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Nature. 2019 Apr;568(7750):49-54. doi: 10.1038/s41586-019-1035-4. Epub 2019 Mar 18.

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

Author information

1
Department of Developmental Biology, Stanford University, Stanford, CA, USA.
2
Department of Genetics, Stanford University, Stanford, CA, USA.
3
Department of Computer Science, Stanford University, Stanford, CA, USA.
4
Department of Developmental Biology, Stanford University, Stanford, CA, USA. boettiger@stanford.edu.

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.

PMID:
30886393
DOI:
10.1038/s41586-019-1035-4

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