{"lab": {"uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@id": "/labs/alistair-boettiger-lab/", "title": "Alistair Boettiger, STANFORD", "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "award": {"uuid": "b7c5d0c8-053e-4da3-b446-b68787a5a738", "status": "current", "center_title": "Bintu", "description": "RT-CDF: Chromatin structure and transcription regulation are essential for cellular function, and their dynamics are highly correlated both in development and in disease. However, despite decades of amazing work identifying the molecular players involved in these processes, and mapping their interactions genome-wide, we are currently unable to describe the function connecting 3D chromatin structure and transcription dynamics. This limitation stems from the fact that chromatin structure and gene expression emerge from intrinsically stochastic transitions at the single-cell level, and we are missing the critical temporal parameters associated with these transitions. Therefore, new tools to measure both chromatin structure and transcription over time in single cells are critical for understanding how the human genome is read and for predictively controlling the epigenome. Here, we propose to develop a new set of live single-cell imaging technologies to simultaneously measure changes in 3D chromatin structures and their associated dynamics of gene expression across a large range of timescales: from dynamics of individual topologically associated domains and enhancer-promoter interactions, to changes associated with stable epigenetic memory across cell cycles. For the shorter timescales (under a cell cycle), our new imaging approach combines live super-resolution microscopy of fluorescently labeled loci with end-point demultiplexing of loci identity using Optical Reconstruction of Chromatin Architecture (ORCA), in order to track and trace 3-12 points within a functional chromatin unit. This new technique, which we call live-ORCA, will allow us to measure for the first time the temporal dynamics of an entire topologically associated domain in single cells. We will use live-ORCA in conjunction with time-lapse imaging of transcriptional bursting to study the dynamics of promoter-enhancer activity throughout cell differentiation and under perturbations of the chromatin network. For the longer timescale (across multiple cell cycles), our approach will combine time-lapse microscopy of gene expression, monitoring the distance between two tagged genomic loci as a live reporter of chromatin structure, and end-point chromatin tracing of the entire gene neighborhood using ORCA. We will perform these measurements in two systems: at a highly controlled synthetic reporter where we can induce either short-term silencing or long-term epigenetic memory, and at time points in differentiation when genes commit epigenetically to a new transcriptional state. Moreover, in order to further investigate the mechanism of epigenetic inheritance, we will develop a novel microfluidic device that allows us to track changes in chromatin 3D structures across individual cell lineages. Finally, to test our quantitative understanding, we will go back and forth between these single-cell data and theoretical modelling of chromatin dynamics. This research plan will greatly advance our understanding of chromatin dynamics and its functional role in transcription regulation, while at the same time contributing a whole new set of novel imaging technologies and engineered cell lines that will serve as a jumping board for the 4D Nucleome and broader scientific community.", "@type": ["Award", "Item"], "@id": "/awards/1U01DK127419-01/", "project": "4DN", "display_title": "LIVE-CELL MULTIPLEX SUPER-RESOLUTION IMAGING OF CHROMATIN STATE TRANSITIONS", "name": "1U01DK127419-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"description": "Issues with replicate numbers", "title": "Replicate Numbers", "@type": ["Badge", "Item"], "@id": "/badges/replicate-numbers/", "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "badge_classification": "Warning", "display_title": "Replicate Numbers", "status": "released", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["alistair-boettiger-lab:FubWT"], "accession": "4DNESWM4U8RX", "condition": "WT at Fub locus, 10-kb resolution", "description": "Optical Reconstruction of Chromatin Architecture (ORCA) of a 700-kb region including the bithorax complex (BX-C) and flanking domains at 10-kb steps in fly embryos that are wild-type at the Fub locus (+/+). 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Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).
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"external_references": []}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESWM4U8RX/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "4362e2b4-83b2-48ab-80fa-88bf9eb9cd97", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESWM4U8RX", "external_references": [], "produced_in_pub": {"url": "https://www.ncbi.nlm.nih.gov/pubmed/30886393", "@id": "/publications/6c007db6-3eba-41d8-9d50-cb7e7c05841f/", "status": "current", "abstract": "The establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. We have a limited understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription. Here we describe optical reconstruction of chromatin architecture (ORCA), a method that can trace the DNA path in single cells with nanoscale accuracy and genomic resolution reaching two kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila embryos and labelled around 30 RNA species in parallel. We identified cell-type-specific physical borders between active and Polycomb-repressed DNA, and unexpected Polycomb-independent borders. Deletion of Polycomb-independent borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and developmental defects. Together, these results illustrate an approach for high-resolution, single-cell DNA domain analysis in vivo, identify domain structures that change with cell identity, and show that border elements contribute to the formation of physical domains in Drosophila.", "ID": "PMID:30886393", "date_published": "2019-04", "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "journal": "Nature", "@type": ["Publication", "Item"], "short_attribution": "Mateo LJ et al. (2019)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "@id": "/publications/6c007db6-3eba-41d8-9d50-cb7e7c05841f/", "abstract": "The establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. We have a limited understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription. Here we describe optical reconstruction of chromatin architecture (ORCA), a method that can trace the DNA path in single cells with nanoscale accuracy and genomic resolution reaching two kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila embryos and labelled around 30 RNA species in parallel. We identified cell-type-specific physical borders between active and Polycomb-repressed DNA, and unexpected Polycomb-independent borders. Deletion of Polycomb-independent borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and developmental defects. Together, these results illustrate an approach for high-resolution, single-cell DNA domain analysis in vivo, identify domain structures that change with cell identity, and show that border elements contribute to the formation of physical domains in Drosophila.", "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "journal": "Nature", "date_published": "2019-04", "status": "current", "ID": "PMID:30886393", "display_title": "Mateo LJ et al. 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