{"lab": {"uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "@id": "/labs/sheng-zhong-lab/", "correspondence": [{"contact_email": "c3pob25nQHVjc2QuZWR1", "@id": "/users/5549e16d-fa63-477c-a1ed-6189cecc1304/", "display_title": "Sheng Zhong"}], "title": "Sheng Zhong, UCSD", "status": "current", "display_title": "Sheng Zhong, UCSD", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "award": {"@type": ["Award", "Item"], "center_title": "OH - Zhong", "uuid": "1a4da807-8221-47d2-96ab-7a31485974c3", "display_title": "THE SECOND PHASE OF NIH COMMON FUND 4D NUCLEOME NETWORK ORGANIZATIONAL HUB", "description": "OH: The second phase of the 4DN program requires an efficient organizational center to synergize the activities of all the funded teams and integrate the research products. 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(4) 4DN annual meetings, including the \"\"kick-off\"\" meeting in winter 2020 and the subsequent annual meetings and 4DN-ASCB (American Society of Cell Biology) satellite meetings; (5) 4DN outreach workshops at Keystone symposia and American Society of Human Genetics (ASHG) meetings, and on 4DN YouTube channel.", "name": "2U01CA200147-06", "project": "4DN", "@id": "/awards/2U01CA200147-06/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["sheng-zhong-lab:iMARGI-on-h1-control"], "accession": "4DNESNOJ7HY7", "condition": "No treatment control", "description": "iMARGI on human embryonic stem cells (H1) - Control", "date_created": "2021-07-01T17:48:37.980922+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "iMARGI on H1 cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-12-17T00:46:37.222714+00:00"}, "public_release": "2021-07-27", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEXD9E1MAB", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "81c90bb4-be64-4340-abca-324823a2a1a8", "display_title": "MARGI on H1-hESC (Tier 1) - 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It is a method analogous to the measurement of DNA-DNA interactions  by Hi-C experiments. MARGI was first published in 2017, and since then, the protocol has been rapidly improved. MARGI 2.0 is the latest version that introduced RNA-DNA proximity ligation *in situ* inside intact nuclei instead of in solution in order to reduce the rate of random ligation. In addition, this version also reduces the necessary amount of cell input 100-fold and shortens experimental processing time.\n\nThe protocol involves crosslinking the cells with formaldehyde to form links between physically adjacent RNA-DNA molecules. The intact nuclei are collected from fixed cells and permeabilized with SDS. A restriction enzyme (AluI) is used to digest chromatin into DNA fragments and RNase I is used to fragment RNA. A specially designed biotinylated linker is introduced to ligate to 3\u00b4-end of RNA first and then this RNA-ligated linker is ligated to DNA. These ligation steps are controlled by the configuration of the linker and by sequential applications of different end modifications and ligation enzymes. Nuclei are lysed, and successfully ligated products, in the form of RNA-linker-DNA, are selected with streptavidin beads, followed by converting the RNA part of the chimera into cDNA on beads. cDNA-linker-DNA is circularized and then cut in the middle, producing DNAs with the configuration left.half.Linker-RNA-DNA-right.half.Linker, which are subjected to library amplification and paired-end sequencing.\n\n<div> \n<img style=\"width:400px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/MARGI2.png\" />\n    <br/><br/>\n    <em> Image Source: Weixin Wu, Xingzhao Wen, Sheng Zhong, private communication </em>\n</div>                                                                                                              \n", "name": "item-page-headers.ExperimentType.margi", "award": {"@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:4dn-dcic-lab:4dn-dcic-lab:experiment_infobox_margi"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-09-20T19:17:26.139621+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-15T16:58:04.692266+00:00"}, "schema_version": "2", "@id": "/static-sections/0c2ba23e-b256-47ce-a37c-0f1282471789/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "0c2ba23e-b256-47ce-a37c-0f1282471789", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**MARGI**\n\nMARGI is a method to map native RNA-DNA interactions from unperturbed cells at a global scale. It is a method analogous to the measurement of DNA-DNA interactions  by Hi-C experiments. MARGI was first published in 2017, and since then, the protocol has been rapidly improved. MARGI 2.0 is the latest version that introduced RNA-DNA proximity ligation *in situ* inside intact nuclei instead of in solution in order to reduce the rate of random ligation. In addition, this version also reduces the necessary amount of cell input 100-fold and shortens experimental processing time.