{"ID": "PMID:34591592", "lab": {"correspondence": [{"contact_email": "bGNhaUBjYWx0ZWNoLmVkdQ==", "@id": "/users/5b7ed4cb-4848-4eee-9dd5-75edde523b0f/", "display_title": "Long Cai"}], "@type": ["Lab", "Item"], "title": "Long Cai, CALTECH", "status": "current", "@id": "/labs/long-cai-lab/", "display_title": "Long Cai, CALTECH", "uuid": "6384bbb3-d82f-4584-8a6a-4b4e7c988d14", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6384bbb3-d82f-4584-8a6a-4b4e7c988d14"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/34591592", "award": {"description": "RT-CDF: Cellular differentiation involves tightly coupled changes in gene expression, chromatin state, and sub-nuclear arrangements of chromosomes. 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. The technology developed in this project can be readily implemented in human cell lines and adopted by other labs in the 4DN consortium.", "name": "1U01DK127420-01", "status": "current", "display_title": "DYNAMICS OF CHROMOSOME ORGANIZATION AND CHROMATIN STATES IN SINGLE CELLS", "project": "4DN", "center_title": "Cai", "uuid": "795c8991-3773-440d-bb4c-4cf69105adfb", "@type": ["Award", "Item"], "@id": "/awards/1U01DK127420-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Single-cell nuclear architecture across cell types in the mouse brain.", "status": "current", "aliases": ["long-cai-lab:publication_DNA_seqFISH_plus_brain"], "authors": ["Takei Y", "Zheng S", "Yun J", "Shah S", "Pierson N", "White J", "Schindler S", "Tischbirek CH", "Yuan GC", "Cai L"], "journal": "Science (New York, N.Y.)", "abstract": "Diverse cell types in tissues have distinct gene expression programs, chromatin states, and nuclear architectures. To correlate such multimodal information across thousands of single cells in mouse brain tissue sections, we use integrated spatial genomics, imaging thousands of genomic loci along with RNAs and epigenetic markers simultaneously in individual cells. We reveal that cell type-specific association and scaffolding of DNA loci around nuclear bodies organize the nuclear architecture and correlate with differential expression levels in different cell types. At the submegabase level, active and inactive X chromosomes access similar domain structures in single cells despite distinct epigenetic and expression states. This work represents a major step forward in linking single-cell three-dimensional nuclear architecture, gene expression, and  epigenetic modifications in a native tissue context.", "date_created": "2022-05-16T12:29:14.205103+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-06-16T12:27:50.001381+00:00"}, "date_published": "2021-10-29", "public_release": "2022-06-16", "schema_version": "2", "static_content": [{"content": {"content_as_html": "<div class=\"markdown-container\"><p>This dataset was initially published on Zenodo (doi: <a href=\"https://doi.org/10.5281/zenodo.4708112\" rel=\"noopener noreferrer\" target=\"_blank\">10.5281/zenodo.4708112</a>) in a lab-specified format. \nData in the 4DN portal is derived from the same experiments, but has been formatted according to the 4DN standard <a href=\"https://fish-omics-format.readthedocs.io/en/latest/\" rel=\"noopener noreferrer\" target=\"_blank\">FOF-CT</a>.</p></div>", "status": "released", "uuid": "85ff334a-2647-41f8-8e3b-f3d67d332183", "options": {"filetype": "md", "collapsible": false, "default_open": true}, "display_title": "takei-zenodo-brain", "@type": ["StaticSection", "UserContent", "Item"], "award": {"status": "current", "@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "content": "This dataset was initially published on Zenodo (doi: [10.5281/zenodo.4708112](https://doi.org/10.5281/zenodo.4708112)) in a lab-specified format. \nData in the 4DN portal is derived from the same experiments, but has been formatted according to the 4DN standard [FOF-CT](https://fish-omics-format.readthedocs.io/en/latest/).", "lab": {"uuid": "6384bbb3-d82f-4584-8a6a-4b4e7c988d14", "@id": "/labs/long-cai-lab/", "display_title": "Long Cai, CALTECH", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6384bbb3-d82f-4584-8a6a-4b4e7c988d14"]}}, "filetype": "md", "@id": "/static-sections/85ff334a-2647-41f8-8e3b-f3d67d332183/", "name": "takei-zenodo-brain", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}}, "location": "tab:attribution"}], "project_release": "2022-06-16", "exp_sets_prod_in_pub": [{"status": "released", "accession": "4DNES53WJMNL", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES53WJMNL/", "display_title": "4DNES53WJMNL", "uuid": "497d7102-4fcd-4788-b41d-f3577c74ab59", "experiments_in_set": [{"uuid": "59fa8ecd-0748-451b-976b-911cf7928de4", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXWI45RB4/", "status": "released", "display_title": "multiplexed FISH on cerebral cortex - 4DNEXWI45RB4", "experiment_type": {"title": "multiplexed FISH", "@id": "/experiment-types/multiplexed-fish/", "status": "released", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "display_title": "multiplexed FISH", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "7e9e5cce-a2f1-4b2e-895c-d8df929ad06d", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEX3SA9WZZ/", "status": "released", "display_title": "multiplexed FISH on cerebral cortex - 4DNEX3SA9WZZ", "experiment_type": {"title": "multiplexed FISH", "@id": "/experiment-types/multiplexed-fish/", "status": "released", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "display_title": "multiplexed FISH", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "4d9624dd-20c8-4c57-b6c3-02bfd073a66d", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXELZLJ72/", "status": "released", "display_title": "multiplexed FISH on cerebral cortex - 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