Fig. 4

VPA induces DHSS at retrotransposon elements. a Genomic distribution of DHSS with respect to repeat regions (defined by RepeatMasker [http://www.repeatmasker.org]). In cases where the same DHSS overlapped several repeats, the overlap with the greatest length was chosen. b Genomic distribution of SINEs overlapping non-induced (non-i) DHSS (leftmost bar), VPA-induced (VPA-i) DHSS (mid bar), and all SINEs (rightmost bar), with respect to RefSeq gene models. c Over-representation of forkhead motifs in induced SINE DHSS compared to all other DHSS. For each JASPAR forkhead motif, the number of matches (obtained using the TFBS toolkit) with at least 80 % similarity were compared between the two groups using one-tailed Wilcoxon rank-sum test. In all cases, p < 1.5e−16. d Overlap between SINEs and Foxa2 binding sites in mouse liver. “non-induced (non-i)/VPA-induced (VPA-i) SINEs” indicates DHSS clusters that overlap SINEs, and “non-induced/induced n.o. SINEs” indicates clusters that do not overlap SINEs. “Top 50 VPA SINEs/n.o. SINEs” indicates the 50 VPA DHSS clusters with highest DHSS tag count in the VPA-i sample, which do or do not overlap SINEs, respectively. e Genome browser view of the 3′ end of the Hectd1 gene (NM_144788), indicating an overlap between VPA DHSS, SINEs and Foxa2 binding sites