{"lab": {"@id": "/labs/thomas-gregor-lab/", "@type": ["Lab", "Item"], "display_title": "Thomas Gregor, PRINCETON", "title": "Thomas Gregor, PRINCETON", "uuid": "41cedc04-1e04-423a-8d08-0fc181409ee7", "correspondence": [{"contact_email": "dGcyQHByaW5jZXRvbi5lZHU=", "@id": "/users/e46f310b-2ed3-4b05-8d78-37456688a86d/", "display_title": "Thomas Gregor"}], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.41cedc04-1e04-423a-8d08-0fc181409ee7"]}}, "tags": ["many_replicates"], "award": {"name": "1U01EB021239-01", "@type": ["Award", "Item"], "@id": "/awards/1U01EB021239-01/", "uuid": "4a3ea2f9-864b-429d-9948-54dbe0d7958d", "status": "current", "display_title": "IMAGING CHROMOSOME DYNAMICS AND MEASURING ITS IMPACT ON TRANSCRIPTIONAL ACTIVITY", "project": "4DN", "center_title": "IT - Gregor", "description": "IT: One of the most fundamental problems in modern biology is to understand dynamic gene activity in time and space in the context of native chromosomes in living cells. The goal of the proposed study is to measure the levels of transcription produced by defined long-range chromosomal interactions in living cells. Traditional live imaging methods lack the spatial resolution to accurately determine the dynamics of gene activity, while bulk assays using fixed material strongly limit investigation of temporal dynamics. Here we propose to overcome these limitations by developing new methods of microscopy and computational analysis. Most of the studies will exploit the unique advantages of the early Drosophila embryo for the development of quantitative live cell imaging methods. Previous studies have identified hundreds of such interactions, and we will sample several of these to provide a \"titration\" of varying distances, from tens to hundreds of kilobases, as seen in mammalian systems. There are two specific aims: 1. Develop high-resolution imaging methods and associated computational algorithms for the visualization and quantification of dynamic enhancer-promoter interactions at select endogenous loci in living embryos. 2. Label regulatory regions and associated transcription units of individual genetic loci exhibiting long-range interactions, including trans-homolog associations during transvection at Hox loci, to measure in vivo the effect of chromosome topology on transcriptional activity. We plan to extend this approach to include the visualization of several hundred fluorescent DNA foci in a library of genetically engineered fly lines to establish a general overview of the dynamics of an entire chromosome in a living embryo and its impact on transcription. The successful realization of the proposed studies will greatly augment our current capacity to superimpose whole-genome maps based on fixed tissues onto the dynamic chromosomes of living cells. The resulting technologies will be immediately applied to the visualization of chromosome dynamics in mammalian tissues, particularly multipotent progenitor cells such as mouse hepatoblasts.", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [], "status": "released", "aliases": ["thomas-gregor-lab:experimentset_parS-homie-noPr-PP7_eveMS2"], "accession": "4DNES1U49MZQ", "condition": "parS-homie-noPr-PP7 (control without promoter)", "description": "Single particle tracking experiments (n = 29) on Drosophila embryos carrying the construct parS-homie-noPr-PP7 (control without promoter), located at 142kb upstream to the eveMS2 allele (2R:9,836,451, dm6). Male flies with this construct were crossed with MCP::3xtagBFP/PCP::3xmKate2; parB::eGFP/+ females to produce embryos for imaging.", "date_created": "2021-01-13T23:42:35.576096+00:00", "sample_image": {"uuid": "14ff0317-3000-481b-974d-ae317bc11c0c", "status": "released", "@id": "/images/14ff0317-3000-481b-974d-ae317bc11c0c/", "display_title": "Thumbnail for parS-homie-noPr-PP7_eveMS2", "caption": "Sample image snapshot from live cell imaging of a Drosophila embryo with parS-homie-noPr-PP7 eveMS2", "@type": ["Image", "Item"], "microscopy_file": {"display_title": "4DNFIUTWRT8J.tiff", "@type": ["FileMicroscopy", "File", "Item"], "accession": "4DNFIUTWRT8J", "omerolink": "https://omero.hms.harvard.edu/pathviewer/viewer/untiled/1401668", "uuid": "f17e268a-e5aa-43e8-9696-0b4df57ff303", "@id": "/files-microscopy/4DNFIUTWRT8J/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "attachment": {"md5sum": "b8390787b4f2b718acd6f7115f46547b", "height": 402, "href": "@@download/attachment/nopromoter.jpg", "download": "nopromoter.jpg", "type": "image/jpeg", "width": 600}}, "submitted_by": {"error": "no view permissions"}, "dataset_label": "Live imaging of chromatin topology and transcription", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-27T14:59:32.581254+00:00"}, "public_release": "2021-01-25", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "4a0fa2a7-8c66-41db-b2a5-a0c08c2fcfb7", "status": "released", "accession": "4DNEXPZO7ZFU", "display_title": "SPT on Drosophila embryo - 4DNEXPZO7ZFU", "@id": "/experiments-mic/4DNEXPZO7ZFU/", "@type": ["ExperimentMic", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "This Experiment Set collects many replicates (the number is indicated in the description above).