Fig. 3: cCRE-enriched TF motifs are mostly ancestral except in SINE.
From: Regulatory transposable elements in the encyclopedia of DNA elements
A Calculation of ancestral origin percentage for cCRE-associated TF motifs. For TF motifs found in the TE subfamily consensus sequence (motif #1), percent ancestral origin was calculated as the percentage of motifs in individual TE copies that align to within 10 bp of the consensus motif (dotted line). For TF motifs that are not found in the consensus sequence (motif #2), we assumed that the TE subfamily’s ancestral sequence did not contain the TF motif and all instances of the motif arose through mutation. The mean percentage was taken across all cCRE-associated TF motifs for a TE subfamily to equally weight each TF motif. B Distribution of mean percent ancestral origin of cCRE-associated TF motif for each TE subfamily, separated by TE class. Two-sided Wilcoxon rank-sum test with Benjamini–Hochberg correction was performed to compare percent ancestral origin between observed cCRE-associated TF motifs and randomly selected TF motifs (DNA transposons p-value = 1.17 × 10−8, LINE p-value = 8.71 × 10−8, LTR p-value < 1.1 × 10−15, ERV-int p-value = 0.00668, SINE p-value = 0.863), and to compare percent ancestral origin between TE classes (DNA transposon vs. SINE p-value = 0.0097, LTR vs. LINE p-value = 0.0239, LTR vs. SINE p-value = 0.0002). C Correlation between TE subfamily Kimura divergence and cCRE-associated TF motif percent ancestral origin. R-squared and p-values for each linear regression is shown along with the 95% confidence interval band. The TE subfamily Kimura divergence represents the age of the TE subfamily given the neutral evolution of most TEs. *p < 0.05, **p < 0.01, ***p < 0.001.
