Extended Data Fig. 12: Enhancer switching is a prominent feature of development.

a. Heatmap showing 458 enhancers that undergo a switch from one cell type to another. Enhancers are grouped based on whether the switch is from (non)neuronal to (non)neuronal. Heatmap shows standardized average accessibility (RPGC): ET: early timepoints (larva-12h APF), MT: middle timepoints (24-48h APF), LT: late timepoints (72h APF-adult). b. Examples of enhancers that switch between cell types for different categories. Given that one region can contain multiple enhancers, it is hard to separate enhancer switches from shifters: the glia enhancer (right) shows a shift, where one peak goes down and an adjacent one becomes accessible. c. t-SNE from the cisTopic analysis on the subset of 18 cell types used for the deep learning (DL) analysis. d. Performance of the DL model for the different topics. e. Examples of topics linked to progenitor cell types (left) and to Kenyon cell subtypes (right).  f. TF-MoDISco results for topics linked to progenitors (left) and to Kenyon cells (right), highlighting motifs of TFs expressed in those cell types. The motif for Ase shows negative nucleotide importances, suggesting a chromatin repressing role. g. CG15117 enhancer switches from ensheathing glia (ENS) to T1 neurons. h. Bar plots showing predicted scores of the region for the developmental and adult DL model. i-j. DeepExplainer plot and in-silico mutagenesis plots of the CG15117 enhancer calculated with (i) adult DL model and (j) development DL model. According to the models, the enhancer is repressed in adult ensheathing glia and developing T1 neurons by the same binding site (highlighted with orange box).