\nThe complete processed data from all of the replicates in this set can be found in the Processed File.\nA Raw File (from one replicate) is presented as an example, for exploratory purposes.", "name": "item-page-headers.note.only-one-repr-raw-file", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on replicates", "status": "released", "aliases": ["4dn-dcic-lab:note_only_one_representative_raw_file"], "options": {"filetype": "md", "collapsible": false, "default_open": true}, "date_created": "2021-01-21T15:39:03.956214+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T23:21:24.067843+00:00"}, "schema_version": "2", "@id": "/static-sections/85520ecd-8df0-4d29-bd78-d8efa1f12ecf/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "85520ecd-8df0-4d29-bd78-d8efa1f12ecf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on replicates", "external_references": [], "content": "This Experiment Set collects many replicates (the number is indicated in the description above).\nThe complete processed data from all of the replicates in this set can be found in the Processed File.\nA Raw File (from one replicate) is presented as an example, for exploratory purposes.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>This Experiment Set collects many replicates (the number is indicated in the description above).\nThe complete processed data from all of the replicates in this set can be found in the Processed File.\nA Raw File (from one replicate) is presented as an example, for exploratory purposes.</p></div>"}, {"lab": {"@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "**SPT**\n\nSingle particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.\n\nThe protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.\n\n4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. \n", "name": "item-page-headers.ExperimentType.spt", "award": {"status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_spt"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-09-07T15:49:58.130720+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-08-04T22:53:31.013900+00:00"}, "schema_version": "2", "@id": "/static-sections/6a313162-e70c-4fbe-93c5-bc78f5faf0c7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "6a313162-e70c-4fbe-93c5-bc78f5faf0c7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**SPT**\n\nSingle particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.\n\nThe protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.\n\n4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. \n", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>SPT</strong></p>\n<p>Single particle tracking (SPT) is a method to track the position\n of a single molecule over time in live cells. Advances in \nmicroscopy and molecular biology techniques have enabled a \nbroad range of applications.</p>\n<p>The protocol involves preparing the target molecule to be \nidentifiable under the microscope, tracking its position over \ntime and analyzing its trajectory. Generally, the preparation \nof the molecule of interest is performed by genetically \nmodifying it with tags followed by the binding of reporter \nmolecules such as fluorescent dyes. However, depending on the \nmolecule of interest, the goal of the experiment and the type \nof microscope used, different techniques are also implemented.\n Following the preparation of the molecule, a high-resolution \nmicroscope is used to take snapshots of the position of the \nmolecule at different intervals of time. Tracking a single \nmolecule in a live cell is a demanding task, requiring both \nsensitivity and accuracy. Tailored to the application, this \ncan be achieved by specialized microscopy techniques like TIRF\n or PALM. Analysis of the resulting images results in a file \nthat describes the trajectory of the molecule.