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Many newly identified peaks are localized along extrusion stripes and form  transitive grids, consistent with their anchors being pause sites impeding cohesin-dependent loop extrusion. Our analyses comprise the highest-resolution maps of chromosome folding in human cells to date, providing a valuable resource  for studies of chromosome organization.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/32213324", "short_attribution": "Krietenstein N et al. (2020)", "date_published": "2020-05-07", "title": "Ultrastructural Details of Mammalian Chromosome Architecture.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [{"@id": "/publications/dfc530f1-82c0-4ddc-8f95-6f40417f87a0/", "status": "current", "uuid": "dfc530f1-82c0-4ddc-8f95-6f40417f87a0", "@type": ["Publication", "Item"], "display_title": "Akgol Oksuz B et al. 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Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a  systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.", "ID": "PMID:34480151", "journal": "Nature methods", "date_published": "2021-09-03", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"title": "Ultrastructural Details of Mammalian Chromosome Architecture.", "status": "current", "uuid": "a716e6b4-9cfa-4f8d-a2c7-cabf21d42b95", "@type": ["Publication", "Item"], "display_title": "Krietenstein N et al. (2020) PMID:32213324", "@id": "/publications/a716e6b4-9cfa-4f8d-a2c7-cabf21d42b95/", "authors": ["Krietenstein N", "Abraham S", "Venev SV", "Abdennur N", "Gibcus J", "Hsieh TS", "Parsi KM", "Yang L", "Maehr R", "Mirny LA", "Dekker J", "Rando OJ"], "abstract": "Over the past decade, 3C-related methods have provided remarkable insights into chromosome folding in vivo. To overcome the limited resolution of prior studies,  we extend a recently developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human ESCs and fibroblasts. Micro-C robustly captures known features of chromosome folding including compartment organization, topologically associating domains, and interactions between CTCF binding sites. In addition, Micro-C provides a detailed map of nucleosome positions and localizes contact domain boundaries with nucleosomal precision. Compared to Hi-C, Micro-C exhibits an order of magnitude greater dynamic range, allowing the identification of approximately 20,000 additional loops in each cell type. Many newly identified peaks are localized along extrusion stripes and form  transitive grids, consistent with their anchors being pause sites impeding cohesin-dependent loop extrusion. Our analyses comprise the highest-resolution maps of chromosome folding in human cells to date, providing a valuable resource  for studies of chromosome organization.", "ID": "PMID:32213324", "journal": "Molecular cell", "date_published": "2020-05-07", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 9, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSC8TU4XY/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSTNNFD79/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample is a stem cell line over 10 passages but missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}