Limits...
The expansion of the PRAME gene family in Eutheria.

Chang TC, Yang Y, Yasue H, Bharti AK, Retzel EF, Liu WS - PLoS ONE (2011)

Bottom Line: The expansion of this gene family as a result of gene duplication has been observed in primates and rodents.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.

View Article: PubMed Central - PubMed

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.

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.

Show MeSH

Related in: MedlinePlus

Expression patterns of PRAME/PRAMEY in cattle.A. RT-PCR results (lanes 2-10). PRAMEY is expressed specifically in the testis, whereas the autosomal PRAME is expressed in the testis (predominantly), kidney, brain and the muscle tissues. Bovine male genomic DNA-specific PCR (lanes 11–12) confirmed that PRAMEY is Y-specific. Te, testis; Li, liver; Ki, kidney; Sp, spleen; Br, brain (cerebrum); Ad, adrenal gland; Mu, muscle; Ly, lymph node; Ov, ovary; ♂, bovine male genomic DNA control; ♀, bovine female genomic DNA control; -, negative control (water); M, 1 kb DNA ladder. B. The expression of the PRAMEY loci by deep-sequencing analysis. The alignment of reads derived from deep-sequencing of selected cDNAs against coding regions of the PRAMEY loci (Table S2) reveals that seven of the 10 active PRAMEY genes are expressed differentially, six of which have significant numbers of both read-pairs matching exactly to the specific loci.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3037382&req=5

pone-0016867-g001: Expression patterns of PRAME/PRAMEY in cattle.A. RT-PCR results (lanes 2-10). PRAMEY is expressed specifically in the testis, whereas the autosomal PRAME is expressed in the testis (predominantly), kidney, brain and the muscle tissues. Bovine male genomic DNA-specific PCR (lanes 11–12) confirmed that PRAMEY is Y-specific. Te, testis; Li, liver; Ki, kidney; Sp, spleen; Br, brain (cerebrum); Ad, adrenal gland; Mu, muscle; Ly, lymph node; Ov, ovary; ♂, bovine male genomic DNA control; ♀, bovine female genomic DNA control; -, negative control (water); M, 1 kb DNA ladder. B. The expression of the PRAMEY loci by deep-sequencing analysis. The alignment of reads derived from deep-sequencing of selected cDNAs against coding regions of the PRAMEY loci (Table S2) reveals that seven of the 10 active PRAMEY genes are expressed differentially, six of which have significant numbers of both read-pairs matching exactly to the specific loci.

Mentions: Two PRAMEY transcripts (PRAMEY1 and PRAMEY2) were identified through a large-scale direct testis cDNA selection using a micro-dissected, PCR amplified BTAY probe. PRAMEY1 is 99% identical to a predicted mRNA (GenBank acc. no. XM_001253165.1) located in a non-annotated bovine bacterial artificial chromosome (BAC) (GenBank acc. no. AC234911.1). This clone was validated as a Y-linked BAC by a male-specific PCR (Fig. 1). PRAMEY2 is 99% identical to an mRNA (GenBank acc. no. NM_001077979) located in a bovine Y-BAC (GenBank acc. no. AC234853.4). Full-length mRNAs of both transcripts were obtained by RACE (rapid amplification of cDNA ends) (Fig. 2). The mRNA of PRAMEY1 (GenBank acc. no. GU144301) is 2747 bp, with an open reading frame (ORF) from nucleotide (nt) 895 to 2436, and it encodes a peptide of 513 amino acids (aa). The mRNA of PRAMEY2 (GenBank acc. no. GU144302) is shorter (1888 bp), with an ORF from nt 104 to 1639, encoding a peptide of 511 aa (Fig. 2). The similarity between the coding regions of PRAMEY1 and PRAMEY2 is 88% at the nucleotide level and 90% at the protein level.


The expansion of the PRAME gene family in Eutheria.

Chang TC, Yang Y, Yasue H, Bharti AK, Retzel EF, Liu WS - PLoS ONE (2011)

Expression patterns of PRAME/PRAMEY in cattle.A. RT-PCR results (lanes 2-10). PRAMEY is expressed specifically in the testis, whereas the autosomal PRAME is expressed in the testis (predominantly), kidney, brain and the muscle tissues. Bovine male genomic DNA-specific PCR (lanes 11–12) confirmed that PRAMEY is Y-specific. Te, testis; Li, liver; Ki, kidney; Sp, spleen; Br, brain (cerebrum); Ad, adrenal gland; Mu, muscle; Ly, lymph node; Ov, ovary; ♂, bovine male genomic DNA control; ♀, bovine female genomic DNA control; -, negative control (water); M, 1 kb DNA ladder. B. The expression of the PRAMEY loci by deep-sequencing analysis. The alignment of reads derived from deep-sequencing of selected cDNAs against coding regions of the PRAMEY loci (Table S2) reveals that seven of the 10 active PRAMEY genes are expressed differentially, six of which have significant numbers of both read-pairs matching exactly to the specific loci.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3037382&req=5

pone-0016867-g001: Expression patterns of PRAME/PRAMEY in cattle.A. RT-PCR results (lanes 2-10). PRAMEY is expressed specifically in the testis, whereas the autosomal PRAME is expressed in the testis (predominantly), kidney, brain and the muscle tissues. Bovine male genomic DNA-specific PCR (lanes 11–12) confirmed that PRAMEY is Y-specific. Te, testis; Li, liver; Ki, kidney; Sp, spleen; Br, brain (cerebrum); Ad, adrenal gland; Mu, muscle; Ly, lymph node; Ov, ovary; ♂, bovine male genomic DNA control; ♀, bovine female genomic DNA control; -, negative control (water); M, 1 kb DNA ladder. B. The expression of the PRAMEY loci by deep-sequencing analysis. The alignment of reads derived from deep-sequencing of selected cDNAs against coding regions of the PRAMEY loci (Table S2) reveals that seven of the 10 active PRAMEY genes are expressed differentially, six of which have significant numbers of both read-pairs matching exactly to the specific loci.
Mentions: Two PRAMEY transcripts (PRAMEY1 and PRAMEY2) were identified through a large-scale direct testis cDNA selection using a micro-dissected, PCR amplified BTAY probe. PRAMEY1 is 99% identical to a predicted mRNA (GenBank acc. no. XM_001253165.1) located in a non-annotated bovine bacterial artificial chromosome (BAC) (GenBank acc. no. AC234911.1). This clone was validated as a Y-linked BAC by a male-specific PCR (Fig. 1). PRAMEY2 is 99% identical to an mRNA (GenBank acc. no. NM_001077979) located in a bovine Y-BAC (GenBank acc. no. AC234853.4). Full-length mRNAs of both transcripts were obtained by RACE (rapid amplification of cDNA ends) (Fig. 2). The mRNA of PRAMEY1 (GenBank acc. no. GU144301) is 2747 bp, with an open reading frame (ORF) from nucleotide (nt) 895 to 2436, and it encodes a peptide of 513 amino acids (aa). The mRNA of PRAMEY2 (GenBank acc. no. GU144302) is shorter (1888 bp), with an ORF from nt 104 to 1639, encoding a peptide of 511 aa (Fig. 2). The similarity between the coding regions of PRAMEY1 and PRAMEY2 is 88% at the nucleotide level and 90% at the protein level.

Bottom Line: The expansion of this gene family as a result of gene duplication has been observed in primates and rodents.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.

View Article: PubMed Central - PubMed

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.

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.

Show MeSH
Related in: MedlinePlus