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

Leslie J. Mateo, Sedona E. Murphy, Antonina Hafner, Isaac S. Cinquini, Carly A. Walker and Alistair N. Boettiger ()
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Leslie J. Mateo: Stanford University
Sedona E. Murphy: Stanford University
Antonina Hafner: Stanford University
Isaac S. Cinquini: Stanford University
Carly A. Walker: Stanford University
Alistair N. Boettiger: Stanford University

Nature, 2019, vol. 568, issue 7750, 49-54

Abstract: 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: 2019
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DOI: 10.1038/s41586-019-1035-4

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