{"lab": {"status": "current", "correspondence": [{"contact_email": "YnJhZGxleS5jYWlybnNAaGNpLnV0YWguZWR1", "@id": "/users/ae9eb991-9a16-4212-8328-74517cd5f26a/", "display_title": "Bradley Cairns"}], "@id": "/labs/brad-cairns-lab/", "@type": ["Lab", "Item"], "title": "Brad Cairns, UTAH", "display_title": "Brad Cairns, UTAH", "uuid": "79c8ecad-9cf2-4bce-a9f8-92b3fa6dbcbf", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.79c8ecad-9cf2-4bce-a9f8-92b3fa6dbcbf"]}}, "award": {"@type": ["Award", "Item"], "center_title": "TCPA - Cairns", "project": "4DN", "description": "TCPA: Three-dimensional (3D) genome organization is important for proper gene regulation, and impacts development and disease. Topological Associating Domains (TADs) comprise the basic unit of organization within the genome, with sharp boundaries characterized by highly transcribed housekeeping genes, short interspersed nuclear elements (SINE) or sites for the DNA-binding protein CCCTC-binding factor (CTCF) \nwhich interacts with Cohesin. This proposal addresses several major unanswered questions and explores new opportunities in the field, including: i) When does 3D genome architecture (TADs and their boundaries) begin to form during early vertebrate embryogenesis? ii) Is genome-wide transcriptional activation in the developing embryo required for the establishment of TADs? iii) How dynamic are individual TADs at the single cell level and what is their effect on gene expression and nuclear architecture? Importantly, our combination of genomics with super-resolution imaging bridges and connects two major disciplines in the 4D Nucleome community. \nOur central goal is to determine when and how higher-order 3D chromatin architecture is first established in early embryos, how is it remodeled during developmental reprograming and what is their impact on transcription. This proposal is significant for several reasons. First, from a standpoint of nuclear architecture, it addresses how TADs are formed over time and what is their effect on genome \nactivation and nuclear architecture. Second, it addresses how positional information in the nucleus plays a role in the fundamental step of transcription in vivo. Third, within the context of the 4D Nucleome initiative and a technological standpoint, the zebrafish embryo is a powerful system for probing different technologies that \nthat can be further applied across the 4D Nucleome initiatives directly relevant to ES cells, mouse embryos and differentiated tissues to understand how nuclear architecture is established in vivo. From a developmental biology and fertility standpoint, we address fundamental mechanisms of initiation of gene expression after fertilization - a universal transition across animals. \nIn our proposal, we provide preliminary evidence supporting the following hypothesis: TADs and their boundary elements are fully established only after the onset of genome-wide transcriptional activation, to refine embryonic transcription. The experiments described below will define the true relationship of TADs \nto transcription, illuminating the fundamental mechanisms responsible for assembling the 4D nuclear architecture during embryogenesis when cells become totipotent. Together, our laboratories will combine advanced genomics techniques (Hi-C, PLAC-seq, others), super-resolution/EM microscopy methods and innovative genetic and molecular approaches in zebrafish embryos, toward addressing these questions.", "display_title": "ESTABLISHING THE 3D CHROMATIN ARCHITECTURAL ORGANIZATION OF THE ZEBRAFISH EMBRYONIC GENOME", "status": "current", "uuid": "a7668120-3722-4ce9-95ac-8dc05b67fe36", "@id": "/awards/TCPA-2017-02/", "name": "TCPA-2017-02", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Hi-C on Zebrafish embryos", "status": "released", "aliases": ["brad-cairns-lab:sperm_Zebrafish"], "accession": "4DNES4G1HPQC", "condition": "pre-fertilization (sperm)", "description": "HiC on WT ZF sperm", "study_group": "Time Course", "date_created": "2020-06-18T14:33:41.417041+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on Zebrafish embryos", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-31T14:46:13.266439+00:00"}, "public_release": "2021-04-05", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "91f14f6e-b51e-483a-8489-58e5281eb9f1", "@id": "/experiments-hi-c/4DNEXXRD6JTM/", "accession": "4DNEXXRD6JTM", "display_title": "in situ Hi-C on