Extended Data Figure 5: Long-range interactions in Drosophila.

a, Zoom-in of the 4C-seq transformed and fitted counts around the apterous (ap) viewpoint (mesoderm 6–8 h). The first fragments around the viewpoint are not included in the monotone fit (red line). b, Frequency of the first identified interaction (green) and the first valid fragment (red) as a function of distance to their respective viewpoints. c, 4C interaction map of the unc-5 and sli loci^52,53. An interaction (blue arrowhead) between the viewpoint (red arrowhead) and the promoter of sli, over half a megabase away, is observed. Inset shows a zoomed-in view of the sli promoter. The location of significant 4C interactions and known enhancers is represented below. WE, whole embryo. d, Double in situ hybridization showing the overlap between sli (green) and unc-5 (red) heart expression (arrowhead) at stage 14. e, 4C interaction map at the scyl and chrb loci²³. Independent of the location of the viewpoint (red arrowhead), the same interacting regions are recovered (blue arrowheads). The location of known enhancers is represented below. The two cloned regions are indicated as ‘new enhancer’ 1 and 2, respectively. WE, whole embryo. f, A non-parametric two-sample Kolmogorov–Smirnov test was used to assess the significance of differences between DNA FISH distance distributions. g, Double in situ hybridization of the chrb gene (red) and the expression driven by two of its interacting regions (green) at stage 11 and 14, showing that both regions recapitulate part of the expression of chrb. The overlap (shown by a white arrowhead) is located in the trunk visceral mesoderm and later in the longitudinal visceral mesoderm for enhancer 1 and in the central nervous system for enhancer 2. New enhancer 1 is overlapping a ChIP-defined CRM (CRM4311), whereas new enhancer 2 is partially overlapping (<10%) an enhancer in the sgs3 locus. Neither region was previously identified as charybde enhancers, and their spatio-temporal activity during development was unknown.