{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/thomas-gregor-lab/", "status": "current", "display_title": "Thomas Gregor, PRINCETON", "title": "Thomas Gregor, PRINCETON", "correspondence": [{"contact_email": "dGcyQHByaW5jZXRvbi5lZHU=", "@id": "/users/e46f310b-2ed3-4b05-8d78-37456688a86d/", "display_title": "Thomas Gregor"}], "uuid": "41cedc04-1e04-423a-8d08-0fc181409ee7", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.41cedc04-1e04-423a-8d08-0fc181409ee7"]}}, "award": {"@type": ["Award", "Item"], "display_title": "IMAGING CHROMOSOME DYNAMICS AND MEASURING ITS IMPACT ON TRANSCRIPTIONAL ACTIVITY", "uuid": "4a3ea2f9-864b-429d-9948-54dbe0d7958d", "name": "1U01EB021239-01", "center_title": "IT - Gregor", "status": "current", "project": "4DN", "@id": "/awards/1U01EB021239-01/", "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.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "status": "released", "aliases": ["thomas-gregor-lab:Kruppel_2colorBlock_B7_experiment_160301_oreR_Kr2colorBlock_13"], "protocol": {"uuid": "e29027dd-f39c-4348-8d18-c0ebac087959", "@type": ["Protocol", "Item"], "display_title": "FISH_Protocol.txt", "status": "released", "@id": "/protocols/e29027dd-f39c-4348-8d18-c0ebac087959/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX5R8XBPD", "biosample": {"@id": "/biosamples/4DNBSLGDCQX6/", "biosource_summary": "Fruit fly (Oregon-R) embryo - NC13", "display_title": "4DNBSLGDCQX6", "modifications_summary": "None", "@type": ["Biosample", "Item"], "uuid": 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"track_and_facet_info": {"experimental_lab": "Thomas Gregor, PRINCETON", "experiment_type": "RNA FISH", "experiment_bucket": "processed file", "assay_info": "8' region of knuppel mRNA (fruit fly), Chromosomes", "dataset": "Dual color smFISH on fruit fly embryo (nuclear cycle 13)", "condition": "Target: wt kruppel mRNA", "replicate_info": "Biorep 7, Techrep 1", "biosource_name": "Fruit fly (Oregon-R) embryo - NC13", "lab_name": "Thomas Gregor, PRINCETON"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "project_release": "2019-12-02", "biosample_quantity": 1.0, "microscopy_technique": "Confocal Laser Scanning", "biosample_quantity_units": "cells", "microscope_settings_master": {"uuid": "50754cf8-bc9e-4709-9b33-a4af88d0dd99", "display_title": "MicroscopeSettingA2 from 2019-11-05", "@type": ["MicroscopeSettingA2", "MicroscopeSetting", "Item"], "@id": "/microscope-settings-a2/50754cf8-bc9e-4709-9b33-a4af88d0dd99/", "status": 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(2018) PMID:30340044", "title": "Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting.", "uuid": "593bf7fe-80fb-4d11-b065-ec23012a1b50", "@id": "/publications/593bf7fe-80fb-4d11-b065-ec23012a1b50/", "ID": "PMID:30340044", "@type": ["Publication", "Item"], "status": "current", "abstract": "How transcriptional bursting relates to gene regulation is a central question that has persisted for more than a decade. Here, we measure nascent transcriptional activity in early Drosophila embryos and characterize the variability in absolute activity levels across expression boundaries. We demonstrate that boundary formation follows a common transcription principle: a single control parameter determines the distribution of transcriptional activity, regardless of gene identity, boundary position, or enhancer-promoter architecture. We infer the underlying bursting kinetics and identify the key regulatory parameter as the fraction of time a gene is in a transcriptionally active state. Unexpectedly, both the rate of polymerase initiation and the switching rates are tightly constrained across all expression levels, predicting  synchronous patterning outcomes at all positions in the embryo. These results point to a shared simplicity underlying the apparently complex transcriptional processes of early embryonic patterning and indicate a path to general rules in transcriptional regulation.", "journal": "Cell", "authors": ["Zoller B", "Little SC", "Gregor T"], "short_attribution": "Zoller B et al. 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Unexpectedly, both the rate of polymerase initiation and the switching rates are tightly constrained across all expression levels, predicting  synchronous patterning outcomes at all positions in the embryo. These results point to a shared simplicity underlying the apparently complex transcriptional processes of early embryonic patterning and indicate a path to general rules in transcriptional regulation.", "date_published": "2018-10-18", "display_title": "Zoller B et al. (2018) PMID:30340044", "uuid": "593bf7fe-80fb-4d11-b065-ec23012a1b50", "journal": "Cell", "ID": "PMID:30340044", "@id": "/publications/593bf7fe-80fb-4d11-b065-ec23012a1b50/", "short_attribution": "Zoller B et al. 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