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. 2019 Oct 21;8:e48216. doi: 10.7554/eLife.48216

Figure 4. Patterns of TF binding site enrichment across retinal cell classes.

Motif enrichment patterns identified in bipolar and photoreceptor ATAC-seq datasets as well as in DNase-seq datasets from adult mouse whole retina, brain, heart, and liver. This analysis included all enhancer (i.e., TSS-distal) open chromatin peaks from each cell class or tissue. Each panel is centered on a 1 kb window around peaks from the indicated dataset. Motif density (motifs per base pair per 1000 peaks) is shown on the Y-axis. Consensus sequences for each motif class and example TFs (in parentheses) expressed in photoreceptors and bipolar cells are shown on the right. Photoreceptor and bipolar cell populations share enrichment for K50 HD motifs, while only photoreceptors show enrichment for Q50 HD motifs.

Figure 4.

Figure 4—figure supplement 1. Enrichment of motif pairs in photoreceptors and bipolar cells.

Figure 4—figure supplement 1.

(A) Scatterplot comparing the difference in proportion of enhancer peaks containing motif pairs in photoreceptors and bipolar cells. Each point corresponds to a distinct motif pair generated by taking all pairs from a list of 67 non-redundant motifs from the HOMER database (see Materials and methods). Statistically significant differences in the proportion of peaks harboring each pair are indicated in red (greater proportion in photoreceptors) or green (greater proportion in bipolar cells) (Fisher's exact test, FDR < 0.01). Motif pairs with the most significant difference in proportion (by p-value) are indicated and include individual motifs which are highly differentially enriched between the two cell classes, including K50 HD (GSC), Q50 HD (LHX3), and E-box (SCL). (B) Scatterplot as in A, showing the proportion of motif pairs within photoreceptor or bipolar cell-enriched peak sets (as defined in Figure 5A). (C) Scatterplot as in A and B, comparing the difference in proportion of motif pairs between enhancer peaks in ON and OFF bipolar cells. Motif pairs with statistically significant differences in proportion are indicated in purple (greater proportion in ON BC) or gold (greater proportion in OFF BC) (Fisher's exact test, FDR < 0.01).
Figure 4—figure supplement 2. Motif spacing and orientation in photoreceptor and bipolar cells.

Figure 4—figure supplement 2.

Peaks from photoreceptors (left) and bipolar cells (right) are centered on K50 HD (A) or Q50 HD motifs (B). Per base-pair counts for secondary motifs (PWM and example TFs shown at the far right) are plotted in a 100 bp window surrounding the primary motif, with counts on the plus strand shown in red, and the minus strand shown in blue. The y-axis was limited to ± 100.