{"lab": {"@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "display_title": "Siyuan Wang, YALE", "title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "correspondence": [{"contact_email": "c2l5dWFuLndhbmdAeWFsZS5lZHU=", "@id": "/users/774c29b8-db1e-48bc-9669-a3e380f435c2/", "display_title": "Siyuan Wang"}], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"name": "1U01CA260701-01", "@type": ["Award", "Item"], "@id": "/awards/1U01CA260701-01/", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "status": "current", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "project": "4DN", "center_title": "OFHHD - Schatz", "description": "OFHHD: During the humoral immune response, somatic hypermutation (SHM) introduces point mutations in rearranged immunoglobulin (Ig) genes of activated germinal center (GC) B cells. SHM is essential for the fine-tuning of antibody affinity, the generation of B cells expressing high-affinity antibody, and the efficacy of many vaccines. Mistargeted SHM activities can lead to mutations and chromosomal translocations that contribute to the development of B cell lymphoma. Recent studies suggest that the three-dimensional (3D) organization of the genome regulates SHM targeting and mistargeting. However, it is largely unknown how the genome is spatially organized across multiple length scales in GC B cell development and lymphoma, and how 3D genome architecture mechanistically affects the targeting and mistargeting of SHM. Conventional approaches cannot address these questions in the primary GC tissue environment due to technical limitations. Here, we propose to apply a new method recently developed by our team, termed Multiplexed Imaging of Nucleome Architectures (MINA), to primary human tonsil tissue samples and malignant GC-derived human B cell lymphomas. We will investigate and test the association between SHM susceptibility and a variety of 3D nucleome architectures, including topologically associating domain (TAD) architecture, phase separation, and nuclear positioning of genomic regions relative to nuclear lamina, nucleoli, and nuclear pores. Through targeted genomic perturbations in human B cell lymphomas, we will test specific hypotheses linking SHM targeting elements to elevated chromatin looping interactions, TAD phase separation, nuclear pore proximity, and mutation vulnerability. Our study will significantly advance our understanding of the role of 3D genome architecture and nuclear organization in GC B cells undergoing SHM in both the developmental and tumorigenesis contexts. We expect this study to establish a new research paradigm and transform 3D nucleome investigations in immunobiology.", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"warning": "Replicate Numbers", "@type": ["Badge", "Item"], "badge_classification": "Warning", "description": "Issues with replicate numbers", "status": "released", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "display_title": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "@id": "/badges/replicate-numbers/", "title": "Replicate Numbers", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["siyuan-wang-lab:expset_A549-Cas9_pooled"], "accession": "4DNES7J5VP92", "condition": "137 genes knocked-down (using 404 sgRNAs and 8 sgNTC)", "description": "Multiplexed FISH of chromosome 22 in A549-Cas9 cancer cells from 17 coverslips, where each coverslip is imaging of the pooled CRISPR screen cells where cells are transduced with sgRNA targeting and knockdown specific genes or sgNTC, non-targeting control. The Crispr screen includes a total of 137 gene targeted by 404 sgRNAs and 8 sgNTC used as controls. The knocked out gene and NTC corresponding to a trace can be found in the associated fof-ct processed files.", "date_created": "2025-03-28T13:38:13.773398+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Multiplexed FISH in A549-Cas9 on Chr22", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-04-21T17:31:30.144892+00:00"}, "public_release": "2025-04-08", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "ef96ddad-5e32-4edc-8a00-b9d9dc92d733", "status": "released", "accession": "4DNEXB98WM6D", "display_title": "multiplexed FISH on A549 - 4DNEXB98WM6D", "@id": "/experiments-mic/4DNEXB98WM6D/", "@type": ["ExperimentMic", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "name": "fof-ct.note", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on FOF-CT file format", "status": "released", "aliases": ["4dn-dcic-lab:fof_ct_note"], "options": {"filetype": "md", "collapsible": true, "default_open": false}, "date_created": "2022-03-07T18:23:27.469177+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-03-08T14:28:37.893086+00:00"}, "schema_version": "2", "@id": "/static-sections/a09a2833-b56b-4e81-8eff-bb8ae6aaa596/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a09a2833-b56b-4e81-8eff-bb8ae6aaa596", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on FOF-CT file format", "external_references": [], "content": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).