{"ID": "PMID:29094699", "lab": {"@id": "/labs/francois-spitz-lab/", "status": "current", "display_title": "Francois Spitz, PASTEUR", "@type": ["Lab", "Item"], "title": "Francois Spitz, PASTEUR", "uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "correspondence": [{"contact_email": "ZnNwaXR6QHVjaGljYWdvLmVkdQ==", "@id": "/users/fbcf7895-3eba-4844-950f-855c02be74a2/", "display_title": "Francois Spitz"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/29094699", "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center": "External", "name": "external-award", "@id": "/awards/external-award/", "project": "External", "center_title": "External", "description": "Funding source is from outside 4DN.", "display_title": "EXTERNAL AWARD", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Two independent modes of chromatin organization revealed by cohesin removal.", "status": "current", "aliases": ["leonid-mirny-lab:29094699"], "authors": ["Schwarzer W", "Abdennur N", "Goloborodko A", "Pekowska A", "Fudenberg G", "Loe-Mie Y", "Fonseca NA", "Huber W", "H Haering C", "Mirny L", "Spitz F"], "journal": "Nature", "abstract": "Imaging and chromosome conformation capture studies have revealed several layers  of chromosome organization, including segregation into megabase-sized active and  inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the  absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by  loop extrusion, which helps to guide distant enhancers to their target genes.", "date_created": "2018-05-10T18:35:25.569390+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2018-10-25T21:03:05.924886+00:00"}, "date_published": "2017-09-27", "public_release": "2018-10-25", "schema_version": "2", "project_release": "2018-10-25", "contributing_labs": [{"@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "status": "current", "correspondence": [{"contact_email": "bGVvbmlkQG1pdC5lZHU=", "@id": "/users/f520d12a-e4c4-4774-a230-08d6dc4f5ef1/", "display_title": "Leonid Mirny"}], "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "exp_sets_prod_in_pub": [{"@id": "/experiment-set-replicates/4DNESWOB3ZGQ/", "display_title": "4DNESWOB3ZGQ", "accession": "4DNESWOB3ZGQ", "uuid": "026db1d0-c159-457c-b555-c9298b35b82e", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "status": "released", "experiments_in_set": [{"display_title": "RNA-seq on hepatocyte - 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