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Visualizing DNA folding and RNA in embryos at single-cell resolution
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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.
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“It also follows from these models that the frequency of enhancer–promoter contacts may have non-linear effects on transcriptional output, consistent with experimental observations [405, 503].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [503]
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“advances in super-resolution imaging (reviewed in [500]) now enable the visualisation of multiple interacting loci to the resolution of a few kilobases in single cells [448, 501–503].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [503]
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Self-citation
Metadata
- Authors
- Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., & Boettiger, A. N.
- Affiliations
- Stanford University (US)
- Corresponding author
- Boettiger, Alistair N.
- Venue
- Nature
- Published
- 2019-03-18
- Volume
- 568
- Issue
- 7750
- Pages
- 49-54
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6556380
- OpenAlex
- W2921773684
- Cited by
- 446
- References
- 62
- Citations by year
- 2026: 43 · 2025: 53 · 2024: 57 · 2023: 61 · 2022: 59 · 2021: 71 · 2020: 68 · 2019: 31
- FWCI
- 19.68
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health (1dp2gm132935-01)
- National Institute of General Medical Sciences (DP2 GM132935)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Keywords
- DNA folding, chromatin structure, polycomb repressive complex, Hox gene clusters, Drosophila embryo, enhancer-promoter interactions, RNA localization, developmental gene regulation, transcriptional repression
- MeSH terms
- Animals, Chromatin, DNA, Drosophila melanogaster, Enhancer Elements, Genetic, Female, Genes, Homeobox, Multigene Family, Male, Nucleic Acid Conformation, Organ Specificity, Promoter Regions, Genetic, RNA, Transcription, Genetic, Gene Expression Regulation, Developmental, Genome, Insect, Single-Cell Analysis, Polycomb-Group Proteins
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