</p>\n<p>This is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. </p>\n<p>The full documentation is available here: https://fish-omics-format.readthedocs.io/</p></div>"}], "project_release": "2025-04-08", "experiments_in_set": [{"accession": "4DNEXB98WM6D", "uuid": "ef96ddad-5e32-4edc-8a00-b9d9dc92d733", "display_title": "multiplexed FISH on A549 - 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4DNSRFLY6T15", "@id": "/biosources/4DNSRFLY6T15/", "cell_line": {"preferred_name": "A549", "status": "released", "term_name": "A549", "display_title": "A549", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0001086/", "uuid": "2fea36d1-69bd-4039-8c58-a5d9bf6bcdad", "synonyms": ["A-549", "A549 cell"], "term_id": "EFO:0001086", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111121bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000925/", "display_title": "endoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "status": "released", "@id": "/organisms/9606/", "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["pulmo"], "uuid": "111186bc-8535-4448-903e-854af460a233", "display_title": "lung", "preferred_name": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0002048", "@id": "/ontology-terms/UBERON:0002048/", "status": "released", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0002048/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["respiratory system", "lung", "endoderm"], "tissue_source": "lung"}}, "processed_files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/65cd0d29-cfac-41e6-b911-dd88af574c0f/4DNFI7XUQN2H.csv", "md5sum": "b037b94aa7a6fdacde4af34ddbbcb4f2", "href": "/files-processed/4DNFI7XUQN2H/@@download/4DNFI7XUQN2H.csv", "genome_assembly": "GRCh38", "uuid": "65cd0d29-cfac-41e6-b911-dd88af574c0f", "display_title": "4DNFI7XUQN2H.csv", "@id": "/files-processed/4DNFI7XUQN2H/", "file_format": {"display_title": "csv", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 876749, "file_type": "FOF-CT - 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(2023)", "url": "https://www.ncbi.nlm.nih.gov/pubmed/36778402", "uuid": "c4d07d85-7bc4-43d4-bc30-ee8b34c1ea8d", "abstract": "Three-dimensional (3D) genome organization becomes altered during development,  aging, and disease(1-23), but the factors regulating chromatin topology are  incompletely understood and currently no technology can efficiently screen for  new regulators of multiscale chromatin organization. Here, we developed an  image-based high-content screening platform (Perturb-tracing) that combines  pooled CRISPR screen, a new cellular barcode readout method (BARC-FISH), and  chromatin tracing. We performed a loss-of-function screen in human cells, and  visualized alterations to their genome organization from 13,000 imaging  target-perturbation combinations, alongside perturbation-paired barcode readout  in the same single cells. Using 1.4 million 3D positions along chromosome traces,  we discovered tens of new regulators of chromatin folding at different length  scales, ranging from chromatin domains and compartments to chromosome territory.  A subset of the regulators exhibited 3D genome effects associated with  loop-extrusion and A-B compartmentalization mechanisms, while others were largely  unrelated to these known 3D genome mechanisms. We found that the ATP-dependent  helicase CHD7, the loss of which causes the congenital neural crest syndrome  CHARGE(24) and a chromatin remodeler previously shown to promote local chromatin  openness(25-27), counter-intuitively compacts chromatin over long range in  different genomic contexts and cell backgrounds including neural crest cells, and  globally represses gene expression. The DNA compaction effect of CHD7 is  independent of its chromatin remodeling activity and does not require other  protein partners. Finally, we identified new regulators of nuclear architectures  and found a functional link between chromatin compaction and nuclear shape.  Altogether, our method enables scalable, high-content identification of chromatin  and nuclear topology regulators that will stimulate new insights into the 3D  genome functions, such as global gene and nuclear regulation, in health and  disease.", "display_title": "Cheng Y et al. (2023) PMID:36778402", "journal": "bioRxiv : the preprint server for biology", "date_published": "2023-11-05", "@type": ["Publication", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"uuid": "c4d07d85-7bc4-43d4-bc30-ee8b34c1ea8d", "ID": "PMID:36778402", "date_published": "2023-11-05", "@type": ["Publication", "Item"], "display_title": "Cheng Y et al. 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Using 1.4 million 3D positions along chromosome traces,  we discovered tens of new regulators of chromatin folding at different length  scales, ranging from chromatin domains and compartments to chromosome territory.  A subset of the regulators exhibited 3D genome effects associated with  loop-extrusion and A-B compartmentalization mechanisms, while others were largely  unrelated to these known 3D genome mechanisms. We found that the ATP-dependent  helicase CHD7, the loss of which causes the congenital neural crest syndrome  CHARGE(24) and a chromatin remodeler previously shown to promote local chromatin  openness(25-27), counter-intuitively compacts chromatin over long range in  different genomic contexts and cell backgrounds including neural crest cells, and  globally represses gene expression. The DNA compaction effect of CHD7 is  independent of its chromatin remodeling activity and does not require other  protein partners. Finally, we identified new regulators of nuclear architectures  and found a functional link between chromatin compaction and nuclear shape.  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