(A) UPGMA tree based on the expression level of 13,832 genes in 4 sample pools. The numbers at the nodes indicate node stability in 1,000 bootstraps over genes. (B) The gene expression divergence between sample pairs plotted against the species divergence time. The box plot represents variation of the divergence estimated from 1,000 bootstraps over genes (same set of genes as (A), see Materials and Methods). (C) The upper panels show genomic annotation of nucleotides covered by at least one sequence read within all HTR identified in at least one sample (Total) and HTR with species-specific expression. Genomic locations of species-specific HTR are listed in Table S8. The lower panels show genomic annotation of nucleotides covered by at least one sequence read within all genomic windows (Total) and genomic windows with species-specific expression. Locations of species-specific genomic windows are listed in Table S10. The colors represent: exons (green), intronic repeats (orange), introns (light orange), intergenic repeats (blue), and intergenic regions (light blue). (D) An example of a genomic window with human-specific expression.

(A) Outer circle: average proportions of transcriptome sequence reads from the two human samples that map within annotated exons (green), introns (light orange), intronic repeats (orange), intergenic repeats (blue), intergenic regions (light blue), mitochondrial DNA (purple), and ncRNA (maroon). Middle circle: the proportions occupied by the corresponding regions in the human genome. Inner circle: the proportions of transcriptome sequence reads for polyadenylated human brain RNA (data adopted from [26]). (B) The transcriptional activity of repeat families located within introns (orange) or intergenic regions (blue) plotted against the total genomic length occupied by the family (see Materials and Methods for details). The labels indicate the repeat families with elevated expression levels. (C and D) The expression levels of twelve TE families normalized by the total genomic length of the corresponding family (C) and by the length corresponding to expressed repeats (D), plotted against their age rank. The expression level 95% confidence intervals are calculated by 1,000 bootstraps over sequence reads. The age rank and the corresponding confidence intervals are plotted according to [39]. Higher age rank corresponds to evolutionary younger TE families.

(A) Examples of igHTR. The black track shows sequence reads density (in counts) in the four samples studied. The blue tracks show human EST density and PhastCon scores. (B) igHTR categories. The inner circle shows the proportion of igHTR with (red) or without (blue) EST support. The outer circle shows proportions of igHTR with protein-coding potential (green), supported by lincRNA (blue) or EvoFold (light blue) ncRNA predictions, adjacent to gene's 5′-UTR (light orange) or 3′-UTR (orange), and uncharacterized igHTR (grey) among EST-supported and non-supported igHTR. (C) Expression levels within intergenic regions (blue), genic regions including both exons and introns (light orange), exons (green), and igHTR (red). (D) Sequence conservation of nucleotides in human exons, genic regions, intergenic regions, and igHTR (all colors as on the panel (C)) based on phastCon scores among 18 placental vertebrates genomes. PhastCon scores close to 1 indicate high conservation. The heights of the bars show mean value and error bars show 95% confident intervals based on sampling of the same number of nucleotides as located within igHTR from the corresponding genomic regions 1,000 times. For igHTR, the values are based on all nucleotides located within them. (E) Size distributions of igHTR in the two human samples (red - Human1, blue - Human2), annotated human exons (grey), and exonic HTR (black) (F) Distributions of genomic distances between nearest pairs of igHTR (red – Human1, blue – Human2), annotated exons (black), and simulated randomly distributed igHTR (grey). The dashed line shows 10 kb distance. (G) Examples of splicing within igHTR clusters (red) and between annotated genes (blue) and downstream igHTR supported by EST (green).