{"lab": {"display_title": "Jennifer Cremins, UPENN", "@id": "/labs/jennifer-cremins-lab/", "status": "current", "correspondence": [{"contact_email": "amNyZW1pbnNAc2Vhcy51cGVubi5lZHU=", "@id": "/users/8773d50c-1716-4153-9a18-d0f5ff2aa5ee/", "display_title": "Jennifer Phillips-Cremins"}], "@type": ["Lab", "Item"], "title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "award": {"center_title": "Phillips-Cremins", "@id": "/awards/1U01DK127405-01/", "name": "1U01DK127405-01", "uuid": "b3046311-087c-4141-8e98-a099b96ac6cd", "status": "current", "display_title": "ENGINEERING AND IMAGING 3D GENOME STRUCTURE-FUNCTION DYNAMICS ACROSS TIME SCALES", "project": "4DN", "@type": ["Award", "Item"], "description": "RT-CDF:The mammalian genome folds into tens of thousands of long-range looping interactions. A critical unknown is whether and how chromatin loops control gene expression, and a major unresolved question is how the temporal progression of loops relates to transcription dynamics. One major barrier to answering this question is that loops change on a range of timescales, necessitating the use of tools and model systems amenable to tracking and engineering loops longitudinally and in real time on both short and long timing. Here, we propose to develop and apply new engineering and imaging tools to measure, induce, and perturb loops with precise temporal control in three different biological systems spanning minutes, hours, and weeks. At the shortest timescale (minutes, Aim 1), we will examine loop dynamics in human induced pluripotent stem cell-derived neurons in response to electrical stimulation, revealing how interaction frequency is functionally connected to transcriptional bursting of immediate early and secondary response genes. On the timescale of hours (Aim 3), we will elucidate how the architectural protein YY1 connects enhancer-promoter loops that re-assemble upon the exit from mitosis by erythroid cells. On the timescale of weeks (Aim 2), we will use a cellular \u201cTime Machine\u201d to longitudinally track the rare cells that undergo cellular reprogramming, allowing us to dissect the functionality of loop formation and dissolution with single-cell and subcellular resolution during the reprogramming of somatic cells to pluripotency and transition of melanoma cancer cells to a resistant phenotype. Our team consists of a highly productive and collaborative set of junior and senior investigators with complementary expertise and overlapping interests, including Dr. Gerd Blobel (epigenetics, mitosis, loop engineering), Dr. Eric Joyce (Oligopaints imaging), Dr. Bomyi Lim (nascent transcript live cell imaging), Dr. Jennifer Phillips-Cremins (chromatin architecture, loop engineering, neurobiology), Dr. Stanley Qi (CRISPR genome engineering, live cell imaging), and Dr. Arjun Raj (single cell genomics, RNA imaging, reprogramming). We will develop and apply live and fixed cell imaging techniques for chromatin contacts, and in the same cells image nascent transcription. We will build a cadre of synthetic architectural proteins to engineer loops in a time-dependent inducible manner. Successful application of our engineering and imaging tools across biological systems will yield a comprehensive and rigorous assessment of the cause-and-effect relationship between loops and distinct biological phenotypes across timescales.", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"upload_key": "06d43159-43cd-4f74-b15e-ca4e6a678231/4DNFIITG12D3.fastq.gz", "accession": "4DNFIITG12D3", "paired_end": "1", "href": "/files-fastq/4DNFIITG12D3/@@download/4DNFIITG12D3.fastq.gz", "notes_to_tsv": ["WARNING - The reads in this file frequently contain adapter sequences and only short regions of genomic sequences. An index file consisting of only the enriched sequence region must be used to produce useful alignments. 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For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "display_title": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "Capture Hi-C", "experiment_bucket": "Derived data files provided by the Cremins Lab", "assay_info": "6MB 5C enriched region", "dataset": "5C on 6Mb of chrX", "condition": "unedited cells", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "7889SA3.5", "lab_name": "Jennifer Cremins, UPENN"}, "last_modified": {"date_modified": "2021-12-16T07:00:46.287279+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "be70ff20-b816-4abc-ab76-02ebd9a32590", "file_type": "counts", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/be70ff20-b816-4abc-ab76-02ebd9a32590/4DNFI2A9E612.txt.gz", "@id": "/files-processed/4DNFI2A9E612/", "accession": "4DNFI2A9E612", "genome_assembly": "GRCh38", "display_title": "4DNFI2A9E612.txt.gz", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFI2A9E612/@@download/4DNFI2A9E612.txt.gz", "file_size": 26826139, "file_type_detailed": "counts (compressed_txt)", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. 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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.", "ID": "PMID:35676475", "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "@type": ["Publication", "Item"], "short_attribution": "Emerson DJ et al. (2022)", "journal": "Nature", "status": "current", "date_published": "2022-06-08", "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"status": "current", "journal": "Nature", "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. 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