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(2019)", "uuid": "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.", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "journal": "Nature", "date_published": "2019-04", "@type": ["Publication", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2019-04", "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "@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.", "@type": ["Publication", "Item"], "ID": "PMID:30886393", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "short_attribution": "Mateo LJ et al. (2019)", "status": "current", "journal": "Nature", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "29 mRNAs and nascent RNAs (fruit fly), 52 consecutive 3-kb loci in the BX-C region (fruit fly)", "combined": "Target: 29 mRNAs and nascent RNAs (fruit fly), 52 consecutive 3-kb loci in the BX-C region (fruit fly)"}, "experiment_summary": "multiplexed FISH on embryo", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}