Fig. 1

Erasure of an epigenetic TAD signature. a Representation of the dac TAD. Hi-C score maps around the dac gene locus in Drosophila embryos [12]. Dac TAD and neighboring TADs are indicated by a black triangle. Below ChIP-seq tracks and RNA-seq track of late embryos are shown (modENCODE). b CUT&RUN profiles for H3 K27 me3 in Drosophila embryos and larval imaginal leg discs from WT flies or Double PRE mutant flies. The left panel shows the dac domain; the right panel shows a neighboring H3 K27 me3 domain (esg/sna genes) which is unaffected by the perturbations. c Hi-C score maps of a 1 Mb kb region (upper panel) or 200 kb region (lower panel) around the dac TAD in WT or Double PRE mutant imaginal leg discs. Dac domain is indicated by a black triangle. PRE loop by a black circle. Violet bars indicate the position of PREs. Gray bars indicate the position of the TAD boundary. Black arrows indicate the promoters of the dac and the CG5888 genes. d Insulation profile shown at 3 kb resolution along the dac 200 kb region in larval WT and Double PRE mutant leg discs is shown as the mean value (line) ± the standard deviation (shaded area) over the insulation scores (IS) computed using 5 different values of the window parameter (w = 100, 150, 200, 250, and 300 kb, see the “Methods” section). eP-values from the comparisons of insulation scores (IS) at the left and right TAD border between the WT and double PRE mutant line (see the “Methods” section). The p-values resulted from a two-sided Welch t-test between the WT condition and the double PRE mutant at the corresponding locus. f Differential Hi-C scores maps (double PRE mutant vs. WT) of a 150 kb region of the dac gene in third instar imaginal leg disc (see Methods). Red regions indicate higher contacts in Double PRE mutant; blue regions indicate higher contacts in WT. Black circle indicates the position of the PRE loop. Violet bars indicate the position of PREs. Black arrows indicate the promoters of the dac and the CG5888 genes. g Quantification of the dac PRE loop Hi-C interaction scores in WT (n = 172) and double PRE (n = 92) mutant flies. Reported p-values result from comparing the WT and double PRE mutant distributions using the unpaired two-sided Wilcoxon statistical test. The number of points per boxplot (bottom) is reported (see the “Methods” section). Boxplots show median (central line), Q1 = 25 th and Q3 = 75 th percentiles (box limits), and Q1 + 1.5 × IQR to Q3 + 1.5 × IQR (wiskers), where IQR is the interquartile range