Zebrafish Embryo with MboI - 4DNEXXRD6JTM", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "376c21f6-d037-42ab-947d-02ff84fc53a9", "@id": "/experiments-hi-c/4DNEXKNKUZZ4/", "accession": "4DNEXKNKUZZ4", "display_title": "in situ Hi-C on Zebrafish Embryo with MboI - 4DNEXKNKUZZ4", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"uuid": "a7668120-3722-4ce9-95ac-8dc05b67fe36", "@id": "/awards/TCPA-2017-02/", "status": "current", "@type": ["Award", "Item"], "display_title": "ESTABLISHING THE 3D CHROMATIN ARCHITECTURAL ORGANIZATION OF THE ZEBRAFISH EMBRYONIC GENOME", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "eac63841-46df-4852-9704-3a37798d0eeb", "title": "4DNES4G1HPQC - Processed files", "contributing_labs": [], "name": "eac63841-46df-4852-9704-3a37798d0eeb", "@id": "/higlass-view-configs/eac63841-46df-4852-9704-3a37798d0eeb/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNES4G1HPQC - Processed files", "description": "4DNES4G1HPQC (HiC on WT ZF sperm): 4DNFITHB7HKC, 4DNFIK36LY3B, 4DNFIPG6ZIGU, 4DNFIPYCL2PF", "filetype": "HiglassViewConfig", "lab": {"status": "current", "uuid": "79c8ecad-9cf2-4bce-a9f8-92b3fa6dbcbf", "display_title": "Brad Cairns, UTAH", "@type": ["Lab", "Item"], "@id": "/labs/brad-cairns-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.79c8ecad-9cf2-4bce-a9f8-92b3fa6dbcbf"]}}, "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": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "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": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "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": [{"accession": "4DNFIFFBCFKN", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCz11", "file_type_detailed": "contact list-combined (pairs)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, 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"tooltip": "Percent of filtered reads (=44.51m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Brad Cairns, UTAH", "uuid": "79c8ecad-9cf2-4bce-a9f8-92b3fa6dbcbf", "name": "brad-cairns-lab", "@type": ["Lab", "Item"], "@id": "/labs/brad-cairns-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.79c8ecad-9cf2-4bce-a9f8-92b3fa6dbcbf"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on Zebrafish embryos", "condition": "pre-fertilization 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["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFITHB7HKC.mcool", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  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.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "md5sum": "738894cf5340ba0a1bdf537bfb6602ec", "file_type": "contact matrix", "file_classification": "processed file", "file_size": 924845470, "upload_key": "0c53b025-21ef-48fe-9212-6e283b39d1dc/4DNFITHB7HKC.mcool", "@id": "/files-processed/4DNFITHB7HKC/", "href": "/files-processed/4DNFITHB7HKC/@@download/4DNFITHB7HKC.mcool", "uuid": "0c53b025-21ef-48fe-9212-6e283b39d1dc", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0c53b025-21ef-48fe-9212-6e283b39d1dc/4DNFITHB7HKC.mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"status": "released", "display_title": "QualityMetricMcool from 2021-05-21", "uuid": "a695f99b-a6c6-4ec3-b89c-998e5126a7a9", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "@id": 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The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated  domains and instead displays \"hinge-like\" domains of approximately 150 kb that repeat every 1-2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of approximately 90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. Together, this study reveals hinge-like domains in histone-packaged zebrafish sperm chromatin and determines that the initial formation of high-order chromatin architecture in zebrafish embryos occurs after ZGA primarily at enhancers bearing high H3K27ac.", "date_published": "2021-06", "uuid": "75fc85cf-66ba-4d08-b50e-e7122482810c", "status": "current", "display_title": "Wike CL et al. 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First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated  domains and instead displays \"hinge-like\" domains of approximately 150 kb that repeat every 1-2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of approximately 90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. 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