Extended Data Figure 8: 4C interactions under different developmental conditions.
From: Enhancer loops appear stable during development and are associated with paused polymerase
a, MA plot of interaction signal between whole embryo 6–8 h and mesoderm 6–8 h. b, 4C interaction map at the Antp locus. Top to bottom: H3K4me3 ChIP-seq signal (RPGC) in whole embryo at 0–4 h and 4–8 h (ref. 49) (green), RNA-seq signal (RPKM, black) in whole embryo at 2–4 h and 6–8 h (ref. 9), 4C interaction map (viewpoint, red arrowhead) in whole embryo at 3–4 h (mauve) and 6–8 h (blue). The differential 4C signal is plotted in between in red with significant differential 4C interactions indicated (asterisk). WE, whole embryo. c, Expression (in situ hybridization) of Antp (red) and the expression driven by a new Antp enhancer (green) at stage 11 (6–8 h). The enhancer’s activity overlaps expression of Antp at 6–8 h; however, the 4C contact between the enhancer and promoter is already present, and at even higher levels, at 3–4 h. d, f, Interaction map at the pdm2 (d) and E2f (f) loci. Top to bottom: Pol II signal (RPGC) in mesoderm at 6–8 h (orange)6, RNA-seq signal (RPKM) in mesoderm and whole embryo at 6–8 h (black)9,54, 4C interaction map (viewpoint location, red arrowhead) in mesoderm (light blue) and whole embryo (dark blue) at 6–8 h. The differential 4C signal is plotted in between in red. Note that the 4C interaction is stronger in mesoderm compared to whole embryo, although those genes are not expressed in the mesoderm. Significant 4C interactions and known enhancers are indicated. WE, whole embryo, MESO, mesoderm (generated by FACS sorting). e, g, Expression (double in situ hybridization) of the pdm2 (e) or E2f (g) genes (green) with a mesoderm-specific marker (mef2, red) at stage 11.
