Abstract
The PRAME gene family belongs to the group of cancer/testis genes whose expression is restricted primarily to the testis and a variety of cancers. The expansion of this gene family as a result of gene duplication has been observed in primates and rodents. We analyzed the PRAME gene family in Eutheria and discovered a novel Y-linked PRAME gene family in bovine, PRAMEY, which underwent amplification after a lineage-specific, autosome-to-Y transposition. Phylogenetic analyses revealed two major evolutionary clades. Clade I containing the amplified PRAMEYs and the unamplified autosomal homologs in cattle and other eutherians is under stronger functional constraints; whereas, Clade II containing the amplified autosomal PRAMEs is under positive selection. Deep-sequencing analysis indicated that eight of the identified 16 PRAMEY loci are active transcriptionally. Compared to the bovine autosomal PRAME that is expressed predominantly in testis, the PRAMEY gene family is expressed exclusively in testis and is up-regulated during testicular maturation. Furthermore, the sense RNA of PRAMEY is expressed specifically whereas the antisense RNA is expressed predominantly in spermatids. This study revealed that the expansion of the PRAME family occurred in both autosomes and sex chromosomes in a lineage-dependent manner. Differential selection forces have shaped the evolution and function of the PRAME family. The positive selection observed on the autosomal PRAMEs (Clade II) may result in their functional diversification in immunity and reproduction. Conversely, selective constraints have operated on the expanded PRAMEYs to preserve their essential function in spermatogenesis.
Highlights
Cancer/testis (CT) genes comprise a group of genes involved primarily in immunity and reproduction
Full-length mRNAs of both transcripts were obtained by rapid amplification of cDNA ends (RACE) (Fig. 2)
We found that the PRAME gene family is present only in Eutheria, indicating that this family may have originated de novo in the eutherian lineages [27]
Summary
Cancer/testis (CT) genes comprise a group of genes involved primarily in immunity and reproduction. They are expressed in various types of cancers when abnormally activated, whereas, the normal expression of CT genes is restricted mainly to the testis, but it has been detected in other tissues such as fetal ovary [1,2,3]. Many amplified CT gene families are located within direct or inverted repeats on the sex chromosomes (chrs) [1,4]. The Y-linked TSPY gene family is conserved among most mammalian species, and has 30–60 copies on the human Y-chr [8]
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