\n\nThe protocol involves crosslinking the cells with formaldehyde to form links between physically adjacent RNA-DNA molecules. The intact nuclei are collected from fixed cells and permeabilized with SDS. A restriction enzyme (AluI) is used to digest chromatin into DNA fragments and RNase I is used to fragment RNA. A specially designed biotinylated linker is introduced to ligate to 3\u00b4-end of RNA first and then this RNA-ligated linker is ligated to DNA. These ligation steps are controlled by the configuration of the linker and by sequential applications of different end modifications and ligation enzymes. Nuclei are lysed, and successfully ligated products, in the form of RNA-linker-DNA, are selected with streptavidin beads, followed by converting the RNA part of the chimera into cDNA on beads. cDNA-linker-DNA is circularized and then cut in the middle, producing DNAs with the configuration left.half.Linker-RNA-DNA-right.half.Linker, which are subjected to library amplification and paired-end sequencing.\n\n<div> \n<img style=\"width:400px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/MARGI2.png\" />\n    <br/><br/>\n    <em> Image Source: Weixin Wu, Xingzhao Wen, Sheng Zhong, private communication </em>\n</div>                                                                                                              \n", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>MARGI</strong></p>\n<p>MARGI is a method to map native RNA-DNA interactions from unperturbed cells at a global scale. It is a method analogous to the measurement of DNA-DNA interactions  by Hi-C experiments. MARGI was first published in 2017, and since then, the protocol has been rapidly improved. MARGI 2.0 is the latest version that introduced RNA-DNA proximity ligation <em>in situ</em> inside intact nuclei instead of in solution in order to reduce the rate of random ligation. In addition, this version also reduces the necessary amount of cell input 100-fold and shortens experimental processing time.</p>\n<p>The protocol involves crosslinking the cells with formaldehyde to form links between physically adjacent RNA-DNA molecules. The intact nuclei are collected from fixed cells and permeabilized with SDS. A restriction enzyme (AluI) is used to digest chromatin into DNA fragments and RNase I is used to fragment RNA. A specially designed biotinylated linker is introduced to ligate to 3\u00b4-end of RNA first and then this RNA-ligated linker is ligated to DNA. These ligation steps are controlled by the configuration of the linker and by sequential applications of different end modifications and ligation enzymes. Nuclei are lysed, and successfully ligated products, in the form of RNA-linker-DNA, are selected with streptavidin beads, followed by converting the RNA part of the chimera into cDNA on beads. cDNA-linker-DNA is circularized and then cut in the middle, producing DNAs with the configuration left.half.Linker-RNA-DNA-right.half.Linker, which are subjected to library amplification and paired-end sequencing.</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/MARGI2.png\" style=\"width:400px;\"/>\n<br/><br/>\n<em> Image Source: Weixin Wu, Xingzhao Wen, Sheng Zhong, private communication </em>\n</div>\n<pre>\n</pre></div>"}], "processed_files": [{"display_title": "4DNFIGDJIRV3.pairs.gz", "file_type": "contact list-combined", "status": "released", "href": "/files-processed/4DNFIGDJIRV3/@@download/4DNFIGDJIRV3.pairs.gz", "@id": "/files-processed/4DNFIGDJIRV3/", "accession": "4DNFIGDJIRV3", "genome_assembly": "GRCh38", "file_classification": "processed file", "uuid": "db03c6f6-102c-40fe-9a14-36ee53d97e8f", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type_detailed": "contact list-combined (pairs)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/db03c6f6-102c-40fe-9a14-36ee53d97e8f/4DNFIGDJIRV3.pairs.gz", "md5sum": "f5d1f95a763065592987fc123981bd01", "@type": ["FileProcessed", "File", "Item"], "upload_key": "db03c6f6-102c-40fe-9a14-36ee53d97e8f/4DNFIGDJIRV3.pairs.gz", "file_size": 8838447632, "extra_files": [{"md5sum": "1dfa8aab4a8c61964c380cfd836dc467", "href": "/files-processed/4DNFIGDJIRV3/@@download/4DNFIGDJIRV3.pairs.gz.px2", "file_size": 17260925, "file_format": {"display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "pairs_px2", "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"status": "released", "display_title": "QualityMetricMargi from 2021-07-26", "@type": ["QualityMetricMargi", "QualityMetric", "Item"], "@id": "/quality-metrics-margi/bad7fc84-7275-4e46-b1a3-1a9b35b6f761/", "overall_quality_status": "PASS", "uuid": "bad7fc84-7275-4e46-b1a3-1a9b35b6f761", "quality_metric_summary": [{"title": "Filtered Reads", "value": "285576525", "numberType": "integer"}, {"title": "Cis reads (>200000)", "value": "12.286", "tooltip": "Percent of total interactions (=35.09m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "28.744", "tooltip": "Percent of total interactions (=82.09m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "58.97", "tooltip": "Percent of total interactions (=168.4m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "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"]}}, "track_and_facet_info": {"dataset": "iMARGI on H1 cells", "condition": "No treatment control", "experimental_lab": "Sheng Zhong, UCSD", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "MARGI", "assay_info": "AluI", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-07-27T19:52:23.022994+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIKWK6NSD.mcool", "file_type": "contact matrix", "status": "released", "higlass_uid": "b6c53f63-2b12-478e-9f7e-eb5b8ab93ae0", "href": "/files-processed/4DNFIKWK6NSD/@@download/4DNFIKWK6NSD.mcool", "@id": "/files-processed/4DNFIKWK6NSD/", "accession": "4DNFIKWK6NSD", "genome_assembly": "GRCh38", "file_classification": "processed file", "uuid": "180fc3bd-e704-45e1-ab0d-e1410f4251a1", "file_format": {"@id": "/file-formats/mcool/", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type_detailed": "contact matrix (mcool)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/180fc3bd-e704-45e1-ab0d-e1410f4251a1/4DNFIKWK6NSD.mcool", "md5sum": "16ef2fdad5e114184c29c4ff49ba20a0", "@type": ["FileProcessed", "File", "Item"], "upload_key": "180fc3bd-e704-45e1-ab0d-e1410f4251a1/4DNFIKWK6NSD.mcool", "file_size": 2344204612, "notes_to_tsv": ["WARNING - 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Conversely, stopping transcription or acute  depletion of RNA induces thousands of chromatin loops genome-wide. Activation or  suppression of the transcription of specific genes suppresses or creates  chromatin loops straddling these genes. Deletion of a specific caRNA-producing  genomic sequence promotes chromatin loops that straddle the interchromosomal  target sequences of this caRNA. 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It remains unclear whether the genome  architecture modulates the spatial distribution of caRNA and vice versa. Here, we  generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human  cells. These maps reveal the chromosomal domains demarcated by locally  transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the  spreading of caRNA is constrained by the boundaries of topologically associating  domains (TADs), demonstrating the role of the 3D genome structure in modulating  the spatial distribution of RNA. Conversely, stopping transcription or acute  depletion of RNA induces thousands of chromatin loops genome-wide. Activation or  suppression of the transcription of specific genes suppresses or creates  chromatin loops straddling these genes. Deletion of a specific caRNA-producing  genomic sequence promotes chromatin loops that straddle the interchromosomal  target sequences of this caRNA. These data suggest a feedback loop where the 3D  genome modulates the spatial distribution of RNA, which in turn affects the  dynamic 3D genome organization.", "date_published": "2023-10-16", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "display_title": "Calandrelli R et al. 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