</p>\n<p>4DN processed files are in a format that includes the ID of a \ntrajectory, the time interval, and the coordinates of the \nposition. Further analysis of the trajectory of the molecule \nis necessary to gain biological insight. </p></div>"}], "processed_files": [{"file_type": "spt results, submitter format", "accession": "4DNFILJ2WX5N", "@type": ["FileProcessed", "File", "Item"], "upload_key": "ca3c06cb-8c49-4746-9c37-18096f18c7cd/4DNFILJ2WX5N.csv", "file_type_detailed": "spt results, submitter format (csv)", "uuid": "ca3c06cb-8c49-4746-9c37-18096f18c7cd", "display_title": "4DNFILJ2WX5N.csv", "href": "/files-processed/4DNFILJ2WX5N/@@download/4DNFILJ2WX5N.csv", "md5sum": "6a0971302b0b92e4e243d7aef28b7d9e", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ca3c06cb-8c49-4746-9c37-18096f18c7cd/4DNFILJ2WX5N.csv", "file_classification": "processed file", "status": "released", "file_size": 41710326, "@id": "/files-processed/4DNFILJ2WX5N/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "csv", "@id": "/file-formats/csv/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Thomas Gregor, PRINCETON", "uuid": "41cedc04-1e04-423a-8d08-0fc181409ee7", "@id": "/labs/thomas-gregor-lab/", "@type": ["Lab", "Item"], "status": "current", "name": "thomas-gregor-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.41cedc04-1e04-423a-8d08-0fc181409ee7"]}}, "last_modified": {"date_modified": "2021-01-25T23:21:25.253472+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Live imaging of chromatin topology and transcription", "condition": "parS-homie-noPr-PP7 (control without promoter)", "experimental_lab": "Thomas Gregor, PRINCETON", "replicate_info": "unreplicated", "experiment_bucket": "processed file", "experiment_type": "SPT", "assay_info": "MS2-tagged endogenous eve transcript and enhancer (fruit fly), ParS-tagged homie (no promoter) cassette (engineered reagent), PP7-tagged transcript from homie (no promoter) cassette (engineered reagent)", "biosource_name": "Drosophila embryo", "lab_name": "Thomas Gregor, PRINCETON"}, "external_references": []}], "project_release": "2021-01-25", "experiments_in_set": [{"accession": "4DNEXPZO7ZFU", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f17e268a-e5aa-43e8-9696-0b4df57ff303/4DNFIUTWRT8J.tiff", "file_type": "time-series", "md5sum": "2c0adcdc7d6e981fed58e09881e3b51f", "status": "released", "href": "/files-microscopy/4DNFIUTWRT8J/@@download/4DNFIUTWRT8J.tiff", "file_size": 1731672586, "@id": "/files-microscopy/4DNFIUTWRT8J/", "file_type_detailed": "time-series (tiff)", "@type": ["FileMicroscopy", "File", "Item"], "accession": "4DNFIUTWRT8J", "display_title": "4DNFIUTWRT8J.tiff", "uuid": "f17e268a-e5aa-43e8-9696-0b4df57ff303", "upload_key": "f17e268a-e5aa-43e8-9696-0b4df57ff303/4DNFIUTWRT8J.tiff", "file_classification": "raw file", "track_and_facet_info": {"experimental_lab": "Thomas Gregor, PRINCETON", "experiment_type": "SPT", "experiment_bucket": "raw file", "assay_info": "MS2-tagged endogenous eve transcript and enhancer (fruit fly), ParS-tagged homie (no promoter) cassette (engineered reagent), PP7-tagged transcript from homie (no promoter) cassette (engineered reagent)", "dataset": "Live imaging of chromatin topology and transcription", "condition": "parS-homie-noPr-PP7 (control without promoter)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Drosophila embryo", "lab_name": "Thomas Gregor, PRINCETON"}, "file_format": {"display_title": "tiff", "uuid": "d13d06cf-218e-4f61-33f0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/tiff/", "status": "released", "file_format": "tiff", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"name": "thomas-gregor-lab", "status": "current", "@id": "/labs/thomas-gregor-lab/", "uuid": "41cedc04-1e04-423a-8d08-0fc181409ee7", "@type": ["Lab", "Item"], "display_title": "Thomas Gregor, PRINCETON", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.41cedc04-1e04-423a-8d08-0fc181409ee7"]}}, "external_references": []}], "uuid": "4a0fa2a7-8c66-41db-b2a5-a0c08c2fcfb7", "display_title": "SPT on Drosophila embryo - 4DNEXPZO7ZFU", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXPZO7ZFU/", "status": "released", "experiment_type": {"assay_classification": "Fluorescence Localization", "experiment_category": "Microscopy", "assay_subclassification": "Single Particle Tracking", "assay_subclass_short": "SPT", "display_title": "SPT", "@id": "/experiment-types/spt/", "@type": ["ExperimentType", "Item"], "status": "released", "title": "SPT", "uuid": "d654c884-fc4f-4d53-818c-fc06fc33dfb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Target: MS2-tagged endogenous eve transcript and enhancer (fruit fly), ParS-tagged homie (no promoter) cassette (engineered reagent), PP7-tagged transcript from homie (no promoter) cassette (engineered reagent)", "value": "MS2-tagged endogenous eve transcript and enhancer (fruit fly), ParS-tagged homie (no promoter) cassette (engineered reagent), PP7-tagged transcript from homie (no promoter) cassette (engineered reagent)", "field": "Target"}, "biosample": {"treatments_summary": "None", "biosample_type": "whole organisms", "uuid": "82201a3d-d410-454e-a045-43b60e2e47ca", "modifications_summary": "None", "biosample_category": ["Multicellular Tissue"], "status": "released", "@type": ["Biosample", "Item"], "display_title": "4DNBS4SH18JM", "biosource_summary": "Drosophila embryo", "accession": "4DNBS4SH18JM", "@id": "/biosamples/4DNBS4SH18JM/", "biosource": [{"biosource_type": "multicellular organism", "override_biosource_name": "Drosophila embryo", "status": "released", "cell_line_tier": "Unclassified", "accession": "4DNSR5R3TLWS", "@type": ["Biosource", "Item"], "uuid": "c672da47-5283-4892-b626-f261e426f8df", "display_title": "Drosophila embryo - 4DNSR5R3TLWS", "@id": "/biosources/4DNSR5R3TLWS/", "organism": {"scientific_name": "Drosophila melanogaster", "@type": ["Organism", "Item"], "display_title": "D. melanogaster", "status": "released", "@id": "/organisms/7227/", "name": "fruit fly", "uuid": "b3911449-1b28-44cf-af23-084ae4eff147", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["embryonic organism"], "uuid": "94a7d7e3-b38e-462a-91e6-55df4a2c120f", "display_title": "embryo", "preferred_name": "embryo", "term_name": "embryo", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0000922", "@id": "/ontology-terms/UBERON:0000922/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "embryo"}}, "processed_files": [], "last_modified": {"date_modified": "2021-01-25T23:21:27.020671+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES1U49MZQ/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "2c9571ac-7c1d-4a10-b1a8-85b3a92b0daf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES1U49MZQ", "external_references": [], "produced_in_pub": {"authors": ["Chen H", "Levo M", "Barinov L", "Fujioka M", "Jaynes JB", "Gregor T"], "@id": "/publications/53073dd7-84ec-4abd-aa88-a33342685eef/", "title": "Dynamic interplay between enhancer-promoter topology and gene activity.", "ID": "PMID:30038397", "short_attribution": "Chen H et al. (2018)", "url": "https://www.ncbi.nlm.nih.gov/pubmed/30038397", "uuid": "53073dd7-84ec-4abd-aa88-a33342685eef", "abstract": "A long-standing question in gene regulation is how remote enhancers communicate with their target promoters, and specifically how chromatin topology dynamically  relates to gene activation. Here, we combine genome editing and multi-color live  imaging to simultaneously visualize physical enhancer-promoter interaction and transcription at the single-cell level in Drosophila embryos. By examining transcriptional activation of a reporter by the endogenous even-skipped enhancers, which are located 150 kb away, we identify three distinct topological  conformation states and measure their transition kinetics. We show that sustained proximity of the enhancer to its target is required for activation. Transcription in turn affects the three-dimensional topology as it enhances the temporal stability of the proximal conformation and is associated with further spatial compaction. Furthermore, the facilitated long-range activation results in transcriptional competition at the locus, causing corresponding developmental defects. Our approach offers quantitative insight into the spatial and temporal determinants of long-range gene regulation and their implications for cellular fates.", "display_title": "Chen H et al. (2018) PMID:30038397", "journal": "Nature genetics", "date_published": "2018-09", "@type": ["Publication", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"uuid": "53073dd7-84ec-4abd-aa88-a33342685eef", "ID": "PMID:30038397", "date_published": "2018-09", "@type": ["Publication", "Item"], "display_title": "Chen H et al. (2018) PMID:30038397", "journal": "Nature genetics", "@id": "/publications/53073dd7-84ec-4abd-aa88-a33342685eef/", "status": "current", "title": "Dynamic interplay between enhancer-promoter topology and gene activity.", "abstract": "A long-standing question in gene regulation is how remote enhancers communicate with their target promoters, and specifically how chromatin topology