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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.", "short_attribution": "Mateo LJ et al. (2019)", "status": "current", "ID": "PMID:30886393", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"ID": "PMID:30886393", "short_attribution": "Mateo LJ et al. (2019)", "date_published": "2019-04", "display_title": "Mateo LJ et al. 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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. 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