWJ8O.pairs.gz", "extra_files": [{"href": "/files-processed/4DNFIGTUWJ8O/@@download/4DNFIGTUWJ8O.pairs.gz.px2", "md5sum": "96c2f55a73ad0556ac98921831893839", "file_size": 13521492, "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "status": "released", "display_title": "pairs_px2", "file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"name": "katherine-pollard-lab", "status": "current", "uuid": "bae16ec7-6e90-48ec-ba27-fa4f6510489c", "display_title": "Katherine Pollard, UCSF", "@type": ["Lab", "Item"], "@id": "/labs/katherine-pollard-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.bae16ec7-6e90-48ec-ba27-fa4f6510489c"]}}, {"name": "benoit-bruneau-lab", "status": "current", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "display_title": "Benoit Bruneau, UCSF", "@type": ["Lab", "Item"], "@id": "/labs/benoit-bruneau-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "Total reads": 924025865, "uuid": "5f6c8d4b-192d-4877-b4d0-7e7cf7428b94", "status": "released", "display_title": "QualityMetricPairsqc from 2025-01-05", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGTUWJ8O/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/5f6c8d4b-192d-4877-b4d0-7e7cf7428b94/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "924025865", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "36.945", "tooltip": "Percent of filtered reads (=341.39m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "49.463", "tooltip": "Percent of filtered reads (=457.05m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "13.592", "tooltip": "Percent of filtered reads (=125.59m)", "numberType": "percent"}]}, "track_and_facet_info": {"dataset": "Hi-C on WTC-11 differentiated to cardiac muscle cell", "condition": "20 day differentiatiation to cardiac cells - 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Here, we  show dose-dependent regulation of chromatin organization by the congenital heart  disease (CHD)-linked, lineage-restricted TF TBX5 in human cardiomyocyte  differentiation. Genome organization, including compartments, topologically  associated domains, and chromatin loops, are sensitive to reduced TBX5 dosage in  a human model of CHD, with variations in response across individual cells.  Regions normally bound by TBX5 are especially sensitive, while co-occupancy with  CTCF partially protects TBX5-bound TAD boundaries and loop anchors. These results  highlight the importance of lineage-restricted TF dosage in cell-type specific 3D  chromatin dynamics, suggesting a new mechanism for TF-dependent disease.", "date_published": "2025-01-12", "title": "Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked  transcription factor.", "short_attribution": "Grant ZL et al. 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