Duplication and positive selection among hominin-specific PRAME genes

Abstract

Background: The physiological and phenotypic differences between human and chimpanzee are largely specified by our genomic differences. We have been particularly interested in recent duplications in the human genome as examples of relatively large-scale changes to our genome. We performed an in-depth evolutionary analysis of a region of chromosome 1, which is copy number polymorphic among humans, and that contains at least 32 PRAME (Preferentially expressed antigen of melanoma) genes and pseudogenes. PRAME-like genes are expressed in the testis and in a large number of tumours, and are thought to possess roles in spermatogenesis and oogenesis.

Results: Using nucleotide substitution rate estimates for exons and introns, we show that two large segmental duplications, of six and seven human PRAME genes respectively, occurred in the last 3 million years. These duplicated genes are thus hominin-specific, having arisen in our genome since the divergence from chimpanzee. This cluster of PRAME genes appears to have arisen initially from a translocation approximately 95-85 million years ago. We identified multiple sites within human or mouse PRAME sequences which exhibit strong evidence of positive selection. These form a pronounced cluster on one face of the predicted PRAME protein structure.

Conclusion: We predict that PRAME genes evolved adaptively due to strong competition between rapidly-dividing cells during spermatogenesis and oogenesis. We suggest that as PRAME gene copy number is polymorphic among individuals, positive selection of PRAME alleles may still prevail within the human population.

Figure 1

Dot plot representation [63] of a 0.74 Mb region of human chromosome 1 (bases 1276000–1350000) annotated (below) according to the locations of PRAME genes (blue arrowheads) and pseudogenes (red arrowheads), approximately to scale. Gene or pseudogene orientation is indicated by arrowhead direction. PRAME gene or pseudogene numbers are provided beneath the arrowheads. Single short diagonals represent alignments of two PRAME genes or pseudogenes. Gaps in the assembly (bases 13015219–13065218 and 13302469–13352468) are indicated, on the axes, by thick black bars. Two recent segmental duplications (Homo_7–12 and 15–20, and Homo_19–25 and 26–32; see text) are highlighted in blue and pink, respectively. Regions identified by Sebat et al. [12] or by Iafrate et al. [36], as being copy number polymorphic are indicated by a yellow, or a black-and-yellow-striped, bar, respectively.

Figure 2

Phylogenetic relationships of mouse and human full-length PRAME homologues, inferred using K_S as a distance metric. Mouse PRAME homologues (blue lineages) are monophyletic, as are human PRAME homologues (red lineages).

Figure 3

Phylogenetic relationships of exons A of human and chimpanzee PRAME homologues, inferred using K_S as a distance metric. Phylogenetic relationships derived using alignments of exons B and C are available as Additional files 1 and 2. Homo_9 and Homo_18 are not shown, as these pseudogenes each appears to lack exon A.

Figure 4

Phylogenetic relationships of introns a of human and chimpanzee PRAME homologues, inferred using K>_I as a distance metric, and a neighbour-joining tree. Percentage bootstrap support (1000 iterations) is shown on branches where the support was less than 50%. Phylogenetic relationships derived using an alignment of intron b is available as Additional file 3.

Figure 5

Scatter plot of the lowest neutral rate estimates (either K_S calculated from exon, or K_I for intron, alignments) for human PRAME genes and either their human paralogues (indicated in red) or their chimpanzee orthologues (indicated in black). Circles represent averages of intronic rate (K_I) estimates, whereas squares represent averages of exonic rate (K_S) estimates. The horizontal axis represents genomic location within a 0.74 Mb region of human chromosome 1 (see Figure 1). Two recent segmental duplications (Homo_7–12 and 15–20, and Homo_19–25 and 26–32; see text) are highlighted in blue and pink, respectively. The dark line represents the median K_S value (3.58 × 10^-3) for human paralogues. The grey band identifies 25–75% of this median value (second and third quartiles). The blue line represents the median K_S (0.011) for human-chimpanzee coding sequence [30, 31]. The exonic K_S value for Homo_12 vs Homo_15 is not shown due to incongruencies in K_S-derived phylogenetic trees (see text). Homo-Pan rate estimates are missing when the most-closely related sequences, that are available, are relatively divergent K_I or K_S > 0.1. These missing values are likely to reflect the incompleteness of the current chimpanzee genome assembly. Homo-Homo rate estimates are missing for 4 genes (Homo_1, 3, 5 and 13) which appear not to have duplicated recently (K_I or K_S > 0.1).

Figure 6

Structure of porcine ribonuclease inhibitor (PDB code 2BNH) with amino acid sites that are positively-selected among human and mouse PRAME proteins shown in red and blue, respectively, ((A) front view, (B) rear view).