Extended Data Fig. 2: doc genes are highly co-expressed and doc CRMs spatially cluster, as do CRMs in the sna locus.

a, RNA-FISH staining for doc1, doc2 and doc3 in late nc14 embryos. Scale bars: 50 𝜇m/ 5 𝜇m (inset). b, Percentage of one or two active transcription sites/nuclei for doc1 and doc2. c. Percentage of cells displaying active transcription spots from 2-color RNA-FISH imaging of doc1-doc2 and doc2-doc3. Most nuclei (>70%) displayed co-activation of doc1 + doc2 and of doc2 + doc3. For this latter, a larger percentage of nuclei expressed only doc2 (~40%), because of the low efficiency of labeling of doc3 nascent mRNA (small intronic size). d, Comparison of contact maps from nuclei displaying at least one active doc1 RNA-FISH spot (top right matrix) and from a subset (33%) of nuclei displaying the strongest doc1 RNA-FISH signals. e, 4 M profiles derived from Hi-M maps of dorsal ectoderm cells in nc14. f, 4 M virtual profile for nuclei displaying at least one active doc1 RNA-FISH spot (solid pink line) and from a subset of nuclei (33%) with the highest doc1 signals (dashed dark pink). g, Epigenetic profile of selected regions around the esg and sna genes within the sna-TAD. Accessibility (ATAC-seq), pioneer factor binding (Zelda), transcriptional activity (RNA-seq), chromatin marks for active enhancers marks (H3K4me1), and for the transcriptional activators Dorsal, Zen and Mad are shown. A subset of barcodes were annotated as cis-regulatory modules (shown in cyan): CRM₁₆₉ harbors the canonical H3K4me1 active enhancer mark; CRM₁₆₀, and shadow sna enhancer were described in the RedFly database. Magenta barcode harbours the esg promoter and the blue barcode contains the sna promoter and its primary enhancer. See Supplementary Table 1 for more details. h, Hi-M contact probability map of the sna locus. Yellow arrow shows interactions between CRMs, red arrow between CRMs and promoters, and green arrow between promoters. i, Multi-way interactions between promoters (panels (i-iii) and CRMs (panels iv-vi). Number of nuclei and embryos examined as in panel r. j, 3D topological representation of the sna-TAD. Bead colors are as in panel d. Barcode 44 contains the wor promoter.