{"lab": {"uuid": "bcf64dc2-a84f-47a2-bd72-5800512d86ee", "@id": "/labs/lacramioara-bintu-lab/", "correspondence": [{"contact_email": "bGJpbnR1QHN0YW5mb3JkLmVkdQ==", "@id": "/users/8fee1ce2-a289-44a0-861f-a4657e20e103/", "display_title": "Lacra Bintu"}], "status": "current", "title": "Lacramioara Bintu, STANFORD", "@type": ["Lab", "Item"], "display_title": "Lacramioara Bintu, STANFORD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.bcf64dc2-a84f-47a2-bd72-5800512d86ee"]}}, "award": {"center_title": "Bintu", "name": "1U01DK127419-01", "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. 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(2023) doi:10.1101/2023.10.03.560616", "status": "current", "@type": ["Publication", "Item"], "abstract": "Repressive chromatin modifications are thought to compact chromatin to silence  transcription. However, it is unclear how chromatin structure changes during  silencing and epigenetic memory formation. We measured gene expression and  chromatin structure in single cells after recruitment and release of repressors  at a reporter gene. Chromatin structure is heterogeneous, with open and compact  conformations present in both active and silent states. Recruitment of repressors  associated with epigenetic memory produces chromatin compaction across 10-20  kilobases, while reversible silencing does not cause compaction at this scale.  Chromatin compaction is inherited, but changes molecularly over time from histone  methylation (H3K9me3) to DNA methylation. The level of compaction at the end of  silencing quantitatively predicts epigenetic memory weeks later. Similarly,  chromatin compaction at the Nanog locus predicts the degree of stem-cell fate  commitment. These findings suggest that the chromatin state across tens of  kilobases, beyond the gene itself, is important for epigenetic memory formation.", "@id": "/publications/109b2954-d7d8-43a2-b7a2-83e3fddaa5dc/", "authors": ["Fujimori T", "Rios-Martinez C", "Thurm AR", "Hinks MM", "Doughty BR", "Sinha J", "Le D", "Hafner A", "Greenleaf WJ", "Boettiger AN", "Bintu L"], "ID": "doi:10.1101/2023.10.03.560616", "uuid": "109b2954-d7d8-43a2-b7a2-83e3fddaa5dc", "journal": "bioRxiv : the preprint server for biology", "date_published": "2023-10-05", "short_attribution": "Fujimori T et al. (2023)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2023-10-05", "abstract": "Repressive chromatin modifications are thought to compact chromatin to silence  transcription. However, it is unclear how chromatin structure changes during  silencing and epigenetic memory formation. We measured gene expression and  chromatin structure in single cells after recruitment and release of repressors  at a reporter gene. Chromatin structure is heterogeneous, with open and compact  conformations present in both active and silent states. Recruitment of repressors  associated with epigenetic memory produces chromatin compaction across 10-20  kilobases, while reversible silencing does not cause compaction at this scale.  Chromatin compaction is inherited, but changes molecularly over time from histone  methylation (H3K9me3) to DNA methylation. The level of compaction at the end of  silencing quantitatively predicts epigenetic memory weeks later. Similarly,  chromatin compaction at the Nanog locus predicts the degree of stem-cell fate  commitment. These findings suggest that the chromatin state across tens of  kilobases, beyond the gene itself, is important for epigenetic memory formation.", "journal": "bioRxiv : the preprint server for biology", "status": "current", "short_attribution": "Fujimori T et al. (2023)", "display_title": "Fujimori T et al. (2023) doi:10.1101/2023.10.03.560616", "title": "Single-cell chromatin state transitions during epigenetic memory formation.", "uuid": "109b2954-d7d8-43a2-b7a2-83e3fddaa5dc", "ID": "doi:10.1101/2023.10.03.560616", "@type": ["Publication", "Item"], "authors": ["Fujimori T", "Rios-Martinez C", "Thurm AR", "Hinks MM", "Doughty BR", "Sinha J", "Le D", "Hafner A", "Greenleaf WJ", "Boettiger AN", "Bintu L"], "@id": "/publications/109b2954-d7d8-43a2-b7a2-83e3fddaa5dc/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "Chromosomes, Custom genome assembly (pJT039-chr19 insert)", "combined": "Target: Chromosomes, Custom genome assembly (pJT039-chr19 insert)"}, "experiment_summary": "multiplexed FISH on 293T", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSC1OEAOP/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}