Visualizing DNA folding and RNA in embryos at single-cell resolution
Establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. Our understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription remains limited. Here we describe op...
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ftpubmed:oai:pubmedcentral.nih.gov:6556380 2023-05-15T17:53:30+02:00 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. 2019-03-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556380/ http://www.ncbi.nlm.nih.gov/pubmed/30886393 https://doi.org/10.1038/s41586-019-1035-4 en eng http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556380/ http://www.ncbi.nlm.nih.gov/pubmed/30886393 http://dx.doi.org/10.1038/s41586-019-1035-4 Reprints and permission information is available at www.nature.com/reprints (http://www.nature.com/reprints) . Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms Article Text 2019 ftpubmed https://doi.org/10.1038/s41586-019-1035-4 2019-09-22T00:11:37Z Establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. Our understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription remains limited. Here we describe optical reconstruction of chromatin architecture (ORCA), a method to trace the DNA path in single cells with nanoscale accuracy and genomic resolution reaching 2 kilobases. We applied ORCA to a Hox gene cluster in cryosectioned Drosophila embryos and labelled ~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, reveal domain structures that change with cell identity, and show that border elements contribute to formation of physical domains in Drosophila. Text Orca PubMed Central (PMC) Nature 568 7750 49 54 |
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Article Mateo, Leslie J. Murphy, Sedona E. Hafner, Antonina Cinquini, Isaac S. Walker, Carly A. Boettiger, Alistair N. Visualizing DNA folding and RNA in embryos at single-cell resolution |
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Establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. Our understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription remains limited. Here we describe optical reconstruction of chromatin architecture (ORCA), a method to trace the DNA path in single cells with nanoscale accuracy and genomic resolution reaching 2 kilobases. We applied ORCA to a Hox gene cluster in cryosectioned Drosophila embryos and labelled ~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, reveal domain structures that change with cell identity, and show that border elements contribute to formation of physical domains in Drosophila. |
format |
Text |
author |
Mateo, Leslie J. Murphy, Sedona E. Hafner, Antonina Cinquini, Isaac S. Walker, Carly A. Boettiger, Alistair N. |
author_facet |
Mateo, Leslie J. Murphy, Sedona E. Hafner, Antonina Cinquini, Isaac S. Walker, Carly A. Boettiger, Alistair N. |
author_sort |
Mateo, Leslie J. |
title |
Visualizing DNA folding and RNA in embryos at single-cell resolution |
title_short |
Visualizing DNA folding and RNA in embryos at single-cell resolution |
title_full |
Visualizing DNA folding and RNA in embryos at single-cell resolution |
title_fullStr |
Visualizing DNA folding and RNA in embryos at single-cell resolution |
title_full_unstemmed |
Visualizing DNA folding and RNA in embryos at single-cell resolution |
title_sort |
visualizing dna folding and rna in embryos at single-cell resolution |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556380/ http://www.ncbi.nlm.nih.gov/pubmed/30886393 https://doi.org/10.1038/s41586-019-1035-4 |
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Orca |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556380/ http://www.ncbi.nlm.nih.gov/pubmed/30886393 http://dx.doi.org/10.1038/s41586-019-1035-4 |
op_rights |
Reprints and permission information is available at www.nature.com/reprints (http://www.nature.com/reprints) . Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
op_doi |
https://doi.org/10.1038/s41586-019-1035-4 |
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Nature |
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