title: The expansion of the PRAME gene family in Eutheria.
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.
authors.affiliation: Department of Dairy and Animal Science, The Center for Reproductive Biology and Health, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Ti-Cheng
authors.initials: TC
authors.lastname: Chang
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yasue
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Ernest F
authors.initials: EF
authors.lastname: Retzel
authors.forename: Wan-Sheng
authors.initials: WS
authors.lastname: Liu
mesh_terms: D000818:Animals; D000951:Antigens, Neoplasm / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D002417:Cattle; D019143:Evolution, Molecular; D006801:Humans; D008297:Male; D008958:Models, Molecular; D010802:Phylogeny; D011487:Protein Conformation; D012641:Selection, Genetic; D012689:Sequence Homology, Nucleic Acid; D013087:Spermatids / Q000166:cytology / Q000378:metabolism; D013091:Spermatogenesis; D014998:Y Chromosome / Q000235:genetics
chemical_list: D000951:Antigens, Neoplasm; C404944:PRAME protein, human