Figure 2.

Features of genomic compartments based on NSUMA coverage and differential methylation (Supplemental Methods; Supplemental Tables S4, S6). (A) Box plot of the number of CpGs within the Alu (blue boxes) and in the 500-bp flanking regions (yellow boxes). Flanking regions have been arranged by CpG content: low to the left and high to the right. Alu repeats unmethylated in all tissues (UNM All) tend to localize in the boundaries of regions with large differences in CpG content (*). Statistical analyses are shown in Supplemental Table S7. (B) Box plot of the genomic distances between Alu repeats classified in different compartments and TSSs, CpG islands, and LINEs. ANOVA P-values for comparisons between Alu repeat subsets are indicated at the bottom of each graph. (C) Transcription factor binding motif enrichment in different subsets of Alu repeats. Full markers correspond to putative binding sites located inside the Alu sequence, and empty markers indicate motifs located within flanking sequences (500 bp).