Figure 3—figure supplement 2.

(A) Heatmaps showing ATAC-seq peaks divided into predicted high-confidence enhancers with H3K27ac CUT&RUN enrichment in ≥3 of four individual replicates, lower-confidence enhancers with pooled H3K27ac CUT&RUN enrichment, and non-enhancers lacking H3K27ac enrichment. (B) Proportion of predicted homeologous enhancers that are flanked upstream and downstream by homeologous genes (at least one of the five nearest genes up/downstream). Only high-confidence enhancers that lift over to the other subgenome were considered. (C) Heatmaps of later-stage ATAC-seq (Esmaeili et al., 2020) and H3K27ac CUT&RUN coverage (this study) plotted over predicted enhancers and homeologous regions. (D) Similar to Figure 3C, maps comparing all (high and lower confidence) predicted enhancer density near homeologous TSSs (middle). Differential predicted enhancers are active in only one subgenome, conserved predicted enhancers are active in both. Average densities are plotted to the right of each paired map. Gene pairs are sorted according to L versus S subgenome RNA-seq activation ratio (right). Differential predicted enhancer density correlates with differential homeolog RNA-seq expression (p=1.0 × 10^–30, Pearson’s correlation test), while conserved predicted enhancer density does not (p=0.06). (E) Maternal (stage 5) RNA-seq levels for L and S sequence-specific transcription factors, as annotated by Gene Ontology. pou5f3.3 and sox3 are the top expressed transcription factors for both L and S. pou5f3.2 is also maternally contributed at lower levels. pou5f3.1 is not maternal.