{"lab": {"uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "@type": ["Lab", "Item"], "title": "Wei Xie, TSINGHUA", "status": "current", "@id": "/labs/wei-xie-lab/", "display_title": "Wei Xie, TSINGHUA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "award": {"name": "external-award", "@type": ["Award", "Item"], "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "center_title": "External", "center": "External", "status": "current", "project": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Embryo Development", "status": "released", "aliases": ["4dn-dcic-lab:sisHi-C_late_2-cell"], "accession": "4DNESXZHIUAU", "condition": "Late 2-cell embryos", "description": "Small-scale in situ Hi-C on mouse late 2-cell embryos", "study_group": "Time Course", "date_created": "2020-01-10T15:45:02.280217+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_group": "sisHi-C during early embryonic development", "dataset_label": "sisHi-C during early embryonic development", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T05:00:43.391227+00:00"}, "public_release": "2020-02-07", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"display_title": "in situ Hi-C on Late 2-cell stage embryo with MboI - 4DNEXOSG8OXE", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXOSG8OXE", "uuid": "32c919ae-957b-448c-8b8c-f47f6009e234", "status": "released", "@id": "/experiments-hi-c/4DNEXOSG8OXE/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"display_title": "in situ Hi-C on Late 2-cell stage embryo with MboI - 4DNEXM5XEQNN", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXM5XEQNN", "uuid": "c53c4771-5da6-42e1-b838-9cce28145c98", "status": "released", "@id": "/experiments-hi-c/4DNEXM5XEQNN/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"display_title": "in situ Hi-C on Late 2-cell stage embryo with MboI - 4DNEX4U1GKC1", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX4U1GKC1", "uuid": "adff3ed9-5d76-42f1-afbe-0f22cb43c300", "status": "released", "@id": "/experiments-hi-c/4DNEX4U1GKC1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"display_title": "in situ Hi-C on Late 2-cell stage embryo with MboI - 4DNEXHFCMUAI", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXHFCMUAI", "uuid": "9feab756-9dc5-40e9-a96a-ae48dc2721aa", "status": "released", "@id": "/experiments-hi-c/4DNEXHFCMUAI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"@id": "/higlass-view-configs/a9b20439-30fe-45b4-8cc2-1d34e20f9f2a/", "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "4DNESXZHIUAU (Small-scale in situ Hi-C on mouse late 2-cell embryos): 4DNFIIWW8LIF", "name": "a9b20439-30fe-45b4-8cc2-1d34e20f9f2a", "uuid": "a9b20439-30fe-45b4-8cc2-1d34e20f9f2a", "status": "released", "lab": {"@type": ["Lab", "Item"], "@id": "/labs/wei-xie-lab/", "status": "current", "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "title": "4DNESXZHIUAU - Processed files", "display_title": "4DNESXZHIUAU - Processed files", "@type": ["HiglassViewConfig", "UserContent", "Item"], "contributing_labs": [], "filetype": "HiglassViewConfig", "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": {"display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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. 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The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. 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(2017) PMID:28703188", "short_attribution": "Du Z et al. (2017)", "journal": "Nature", "title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "date_published": "2017-07-12", "authors": ["Du Z", "Zheng H", "Huang B", "Ma R", "Wu J", "Zhang X", "He J", "Xiang Y", "Wang Q", "Li Y", "Ma J", "Zhang X", "Zhang K", "Wang Y", "Zhang MQ", "Gao J", "Dixon JR", "Wang X", "Zeng J", "Xie W"], "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "status": "current", "ID": "PMID:28703188", "url": "https://www.ncbi.nlm.nih.gov/pubmed/28703188", "abstract": "In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs)  and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "abstract": "In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs)  and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.", "date_published": "2017-07-12", "ID": "PMID:28703188", "authors": ["Du Z", "Zheng H", "Huang B", "Ma R", "Wu J", "Zhang X", "He J", "Xiang Y", "Wang Q", "Li Y", "Ma J", "Zhang X", "Zhang K", "Wang Y", "Zhang MQ", "Gao J", "Dixon JR", "Wang X", "Zeng J", "Xie W"], "status": "current", "display_title": "Du Z et al. (2017) PMID:28703188", "journal": "Nature", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 4, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}