Mateo, L. J. et al. Nature https://doi.org/10.1038/s41586-019-1035-4 (2019).

The 3D organization of the genome and how it relates to gene expression are fundamental questions in biology. This regulation may be especially important in embryos, where the timing and nature of gene expression are crucial for proper development. Mateo et al. have developed optical reconstruction of chromatin architecture (ORCA), a method that uses Oligopaint probes to label the genome with resolution reaching two kilobases. The probes are tiled over the genome sequentially to enable 3D reconstruction of genomic organization. The method can be combined with single-molecule RNA fluorescence in situ hybridization to examine gene expression in the same cells. The researchers used ORCA to study genome organization in Drosophila embryos, where they observed Polycomb-independent borders between active and Polycomb-repressed DNA, the deletion of which led to aberrant gene expression and developmental defects.