Figure 2. Despite binding motif divergence and general transcriptome divergence, DUX4 transcriptome in mouse muscle cells is enriched for the 2C-like gene signature.

(a) Dux and DUX4 binding motifs as derived de novo from ChIP-seq peaks using MEME algorithm. DUX4 ChIP-seq data was previously published⁶, but re-analyzed using the methods of this study. Note the divergence in the first half of the motif and the conservation of the second half of the motif. E-values listed reflect an estimate of the expected number of motifs, with the given motif’s log likelihood ratio (or higher) and with the same width and site count, that one would find in a similarly sized set of random sequences (where each position in each sequence is independent and letters are chosen according to the background letter frequencies). Histogram to the right shows that 578 peaks out of the 600 used to generate the Dux motif carry a match to the motif and that the motifs are centrally located within each ChIP-seq peak. DUX4 histogram is also shown.

(b) GSEA: gene set is the mouse 2C-like gene signature, x-axis is the log2FoldChange-ranked DUX4 transcriptome in mouse cells. Since the mouse 2C-like gene signature and this DUX4 transcriptome were both identified in mouse cells, neither gene set nor transcriptome was limited to genes with 1:1 mouse-to-human orthology.