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A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. 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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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>\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n</p>\n<p>\nSee <a href=\"http://science.sciencemag.org/content/326/5950/289\" rel=\"noopener noreferrer\" target=\"_blank\">Lieberman-aiden et al., 2009</a> for more details on dilution Hi-C.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/dHiC.png\" style=\"width: 600px;\"/>\n<br/><br/>\n<em>Image source: Lieberman-aiden et al., 2009, Figure 1A</em>\n</div></div>"}], "processed_files": [{"file_type_detailed": "contact list-combined (pairs)", "display_title": "4DNFIQJLTRNZ.pairs.gz", "file_size": 14400151050, "accession": "4DNFIQJLTRNZ", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIQJLTRNZ/", "upload_key": "27649613-6f97-4774-a72d-bf78bdb231b6/4DNFIQJLTRNZ.pairs.gz", "status": "released", "file_type": "contact list-combined", "file_classification": "processed file", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/27649613-6f97-4774-a72d-bf78bdb231b6/4DNFIQJLTRNZ.pairs.gz", "href": "/files-processed/4DNFIQJLTRNZ/@@download/4DNFIQJLTRNZ.pairs.gz", "md5sum": "3713ec7d71ce7fec8be9ca3b0bc48f0a", "uuid": "27649613-6f97-4774-a72d-bf78bdb231b6", "quality_metric": {"display_title": "QualityMetricPairsqc from 2018-04-26", "overall_quality_status": "PASS", "Total reads": 760116700, "uuid": "ab80d99c-abad-4897-a036-d5d0ba529a5c", "status": "released", "@id": "/quality-metrics-pairsqc/ab80d99c-abad-4897-a036-d5d0ba529a5c/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQJLTRNZ/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Filtered Reads", "value": "760116700", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "36.851", "tooltip": "Percent of filtered reads (=280.11m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.082", "tooltip": "Percent of filtered reads (=152.65m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "43.066", "tooltip": "Percent of filtered reads (=327.36m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "extra_files": [{"md5sum": "61b6cea60c6b0343c379f74a5f20551f", "file_size": 27833925, "href": "/files-processed/4DNFIQJLTRNZ/@@download/4DNFIQJLTRNZ.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "last_modified": {"date_modified": "2022-01-10T14:35:24.634962+00:00"}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "name": "job-dekker-lab", "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HFF cells - 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