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Our project uses novel methods for epigenomic profiling that detect 3D contact sites without cross-linking and with much higher resolution than current technologies. We recently introduced a novel strategy for chromatin profiling called CUT&RUN (Cleavage Under Targets & Release Using Nuclease), in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. The method yields precise transcription factor (TF) profiles, yet is simple to perform and is inherently robust, with extremely low backgrounds requiring ~1/10 th the sequencing depth of chromatin immunoprecipitation (ChIP). CUT&RUN binding and cleavage occurs in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the 3D chromatin environment. 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"experimentset_type": "replicate", "uuid": "84d203e2-e3ab-453e-b62b-63e9a0a55480", "display_title": "4DNES1RQBHPK", "accession": "4DNES1RQBHPK", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [{"ID": "PMID:34480151", "title": "Systematic evaluation of chromosome conformation capture assays.", "@type": ["Publication", "Item"], "status": "current", "short_attribution": "Akgol Oksuz B et al. (2021)", "@id": "/publications/dfc530f1-82c0-4ddc-8f95-6f40417f87a0/", "display_title": "Akgol Oksuz B et al. (2021) PMID:34480151", "uuid": "dfc530f1-82c0-4ddc-8f95-6f40417f87a0", "abstract": "Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. 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.", "journal": "Nature methods", "authors": ["Akgol Oksuz B", "Yang L", "Abraham S", "Venev SV", "Krietenstein N", "Parsi KM", "Ozadam H", "Oomen ME", "Nand A", "Mao H", "Genga RMJ", "Maehr R", "Rando OJ", "Mirny LA", "Gibcus JH", "Dekker J"], "date_published": "2021-09", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"ID": "PMID:35676475", "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "@type": ["Publication", "Item"], "status": "current", "short_attribution": "Emerson DJ et al. (2022)", "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability(1,2). At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.", "journal": "Nature", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "date_published": "2022-06-08", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "CTCF protein", "combined": "Target: CTCF protein"}, "experiment_summary": "CUT&RUN against CTCF protein on H1-hESC (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSIDU2JA7/", "embedded_path": "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."}}}]}, "validation-errors": []}