{"ID": "PMID:30886393", "lab": {"title": "Alistair Boettiger, STANFORD", "display_title": "Alistair Boettiger, STANFORD", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "@id": "/labs/alistair-boettiger-lab/", "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"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/30886393", "award": {"name": "external-award", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center_title": "External", "project": "External", "description": "Funding source is from outside 4DN.", "status": "current", "center": "External", "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "status": "current", "aliases": ["alistair-boettiger-lab:publication_ORCA"], "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "journal": "Nature", "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.", "date_created": "2022-05-20T08:49:57.022331+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-03-15T13:06:47.789938+00:00"}, "date_published": "2019-04", "public_release": "2022-06-22", "schema_version": "2", "project_release": "2022-06-22", "exp_sets_prod_in_pub": [{"experimentset_type": "replicate", "display_title": "4DNESEC7D1AH", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "872f56e5-e0f3-42f3-9b71-0137155a1a34", "status": "released", "@id": "/experiment-set-replicates/4DNESEC7D1AH/", "accession": "4DNESEC7D1AH", "experiments_in_set": [{"@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXHCD7KS2/", "display_title": "multiplexed FISH on embryo - 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