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Figure 6 | Genome Biology

Figure 6

From: The genomic landscape shaped by selection on transposable elements across 18 mouse strains

Figure 6

Densities of intergenic TEVs in the proximity of gene boundaries. (a) Densities of TEVs (full lines) or of TEs from the reference C57BL/6J assembly (dashed lines) 5' of genes' transcriptional start sites (left panels) or 3' of genes' transcriptional stop sites (right panels). The top two panels represent TEVs and TEs that occur in the transcriptional sense orientation, whereas the bottom two panels represent those present in the antisense orientation. For each family, the densities of TEVs (y-axis) present within distance bins (x-axis) from the gene are shown relative to the TEV density observed. Bin sizes were selected from the Fibonacci series, which allowed improved visualization of TEV densities compared to linear or logarithmic scales. All TEVs and TEs are depleted in close proximity to the 5' of genes, but SINEs are enriched upstream (approximately 500 bp to 10 kbp) of genes. No significant effects of TEV orientation on density distributions in the vicinity of genes were observed. (b) Densities of intronic TEVs in the proximity of exon boundaries. Densities of intronic TEVs (full lines) or of TEs from the reference C57BL/6J assembly (dashed lines) 5' of exons (left panels) or 3' of exons (right panels). The top two panels represent TEVs and TEs that occur in the transcriptional sense orientation, whereas the bottom two panels represent those present in the antisense orientation. For each family, the densities of TEVs (y-axis) present within distance bins (x-axis) from the gene are shown relative to the TEV density observed. Bin sizes were selected from the Fibonacci series, which allowed improved visualization of TEV densities compared to linear or logarithmic scales. A difference in density profiles of sense and antisense TEVs is observed in proximity to exon boundaries.

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