Extended Data Fig. 7: Extensive pleiotropic effects across the E3N enhancer.
From: Dense and pleiotropic regulatory information in a developmental enhancer
a, b, Plot comparing the percent of lines with pleiotropic or ectopic expression versus the number of mutations based on antibody staining (a) and Beta-Galactosidase staining (b). c–j, A subset of mutants with pleiotropic effects. (c) Line 145-2 drives ectopic expression in the developing wing and haltere discs (7/7 embryos). (d) Line 139-6 drives wider stripes and increased expression, as well as ectopic expression between the stripes and (e) on the dorsal side, (5/5 embryos). (f) Line 40-8 drives a split stripe pattern, where the middle row of nuclei within the stripes is not active (6/6 embryos). (g) Line 93-4 expression varies along the anterior-posterior axis (5/5 embryos). (h) Line 77-9 drives ectopic expression in the salivary glands (5/5 embryos). (i) Line 81-7 drives expression in the developing mouth hooks (5/5 embryos.) (j) Line 15-2v activates expression at stage 10 and drives ectopic expression throughout the embryo in multiple developmental stages (14/14 embryos). k, Plot of footprinting scores versus E3N sequence. Magenta is the footprinting score (σi, see methods). The higher the peak, the higher probability that a mutation will change expression. Gray plots are the mutation coverage for the number of lines screened per base (Mi, see methods). l, EWAC scores represent p-values from a log of odds ratio test for the association of a mutation changing expression. Dashed lines denote p- and q-values11, respectively. See Materials and Methods. m, Plot comparing the percent of lines with changed expression for mutations in the overlapping Pan/Hth site. n, Quantification of the staining intensities in the stripe and naked domains with the indicated reporter construct using the “sliding window” technique (Extended Data Fig. 3e). N = the number of embryos per line measured, from left to right: 10, 10, 7, 9, 10, 7, 10, 6, 10, 8, 4, 8, 10, 10, 10. In box plots, centre line is mean, upper and lower limits are standard deviation and whiskers show 95% CIs. Scale bars, 100 μm. Embryos are matched to scale (c – j).
