Fig. 4

Evolutionary conservation of mouse accessible TEs in the rat and human genome. a The distinct proportion of orthologous mouse accessible TEs in the rat and human genome (left), orthologous mouse background regions in the rat and human genome (middle), and orthologous mouse OCRs without TEs in the rat and human genome (right). b Averaged phastCons score at 10-kb regions centered by accessible TEs (red), OCRs without TEs (blue), gene exon (orange), and intron (gray) in the mouse genome. Accessible TEs showed the lowest phastCons score in the center. c Distinct orthologous conservation of protein-coding genes (left) and lincRNA (right) with TE-derived TSS. In total, 87% of mouse protein-coding genes with TE-derived TSS were ortholog in both human and rat genome, while less than 1% of mouse lincRNAs were ortholog in other two species. d Expression pattern of 117 protein-coding genes with mouse TE-derived TSS in five tissues of mouse and human. e Epigenome browser view of ATAC-seq signals and genome-alignment (mm10, hg38, and rn5) around rodent-specific ORR1A4 TE-derived TSS (left: conserved in mouse and rat) and canonical ortholog TSS (right: conserved in mouse, rat, and human) of Chit1 gene. Top-left: expression pattern of Chit1 in five mouse tissues. Top-right: expression pattern of CHIT1 in five human tissues. ANOVA test: p-value < 0.01