DUX4-bound motifs are evolutionarily conserved.

<p>(A) DUX4 motifs are conserved among placental mammals. We obtained phylogenetic conservation scores for placental mammals (phyloP scores) via the UCSC genome browser for the top-scoring DUX4 motif in each of the 63,795 DUX4 ChIP-seq peaks, along with scores for 20 bp flanking regions on each side. For each position in the motif, we show the mean phyloP score across all 63,795 motifs (black datapoints) or across just motifs overlapping repetitive elements (gray datapoints). The dashed lines show overall mean scores for the entire motif plus their flanking regions. We use blue and red background shading to indicate the 17 nucleotide positions that comprise the DUX4 motif, with light red shading showing the least variable nucleotide positions of the motif. A sequence logo of the motif is shown above each graph. It is clear that most of the nucleotide positions that are least variable in the DUX4 motif have higher conservation scores than the surrounding positions. (B) DUX4 motifs are conserved among primates. Primate phyloP scores, plotted as in panel A. (C) Common SNPs are under-represented in DUX4-bound motifs. We used the UCSC genome browser to determine the locations of common SNPs (≥1% minor allele frequency) within any of the 63,795 DUX4-bound motifs and their flanking regions. We plot the number of SNPs found at each position in any of the 63,795 DUX4-bound motifs (black datapoints), or in just motifs overlapping repetitive elements (gray datapoints). It is clear that there are fewer SNPs in most of the nucleotide positions that are least variable in the DUX4 motif than in the surrounding positions.