{"ID": "doi:10.1101/2021.01.05.425437", "lab": {"title": "Jennifer Cremins, UPENN", "@id": "/labs/jennifer-cremins-lab/", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "correspondence": [{"contact_email": "amNyZW1pbnNAc2Vhcy51cGVubi5lZHU=", "@id": "/users/8773d50c-1716-4153-9a18-d0f5ff2aa5ee/", "display_title": "Jennifer Phillips-Cremins"}], "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "url": "http://biorxiv.org/lookup/doi/10.1101/2021.01.05.425437", "award": {"description": "NT: Critical unanswered questions in the field of genome biology are how the dynamics of chromatin folding shape gene expression patterns. Our knowledge of the dynamics of higher-order 3-D folding of chromatin is severely limited, largely due to the lack of technologies to precisely image, engineer and monitor looping in a precise spatiotemporal manner across a population of cells. Here we propose to address these limitations by developing tools to dynamically alter chromatin folding in a synchronous manner across populations of cells as well as individual cells, and measure chromatin looping and its relationship to transcription at high spatial resolution in single cells. In Specific Aim 1 we will design tools to control looping dynamics. We will modify factors that fold chromatin at various levels, such as Ldb1 and CTCF by fusion to a moiety whose stability can be controlled by diffusible ligands. In combination with hi resolution 5C and single molecule imaging these tools are expected to generate fundamental insights into the relationship of nuclear architecture and gene expression mechanisms. In Specific Aim 2 we plan to engineer light-inducible systems for the precise control of looping dynamics. Using light activated dimerization domains that can be used in conjunction with designer DNA binding proteins we attempt to engineer factors used to rapidly promote or disrupt chromatin looping at various scales. This technology should enable studies not only in populations but also at the single cell level. In Specific Aim 3: we will develp reagents to study the transcriptional dynamics in relation to looping at the single cell level. We will combine RNA FISH with super-resolution imaging to develop a methodology for exploring the spatial and temporal structure of nascent transcription at high resolution. Combined with high-throughput image acquisition, we will discriminate the temporal dynamics of transcription by measuring the relative intensities arising from the different parts of the transcript. We will employ super-resolution imaging (STORM) to measure the spatial structure of transcription sites. These experiments are expected to reveal the impact of forced chromatin looping on distinct stages of the transcription cycle and elucidate the relationship between transcriptional burst kinetics and physical gene structure.", "@id": "/awards/1U01HL129998-01/", "center_title": "NT - Raj", "uuid": "cf0c686c-a3ad-411d-9986-ad42927352c0", "name": "1U01HL129998-01", "display_title": "ENGINEERING AND VISUALIZING GENOME FOLDING AT HIGH SPATIOTEMPORAL RESOLUTION", "@type": ["Award", "Item"], "status": "current", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Cohesin-mediated loop anchors confine the location of human replication origins", "status": "current", "aliases": ["4dn-dcic-lab:cremins-gilbert-biorxiv-doi-10.1101_2021.01.05.425437"], "authors": ["Emerson DJ", "Zhao PA", "Klein K", "Ge C", "Zhou L", "Sasaki T", "Yang L", "Venvev SV", "Gibcus JH", "Dekker J", "Gilbert DM", "Phillips-Cremins JE"], "journal": "bioRxiv", "version": "1", "abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability across dividing cells in metazoans. It is currently unknown how the location of replication origins and the timing of their activation is determined in the human genome. Here, we dissect the role for G1 phase topologically associating domains (TADs), subTADs, and loops in the activation of replication initiation zones (IZs). We identify twelve subtypes of self-interacting chromatin domains distinguished by their degree of nesting, the presence of corner dot structures indicative of loops, and their co-localization with A/B compartments. Early replicating IZs localize to boundaries of nested corner-dot TAD/subTADs anchored by high density arrays of co-occupied CTCF+cohesin binding sites with divergently oriented motifs. By contrast, late replicating IZs localize to weak TADs/subTAD boundaries devoid of corner dots and most often anchored by singlet CTCF+cohesin sites. Upon global knock-down of cohesin-mediated loops in G1, early wave focal IZs replicate later in S phase and convert to diffuse placement along the genome. Moreover, IZs in mid-late S phase are delayed to the final minutes before entry into G2 when cohesin-mediated dot-less boundaries are ablated. We also delete a specific loop anchor and observe a sharp local delay of an early wave IZ to replication in late S phase. Our data demonstrate that cohesin-mediated loops at genetically-encoded TAD/subTAD boundaries in G1 phase are an essential determinant of the