{"ID": "PMID:29348367", "lab": {"status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "title": "Job Dekker, UMMS", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/29348367", "award": {"name": "external-award", "center": "External", "@type": ["Award", "Item"], "status": "current", "center_title": "External", "display_title": "EXTERNAL AWARD", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "project": "External", "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "A pathway for mitotic chromosome formation.", "status": "current", "aliases": ["4dn-dcic-lab:29348367"], "authors": ["Gibcus JH", "Samejima K", "Goloborodko A", "Samejima I", "Naumova N", "Nuebler J", "Kanemaki MT", "Xie L", "Paulson JR", "Earnshaw WC", "Mirny LA", "Dekker J"], "journal": "Science (New York, N.Y.)", "abstract": "Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop  array acquires a helical arrangement with consecutive loops emanating from a central \"spiral staircase\" condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of  condensin I or II shows that nested loops form by differential action of the two  condensins, whereas condensin II is required for helical winding.", "date_created": "2018-10-30T14:35:44.543097+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-08T21:40:16.907628+00:00"}, "date_published": "2018-02-09", "public_release": "2018-10-30", "schema_version": "2", "static_content": [{"content": {"options": {"collapsible": true, "default_open": true}, "filetype": "HiglassViewConfig", "uuid": "f3dfab96-4150-4834-a841-b03fd8f36a2b", "@id": "/higlass-view-configs/f3dfab96-4150-4834-a841-b03fd8f36a2b/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "f3dfab96-4150-4834-a841-b03fd8f36a2b", "display_title": "Hi-C on Synchronized DT40 (chicken) cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C on Synchronized DT40 (chicken) cells", "description": "Cells were arrested in G2 to synchronize, then released from arrest and fixed at several time points. Later timepoints were treated with nocodazole to prevent metaphase to anaphase transition. From left to right, top then bottom: G2 (0m); early prophase (5m); late prophase (10m); early prometaphase (15m); prometaphase (30m, blocked with nocodazole); prometaphase (60m, blocked with nocodazole). Note the large-scale changes in contact frequencies as mitosis begins.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:higlass_displays"}, {"content": {"options": {"collapsible": true, "default_open": false}, "filetype": "HiglassViewConfig", "uuid": "f0b1d7ac-3f8c-42ee-81b3-a0617ed8f17a", "@id": "/higlass-view-configs/f0b1d7ac-3f8c-42ee-81b3-a0617ed8f17a/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "f0b1d7ac-3f8c-42ee-81b3-a0617ed8f17a", "display_title": "Hi-C on Synchronized SMC2-mAID DT40 cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C on Synchronized SMC2-mAID DT40 cells", "description": "When SMC2 is depleted, compartments take longer to disappear and no second diagonal is formed in contact maps as mitosis proceeds, unlike the non-AID-tagged cells. Top: SMC2+ (left) and SMC2- (right) G2 cells. Bottom: SMC2- cells 10m (left), 45m (middle) and 75m (right) after release from G2 arrest.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:higlass_displays"}, {"content": {"options": {"collapsible": true, "default_open": false}, "filetype": "HiglassViewConfig", "uuid": "68e2b628-2e48-402d-bb97-974cd3c906d6", "@id": "/higlass-view-configs/68e2b628-2e48-402d-bb97-974cd3c906d6/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "68e2b628-2e48-402d-bb97-974cd3c906d6", "display_title": "Hi-C of Synchronized CAPH2-mAID cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C of Synchronized CAPH2-mAID cells", "description": "When the condensin II-specific kleisin (CAP-H2) is depleted, compartments still disappear and condensing along the diagonal is observed. However, no second diagonal is formed in contact maps as mitosis proceeds, unlike the non-AID-tagged cells. Top left: CAP-H2+ cells in G2. Other views (left to right, top then bottom): CAP-H2- cells 0m, 8m, 15m, 30m, and 60m after release from G2 arrest.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:higlass_displays"}, {"content": {"options": {"collapsible": true, "default_open": false}, "filetype": "HiglassViewConfig", "uuid": "8b1e8511-d3c8-49e6-a61b-0bc61a767c45", "@id": "/higlass-view-configs/8b1e8511-d3c8-49e6-a61b-0bc61a767c45/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "8b1e8511-d3c8-49e6-a61b-0bc61a767c45", "display_title": "Hi-C of Synchronized CAPH-mAID DT40 cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C of Synchronized CAPH-mAID DT40 cells", "description": "When the condensin I-specific kleisin (CAP-H) is depleted, cells proceed through prophase normally. However, during prometaphase, the second diagonal observed at 30m resembles the wildtype at 60m, indicating faster development of larger helical turns during condensation. Top left: CAP-H+ cells in G2. Other views (left to right, top then bottom): CAP-H- cells 0m, 10m, 15m, 30m, and 60m after release from G2 arrest.