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Figure 4 | BMC Genomics

Figure 4

From: Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

Figure 4

Pairwise analysis of Dichaete binding site turnover. (A) Quantitative differences in Dichaete binding between D. melanogaster and D. simulans. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. simulans (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. simulans clustered by binding affinity scores. The color key and histogram shows the distribution of binding affinity scores (log of normalised read counts) in all bound intervals in each sample. Darker green corresponds to higher affinity scores or stronger binding, while lighter green corresponds to lower affinity scores or weaker binding. Roughly equal numbers of intervals are preferentially bound in each species. (B) Quantitative differences in Dichaete binding between D. melanogaster and D. yakuba. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. yakuba (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. yakuba clustered by binding affinity scores. The color key and histogram are as in (A). Again, rough equal numbers of intervals are preferentially bound in each species, although more differentially bound intervals are identified overall. (C) Example of Dichaete binding site turnover between D. melanogaster (blue) and D. yakuba (orange) at the reduced ocelli (rdo) locus. Binding profiles represent the normalised log2 fold changes between Dichaete-Dam binding and Dam-only control binding in each GATC fragment. Bars represent bound intervals identified at FDR5. Bound intervals that are positionally conserved are not shown. Strong binding is observed in the third, fourth and eleventh introns in D. yakuba; these binding events are lost in D. melanogaster, but several binding intervals are gained in the first and fourth introns.

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