dynamically  relates to gene activation. Here, we combine genome editing and multi-color live  imaging to simultaneously visualize physical enhancer-promoter interaction and transcription at the single-cell level in Drosophila embryos. By examining transcriptional activation of a reporter by the endogenous even-skipped enhancers, which are located 150 kb away, we identify three distinct topological  conformation states and measure their transition kinetics. We show that sustained proximity of the enhancer to its target is required for activation. Transcription in turn affects the three-dimensional topology as it enhances the temporal stability of the proximal conformation and is associated with further spatial compaction. Furthermore, the facilitated long-range activation results in transcriptional competition at the locus, causing corresponding developmental defects. Our approach offers quantitative insight into the spatial and temporal determinants of long-range gene regulation and their implications for cellular fates.", "authors": ["Chen H", "Levo M", "Barinov L", "Fujioka M", "Jaynes JB", "Gregor T"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"display_title": "MS2-tagged endogenous eve transcript and enhancer (fruit fly) targeted by mTagBFP2-labeled MCP", "status": "released", "@id": "/imaging-paths/a2c6894c-62e5-4aec-9574-8cdf83578b2f/", "uuid": "a2c6894c-62e5-4aec-9574-8cdf83578b2f", "@type": ["ImagingPath", "Item"], "labeled_probe": "MCP", "target": [{"feature_mods": [{"mod_type": "MS2"}], "organism_name": "fruit fly", "display_title": "MS2-tagged endogenous eve transcript and enhancer (fruit fly)", "preferred_label": "MS2-tagged endogenous eve transcript and enhancer", "@id": "/bio-features/d0001702-1345-4a94-b63d-7f7f715da483/", "uuid": "d0001702-1345-4a94-b63d-7f7f715da483", "status": "released", "@type": ["BioFeature", "Item"], "feature_type": {"preferred_name": "gene", "status": "released", "@id": "/ontology-terms/SO:0000704/", "term_url": "http://purl.obolibrary.org/obo/SO_0000704", "display_title": "gene", "term_id": "SO:0000704", "term_name": "gene", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"preferred_symbol": "eve", "geneid": "36039", "status": "released", "uuid": "dfc2c7b6-0369-4c66-b49d-a6207e53e860", "display_title": "eve", "@type": ["Gene", "Item"], "@id": "/genes/36039/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}, {"path": {"display_title": "PP7-tagged transcript from homie (no promoter) cassette (engineered reagent) targeted by mKate2-labeled PCP", "status": "released", "@id": "/imaging-paths/cf8c204f-48b6-457b-bbbb-b1a662d76825/", "uuid": "cf8c204f-48b6-457b-bbbb-b1a662d76825", "@type": ["ImagingPath", "Item"], "labeled_probe": "PCP", "target": [{"feature_mods": [{"mod_type": "PP7"}], "organism_name": "engineered reagent", "display_title": "PP7-tagged transcript from homie (no promoter) cassette (engineered reagent)", "preferred_label": "PP7-tagged transcript from homie (no promoter) cassette", "@id": "/bio-features/09197d78-30f9-4f79-aac4-a87cc8807804/", "uuid": "09197d78-30f9-4f79-aac4-a87cc8807804", "status": "released", "@type": ["BioFeature", "Item"], "feature_type": {"preferred_name": "transcript", "status": "released", "@id": "/ontology-terms/SO:0000673/", "term_url": "http://purl.obolibrary.org/obo/SO_0000673", "display_title": "transcript", "term_id": "SO:0000673", "term_name": "transcript", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}, {"path": {"display_title": "ParS-tagged homie (no promoter) cassette (engineered reagent) targeted by eGFP-labeled ParB", "status": "released", "@id": "/imaging-paths/74a3f9e2-9996-4f4b-a90b-640a928ed3b4/", "uuid": "74a3f9e2-9996-4f4b-a90b-640a928ed3b4", "@type": ["ImagingPath", "Item"], "labeled_probe": "ParB", "target": [{"feature_mods": [{"mod_type": "ParS"}], "organism_name": "engineered reagent", "display_title": "ParS-tagged homie (no promoter) cassette (engineered reagent)", "preferred_label": "ParS-tagged homie (no promoter) cassette", "@id": "/bio-features/94b506f7-253a-4231-9da0-ed0481f1c4aa/", "uuid": "94b506f7-253a-4231-9da0-ed0481f1c4aa", "status": "released", "@type": ["BioFeature", "Item"], "feature_type": {"preferred_name": "gene", "status": "released", "@id": "/ontology-terms/SO:0000704/", "term_url": "http://purl.obolibrary.org/obo/SO_0000704", "display_title": "gene", "term_id": "SO:0000704", "term_name": "gene", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch02"}], "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}