Fig. 3.

Characteristics of ATAC-seq peaks associated with the transition to eye field point to enhancer-driven logic and regulatory roles for canonical EFTFs. (A) Mean and variability of ATAC-seq signal in promoter and non-promoter peaks associated with EF genes. (B) ATAC-seq trajectories of EF-up and EF-down gene promoters, and dynamic non-promoter peaks within EF TADs. (C) TF-motif enrichment analysis of peaks with increasing (y-axis) and decreasing (x-axis) accessibility across the transition from day 3 to day 5. (D) TF-expression/TF-motif-accessibility correlations for peaks within EF-up TADs. Plots on the right and left illustrate the median across positive and negative correlations, respectively, indicative of activator-like and repressor-like behaviour of the respective TFs. (E) Coefficients of the logistic-regression model trained to predict opening versus closing ATAC-seq peaks within EF-up TADs, using the presence of TF motifs as input covariates. The magnitude of coefficients is indicative of the importance of the respective TF motifs for these predictions.