precise genomic placement of human replication origins in S phase.", "categories": ["integrative analysis", "basic biology", "genomic annotations"], "date_created": "2021-01-20T21:15:57.605376+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-02-27T09:53:30.261965+00:00"}, "date_published": "2021-01-06", "public_release": "2021-01-20", "schema_version": "2", "static_content": [{"content": {"@id": "/static-sections/94f5d443-c509-435c-b4f9-06ac76d40fcd/", "name": "emerson-etal.summary.temp_intro_blurb", "content": "The current publication info is for the originally submitted preprint and reports on the original analysis. The resubmission is currently under review and the data provided in this summary is that reported in the re-submitted manuscript and a subset of the data presented here has been updated.  You can find information on how to find the original analysis data, which has been archived in favor of the updated analyses, in notes in the sections below. Upon publication the links and information on these pages will be updated to reflect that. Please contact jcremins@seas.upenn.edu for information prior to publication.\n", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "filetype": "md", "title": "Publication Status Update", "uuid": "94f5d443-c509-435c-b4f9-06ac76d40fcd", "contributing_labs": [{"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@id": "/labs/jennifer-cremins-lab/", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@type": ["Lab", "Item"], "status": "current", "display_title": "Jennifer Cremins, UPENN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "@type": ["StaticSection", "UserContent", "Item"], "display_title": "Publication Status Update", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "tab:data_summary"}, {"content": {"@id": "/static-sections/ae5222b1-3758-40c8-8f37-2a968233ccb9/", "name": "emerson-etal.summary.5C-data-table", "content": "\n<EmbeddedItemSearchTable\n    searchHref=\"/search/?experiments_in_set.experiment_type.display_title=Capture+Hi-C&lab.display_title=Jennifer+Cremins%2C+UPENN&type=ExperimentSetReplicate&produced_in_pub.uuid=70a029d4-9432-4ceb-bd11-ad3b30188501\"\n    schemas={schemas}\n    session={session}\n    key=\"anyRandomTextString\"\n    facets={null}\n    columns={{\n        \"display_title\": {\n            \"title\": \"Title\"\n        },\n        \"experiments_in_set.experiment_type.display_title\" : {\n            \"title\" : \"Experiment Type\",\n        },\n        \"experiments_in_set.biosample.biosource_summary\": {\n            \"title\" : \"Biosample\"\n        },\n        \"experiments_in_set.biosample.modifications.display_title\": {\n            \"title\" : \"Modifications\"\n        },\n        \"experiments_in_set.experiment_categorizer.combined\" : {\n            \"title\" : \"Assay Details\"\n        }\n    }}\n/>\n", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - 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the previous calls can be found in the archived collection of supplementary files in <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNES2M5JIGV/#supplementary-files\">4DNES2M5JIGV</a></p>\n\n<EmbeddedItemSearchTable\n    searchHref=\"/search/?type=FileProcessed&track_and_facet_info.experiment_bucket=TADs%2C+subTADs%2C+Boundaries%2C+and+Dot+Calls+-+Cremins+Lab&experiment_sets.accession=4DNESX75DD7R\"\n    schemas={schemas}\n    session={session}\n    key=\"anyRandomTextString\"\n    columns={{\n        \"display_title\": {\n            \"title\": \"Title\"\n        },\n        \"file_type\" : {\n            \"title\" : \"File Type\"\n        },\n        \"file_format.file_format\": {\n            \"title\" : \"File Format\"\n        },\n        \"file_size\" : {\n            \"title\" : \"File Size\"\n        }\n    }}\n    hideFacets={[\"lab.display_title\",\n                 \"track_and_facet_info.experiment_type\",\n                 \"track_and_facet_info.assay_info\",\n                 \"track_and_facet_info.biosource_name\",\n                 \"track_and_facet_info.lab_name\",\n                 \"public_release\",\n                 \"type\",\n                 \"status\",\n                 \"workflow_run_inputs.workflow.title\",\n                 \"workflow_run_outputs.workflow.title\",\n                 \"validation_errors.name\"\n                ]\n               }\n/>\n\n<H3>Feature Calls derived from <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNES2R6PUEK/\">HFFc6 Hi-C - 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4DNES3QAGOZZ</a></H3>\n<p><strong>Note:</strong> these data have been updated from those originally provided here and described in the original Biorxiv paper - the previous calls can be found in the archived collection of supplementary files in <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNES3QAGOZZ/#supplementary-files\">4DNES3QAGOZZ</a>\nAlso note that this dataset is derived from HCT116 cells engineered to contain a Rad21 AID-tagged degron that can be treated with auxin to deplete cohesin.  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