{"ID": "PMID:31036827", "lab": {"title": "Steve Henikoff, FREDHUTCH", "uuid": "3a41e042-a9f3-4205-a28a-4c20ba2edda2", "@type": ["Lab", "Item"], "display_title": "Steve Henikoff, FREDHUTCH", "@id": "/labs/steve-henikoff-lab/", "correspondence": [{"contact_email": "c3RldmVoQGZoY3JjLm9yZw==", "@id": "/users/bed386a9-7ee0-4ac0-ab50-741018edf928/", "display_title": "Steve Henikoff"}], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3a41e042-a9f3-4205-a28a-4c20ba2edda2"]}, "pi": {"error": "no view permissions"}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/31036827", "award": {"status": "current", "display_title": "TETHERED NUCLEASE STRATEGIES FOR IN SITU MAPPING OF 3D NUCLEAR ORGANIZATION", "description": "TCPA: The 4D Nucleome project focuses on describing the 3D organization within the nucleus, with \nthe ultimate goal of understanding this organization in mechanistic terms. 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. Together with our new native ChIP-seq protocol, we distinguish direct \u201canchor\u201d sites of a \nchromatin-bound protein from contacting sites without fixation, a kind of inference has not been possible with current methods of interrogating 3D chromatin architecture. We have two Aims: First, we will annotate the genome at high density for CTCF and cohesin sites, distinguishing between anchor and contact sites in 4D Nucleome cell lines. Second, we will continue development of a new replacement technology for 3D contact mapping, using CUT&RUN as a \u201cfront-end\u201d for proximity ligation (CUT&PASTE \u2013 Cleave Under Targets & Polish And Splice Touching Ends), building on our novel sci-HiC protocol for high-resolution TF-specific 3D interaction mapping. By annotating more contact sites in genomes and assigning the directionality of contacts, we move towards a mechanistic model of how topology within the nucleus is organized. Participation in the 4DN program would provide the opportunity to compare and integrate our CUT&RUN/PASTE datasets with 4DN datasets on common cell lines and differentiating tissues, ideally positioning consortium investigators to adopt our alternative strategy for their own 4DN efforts.", "center_title": "TCPA - Henikoff", "name": "TCPA-2017-04", "project": "4DN", "uuid": "4ddcac2d-72b6-40a7-ac68-67efba21a0d0", "@type": ["Award", "Item"], "@id": "/awards/TCPA-2017-04/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "CUT&Tag for efficient epigenomic profiling of small samples and single cells.", "status": "current", "aliases": ["4dn-dcic-lab:cut_n_tag_publ"], "authors": ["Kaya-Okur HS", "Wu SJ", "Codomo CA", "Pledger ES", "Bryson TD", "Henikoff JG", "Ahmad K", "Henikoff S"], "journal": "Nature communications", "abstract": "Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells  to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone  modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.", "date_created": "2021-02-04T16:40:21.374631+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-02-04T17:14:06.029189+00:00"}, "date_published": "2019-04-29", "public_release": "2021-02-04", "schema_version": "2", "project_release": "2021-02-04", "@id": "/publications/d0ef0d3b-ce23-416a-8e8a-b5b657b23e62/", "@type": ["Publication", "Item"], "uuid": "d0ef0d3b-ce23-416a-8e8a-b5b657b23e62", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Kaya-Okur HS et al. (2019) PMID:31036827", "external_references": [], "short_attribution": "Kaya-Okur HS et al. (2019)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}