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:higlass_displays"}, {"content": {"options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "filetype": "md", "uuid": "43391e8c-bb44-4aa5-b1b2-6c4efeb2d82c", "@id": "/static-sections/43391e8c-bb44-4aa5-b1b2-6c4efeb2d82c/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "content": "This study takes advantage of the chicken cell line DT40 with a\nCdk1as (analog-sensitive) mutant, in which Cdk1 can be \ninactivated with 1NM-PP1 in order to synchronize the cells. \nThis allows the authors to perform Hi-C on cells at different \nstages of mitosis, and they compare control cells to cells with\n condensin I or II depleted to look at chromosome condensation \nand the relative contribution of the condensins.\n\n---------------------\n\n#### HiGlass Displays", "name": "gibcus_et_al.section-top", "display_title": "About this Study", "@type": ["StaticSection", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "About this Study", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}, {"content": {"options": {"collapsible": true, "default_open": true}, "filetype": "HiglassViewConfig", "uuid": "f3dfab96-4150-4834-a841-b03fd8f36a2b", "@id": "/higlass-view-configs/f3dfab96-4150-4834-a841-b03fd8f36a2b/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "f3dfab96-4150-4834-a841-b03fd8f36a2b", "display_title": "Hi-C on Synchronized DT40 (chicken) cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C on Synchronized DT40 (chicken) cells", "description": "Cells were arrested in G2 to synchronize, then released from arrest and fixed at several time points. Later timepoints were treated with nocodazole to prevent metaphase to anaphase transition. From left to right, top then bottom: G2 (0m); early prophase (5m); late prophase (10m); early prometaphase (15m); prometaphase (30m, blocked with nocodazole); prometaphase (60m, blocked with nocodazole). Note the large-scale changes in contact frequencies as mitosis begins.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}, {"content": {"options": {"collapsible": true, "default_open": false}, "filetype": "HiglassViewConfig", "uuid": "f0b1d7ac-3f8c-42ee-81b3-a0617ed8f17a", "@id": "/higlass-view-configs/f0b1d7ac-3f8c-42ee-81b3-a0617ed8f17a/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "f0b1d7ac-3f8c-42ee-81b3-a0617ed8f17a", "display_title": "Hi-C on Synchronized SMC2-mAID DT40 cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C on Synchronized SMC2-mAID DT40 cells", "description": "When SMC2 is depleted, compartments take longer to disappear and no second diagonal is formed in contact maps as mitosis proceeds, unlike the non-AID-tagged cells. Top: SMC2+ (left) and SMC2- (right) G2 cells. Bottom: SMC2- cells 10m (left), 45m (middle) and 75m (right) after release from G2 arrest.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}, {"content": {"options": {"collapsible": true, "default_open": false}, "filetype": "HiglassViewConfig", "uuid": "68e2b628-2e48-402d-bb97-974cd3c906d6", "@id": "/higlass-view-configs/68e2b628-2e48-402d-bb97-974cd3c906d6/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "68e2b628-2e48-402d-bb97-974cd3c906d6", "display_title": "Hi-C of Synchronized CAPH2-mAID cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C of Synchronized CAPH2-mAID cells", "description": "When the condensin II-specific kleisin (CAP-H2) is depleted, compartments still disappear and condensing along the diagonal is observed. However, no second diagonal is formed in contact maps as mitosis proceeds, unlike the non-AID-tagged cells. Top left: CAP-H2+ cells in G2. Other views (left to right, top then bottom): CAP-H2- cells 0m, 8m, 15m, 30m, and 60m after release from G2 arrest.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.e2324f87-0625-4bbc-803b-d47677aebe08"]}}, "location": "tab:overview"}, {"content": {"options": {"collapsible": true, "default_open": false}, "filetype": "HiglassViewConfig", "uuid": "8b1e8511-d3c8-49e6-a61b-0bc61a767c45", "@id": "/higlass-view-configs/8b1e8511-d3c8-49e6-a61b-0bc61a767c45/", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "8b1e8511-d3c8-49e6-a61b-0bc61a767c45", "display_title": "Hi-C of Synchronized CAPH-mAID DT40 cells", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "title": "Hi-C of Synchronized CAPH-mAID DT40 cells", "description": "When the condensin I-specific kleisin (CAP-H) is depleted, cells proceed through prophase normally. 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