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Understanding and controlling differentiation requires understanding how each of these processes occurs dynamically within the same cell and how they influence one another. Existing techniques can provide genome scale analysis of interactions or spatial organization of a few chromosomal positions. However, we have lacked a generalizable framework for simultaneous reconstruction of the overall dynamics of the nucleus across all three levels. Recent work from our labs has opened up the possibility of achieving such coupled analysis. Our track first, identify later approach allows many DNA to be simultaneously tracked in living cells. RNA and DNA seqFISH allows a large number of transcripts and DNA loci to be imaged in single fixed cells and MEMOIR allows lineage information to be recovered from endpoint measurements. In this project, we propose to combine live imaging, multiplexed RNA, DNA, and immunofluorescence measurements, and MEMOIR lineage tracking to capture whole- genome dynamics of chromosomal loci and chromatin states. Using mouse embryonic stem cells (mESCs) as a model system, we will study the transition from the pluripotent state to an earlier 2- cell (2C) like state which shows drastic chromosome re-arrangement and changes in nascent gene expression patterns. In addition, we will study the chromosomal dynamics of X-inactivation based on the initial observations that sister X chromosomes are in contact with each other during early phases of the inactivation process. Both of these biological questions require tracking chromosomal dynamics and chromatin state simultaneously in single cells. The \u201cTrack First and ID later\u201d approach allows a large number of loci to be tracked in living cells. The combined MEMOIR approach with multiplex immunofluorescence allows us to infer the kinetics of chromatin states transitions. Bringing these tools to study X inactivation and 2C state transition will demonstrate the capability of this approach for addressing a broad range of cell fate decision questions. We will also develop analysis and visualization tools to integrate genomics (SPRITE) and imaging data. 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These loci form 'fixed points' in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies  and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states.  Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3-4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems.", "short_attribution": "Takei Y et al. (2021)", "ID": "PMID:33505024", "date_published": "2021-02", "authors": ["Takei Y", "Yun J", "Zheng S", "Ollikainen N", "Pierson N", "White J", "Shah S", "Thomassie J", "Suo S", "Eng CL", "Guttman M", "Yuan GC", "Cai L"], "title": "Integrated spatial genomics reveals global architecture of single nuclei.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"uuid": "04e04160-bbda-4e5b-8d34-3e9c8f460e97", "@id": "/publications/04e04160-bbda-4e5b-8d34-3e9c8f460e97/", "ID": "PMID:36593410", "display_title": "Jia BB et al. (2023) PMID:36593410", "journal": "Nature biotechnology", "@type": ["Publication", "Item"], "short_attribution": "Jia BB et al. 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We  demonstrate that this spatial genome aligner can efficiently model chromosome  architectures from DNA FISH data across multiple scales and be used to predict  chromosome ploidies de novo in interphase cells. Reprocessing of previous  whole-genome chromosome tracing data with this method indicates the spatial  aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse  embryonic stem cells and provides evidence for extranumerary chromosomes that  remain tightly paired in postmitotic neurons of the adult mouse cortex.", "authors": ["Jia BB", "Jussila A", "Kern C", "Zhu Q", "Ren B"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "745502f5-4f9b-41f5-afb4-a8e95d317e58", "@id": "/publications/745502f5-4f9b-41f5-afb4-a8e95d317e58/", "ID": "PMID:33505024", "display_title": "Takei Y et al. (2021) PMID:33505024", "journal": "Nature", "@type": ["Publication", "Item"], "short_attribution": "Takei Y et al. (2021)", "date_published": "2021-02", "title": "Integrated spatial genomics reveals global architecture of single nuclei.", "abstract": "Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies(1-4). Because individual cells appear to be highly variable at all these levels(5), it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence  marks in single mouse ES cells. These loci form 'fixed points' in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies  and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states.  Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3-4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems.", "authors": ["Takei Y", "Yun J", "Zheng S", "Ollikainen N", "Pierson N", "White J", "Shah S", "Thomassie J", "Suo S", "Eng CL", "Guttman M", "Yuan GC", "Cai L"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "70 RNAs (mouse), 7 genomic regions, 17 proteins, Chromosomes", "combined": "Target: 70 RNAs (mouse), 7 genomic regions, 17 proteins, Chromosomes"}, "experiment_summary": "multiplexed FISH on ES-E14TG2a.4", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSX8YDEJ7/", "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": []}