Recent signatures of transcription in <i>de novo</i> genes.

<p><b>a)</b> Overrepresented transcription factor binding sites (TFBS) in the region -100 to 0 with respect to the transcription start site (TSS) in <i>de novo</i> genes. The region from -300 to +300 with respect to the TSS was analysed (n = 3,875). Color code relates to normalized values (highest value is yellow). <b>b)</b> Fine-grained motif density 200bp upstream of the TSS is shown. <b>c)</b> Comparison of motif density in genomic syntenic regions in macaque for <i>de novo</i> transcripts (n = 3,116) and conserved transcripts (n = 4,323, randomly taken human and chimpanzee annotated transcripts not classified as <i>de novo</i>). Significant differences between human/chimpanzee and macaque are indicated; Fisher-test; *, p-value < 0.05; **, p-value < 0.01. <b>d)</b> Density of the main human transposable elements (TE) families around the TSS of <i>de novo</i> and conserved transcripts. Regions -3 kB to +3 kB with respect to the TSS were analyzed. LTR frequency is higher in the region -100 to +100 in de novo genes when compared to conserved genes (Fisher-test p-value < 10⁻¹⁸). <b>e)</b> Comparison of motif density in promoters with and without long terminal repeat (LTR) in the region -500 to 0 with respect to the TSS. Significant differences in motif density in the -100 bp window are indicated. <b>f)</b> Signatures of transcription elongation in <i>de novo</i> and conserved genes. Density of U1 and PAS motifs in the 500bp region upstream and downstream of the TSS. Comparison of U1 and PAS motif density in genomic syntenic regions in macaque for <i>de novo</i> transcripts (n = 3,116) and conserved transcripts (n = 4,323). There is an increase of U1 motifs in <i>de novo</i> transcripts when compared to macaque (indicated by a black arrow, Fisher-test, p-value = 0.016 for the region +100 to +200).