Differential Evolution of MAGE Genes Based on Expression Pattern and Selection Pressure

<div><p>Starting from publicly-accessible datasets, we have utilized comparative and phylogenetic genome analyses to characterize the evolution of the human MAGE gene family. Our characterization of genomic structures in representative genomes of primates, rodents, carnivora, and macroscelidea indicates that both Type I and Type II MAGE genes have undergone lineage-specific evolution. The restricted expression pattern in germ cells of Type I MAGE orthologs is observed throughout evolutionary history. Unlike Type II MAGEs that have conserved promoter sequences, Type I MAGEs lack promoter conservation, suggesting that epigenetic regulation is a central mechanism for controlling their expression. Codon analysis shows that Type I but not Type II MAGE genes have been under positive selection. The combination of genomic and expression analysis suggests that Type 1 MAGE promoters and genes continue to evolve in the hominin lineage, perhaps towards functional diversification or acquiring additional specific functions, and that selection pressure at codon level is associated with expression spectrum.</p> </div

Summary of protein-coding MAGE homologs in each genome.

<p>Summary of protein-coding MAGE homologs in each genome.</p

MAGE gene family expansion along evolution.

<p>Numbers in brackets are number of total MAGE genes detected in the genome. Type I MAGEs emerged after marsupial.</p

Selection pressure on cancer/testis (CT) antigen genes between human-chimpanzee orthologs.

<p>(A), Comparison of Ka/Ks ratios between testis-restricted and testis-selective CT genes. To increase the data entry points, the Ka/Ks ratio is given an arbitrary constant of 3 for Ka/Ks = ∞ which has a Ks = 0. The mean or median of Ka/Ks is significantly higher in the testis-restricted group (<i>P</i> = 0.0001 in Mann-Whitney test) than the testis-selected group. (B), Comparison of Ka/Ks ratios for testis-selective genes located on the X chromosome and on autosomes shows no difference (<i>P</i> = 0.69 by Mann-Whitney test).</p

Phylogenetic trees of MAGEs.

<p>Two clades are formed: one by Type I MAGE genes; the other by Type II MAGE genes. A, Evolution tree of MAGEs in primates. Gene identifier prefixes with species: h stands for human, c for chimpanzee, o for orangutan and r for rhesus. B, Evolution tree of MAGEs in human and rodents. Rodent gene identifier prefixes with m (stands for mouse) or rat. Genes all in capital letters are from human. The MAGEA subfamily is the most divergent between human and rodents by forming monophyletic clusters of Human A and Rodent A. *, rhesus MAGEB16 however is clustered with MAGEC subfamily (see text). In addition to the conserved MAGEC cluster, new Magec(s) derived from Magea exist in rodents labeled as Rodent C. Trees shown are bootstrap consensus tree with 50% cutoff.</p

Amino acids estimated under positive selection in genes of the MAGEA subfamily.

<p>Codon alignment of human MAGEA genes is used as the reference backbone. *, sites under positive selection predicted by at least two methods as presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048240#pone-0048240-t003" target="_blank">Table 3</a>.</p

Likelihood ratio tests for variable selection pressures among lineages.

<p>Reject one-ratio model <i>P</i><0.001 (2δ = 289.46, df = 79); reject neutral model <i>P</i><0.001 (2δ = 14.30, df = 1)</p

Synteny of Type I MAGE clusters on chromosome X among human, mouse and dog.

<p>Approximate coordinates on the X chromosome are labeled under each cluster including MAGEA, MAGEB and MAGEC subfamilies. Arrows represent gene orientation. Anchor genes for synteny other than MAGE genes are represented by orange arrows; copies of MAGE genes are represented by blue arrows; pseudogenes are shown as in white/open arrows. *: gene recruited from unmapped scaffolds in dog genome integrated with phylogeny analysis. Naming of MAGE genes shown are based on RefSeq entries.</p

Likelihood ratio tests for positive selection on specific sites by PAML and HyPhy.

<p>#seq, number of nucleotide sequence entries used in the multi-alignments. Length, nucleotide sequence length in alignment. PSS, positive-selected site, predicted by FEL with cutoff of <i>P</i><0.05, REL with cutoff of <i>P</i>>0.90 or BEB posterior probability (in M8 by PAML) of <i>P</i>>0.90. p1 is proportion of sites in the class with ω>1 and ω1 is the estimate of ω for that class. Numbers in parentheses are codon positions in the alignment. Df, degree of freedom in the LRT. Only significant <i>P</i> values in the LRT are presented in bold.*, positive selected sites predicted by different methods are overlapping.</p