Visualizing DNA folding and RNA in embryos at single-cell resolution

Mateo, Leslie J.; Murphy, Sedona E.; Hafner, Antonina; Cinquini, Isaac S.; Walker, Carly A.; Boettiger, Alistair N.

doi:10.1038/s41586-019-1035-4

Cited by 458Genomics and Chromatin DynamicsEpigenetics and DNA MethylationAdvanced Fluorescence Microscopy Techniques

Visualizing DNA folding and RNA in embryos at single-cell resolution

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Mateo, Leslie J., Murphy, Sedona E., Hafner, Antonina, Cinquini, Isaac S., Walker, Carly A., Boettiger, Alistair N.·2019·Nature

DOI 10.1038/s41586-019-1035-4PMC PMC6556380

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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.

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The frequency of enhancer-promoter contacts may have non-linear effects on transcriptional output.
“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]
In “Cis contacts predict transcription” (page unavailable), the paper reports that enhancer–promoter proximity weakly predicts whether nascent transcription is present. It does not establish how contact frequency affects the amount of transcription or show a non-linear relationship, so that part of the attributed claim is unsupported. (LLM, conf=0.83)
Experimental — accuracy not yet measured
Advances in super-resolution imaging enable visualisation of multiple interacting loci to the resolution of a few kilobases in single cells.
“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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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.
ORCID: Mateo, Leslie J.
Murphy, Sedona E.
Hafner, Antonina
Boettiger, Alistair N.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2019-03-18
Volume: 568
Issue: 7750
Pages: 49-54
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-019-1035-4
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 · 2018: 1
FWCI: 19.68
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

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Visualizing DNA folding and RNA in embryos at single-cell resolution

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