Organization and concerted evolution of the ampliconic Y-chromosomal TSPY genes from cattle

Verkaar, E.L.C.; Zijlstra, C.; Veld, E.M. van 't; Boutaga, Khalil; Boxtel, Dick C.J. van; Lenstra, Johannes A.

doi:10.1016/j.ygeno.2004.05.001

Cited by 19 publications

(11 citation statements)

References 33 publications

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“…1) and supporting the draft sequence assembly and a previous report about the different clusters of the TSPY subfamilies (21). It is important to point out that the number of repeat units on the BTAY varies among individuals and among populations, as evidenced by previous studies on the copy number variations of TSPY, ranging from 45 to ∼200 (21,22).…”

Section: Discussionsupporting

confidence: 76%

Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development

Chang

Yang²,

Retzel

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

118

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The male-specific region of the mammalian Y chromosome (MSY) contains clusters of genes essential for male reproduction. The highly repetitive and degenerative nature of the Y chromosome impedes genomic and transcriptomic characterization. Although the Y chromosome sequence is available for the human, chimpanzee, and macaque, little is known about the annotation and transcriptome of nonprimate MSY. Here, we investigated the transcriptome of the MSY in cattle by direct testis cDNA selection and RNA-seq approaches. The bovine MSY differs radically from the primate Y chromosomes with respect to its structure, gene content, and density. Among the 28 protein-coding genes/families identified on the bovine MSY (12 single- and 16 multicopy genes), 16 are bovid specific. The 1,274 genes identified in this study made the bovine MSY gene density the highest in the genome; in comparison, primate MSYs have only 31–78 genes. Our results, along with the highly transcriptional activities observed from these Y-chromosome genes and 375 additional noncoding RNAs, challenge the widely accepted hypothesis that the MSY is gene poor and transcriptionally inert. The bovine MSY genes are predominantly expressed and are differentially regulated during the testicular development. Synonymous substitution rate analyses of the multicopy MSY genes indicated that two major periods of expansion occurred during the Miocene and Pliocene, contributing to the adaptive radiation of bovids. The massive amplification and vigorous transcription suggest that the MSY serves as a genomic niche regulating male reproduction during bovid expansion.

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Section: Discussionsupporting

confidence: 76%

Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development

Chang

Yang²,

Retzel

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

118

View full text Add to dashboard Cite

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“…Previous studies examining the clustered nature of bovine TSPY have shown conflicting results. Vogel et al [1997a] claim that bovine TSPY is tandemly repeated, while Verkaar et al [2004] claim that it is actually more dispersed. Our fiber-FISH results show the signals arranged in a tight linear sequence, which suggests that bovine TSPY is actually tandemly arranged as it is in humans.…”

Section: Discussionmentioning

confidence: 99%

“…281554) and span the exon 4/exon 5 bor-207 der. This particular area of the gene was used to avoid possible overlap with BRY.2 as described by Verkaar et al [2004]. The SRY primers were designed for the Bos taurus SRY gene sequence (GenBank Accession No.…”

Section: Primer Designmentioning

confidence: 99%

Copy Number Variation of Testis-Specific Protein, Y-Encoded <i>(TSPY)</i> in 14 Different Breeds of Cattle <i>(Bos taurus)</i>

Hamilton

Favetta

Meo

et al. 2009

Sex Dev

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Multi-copied gene families are prevalent in mammalian genomes, especially within the Y chromosome. Testis specific protein Y-encoded (TSPY) is present in variable copy number in many mammalian species. Previous studies have estimated that TSPY ranges from 50–200 copies in cattle. To examine TSPY localization on the Y chromosome we employed fluorescence in situ hybridization (FISH) and fiber-FISH. The results show a strong signal on the short arm of the Y chromosome (Yp). To investigate TSPY copy number we used relative real-time polymerase chain reaction (PCR) to analyze the DNA of 14 different cattle breeds. Variation both within and between breeds was observed. All breeds show significant variation in TSPY copy number among individual members. Brown Swiss (161 copies, CI = 133–195) had higher average levels of TSPY and Western Fjord Cattle (63 copies, CI = 45–86) had lower levels than some breeds. Overall, however, most breeds had a similar average TSPY copy number. The pooled average was 94 copies (CI = 88–100). The significance of the TSPY array remains uncertain, but as the function of TSPY is unraveled the purpose of the array may become clearer.

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“…PCR product smaller than the expected size). Intron-containing pseudogenes have also been reported for TSPY (known as TSPY-C ) [Verkaar et al, 2004] so to avoid amplification of these pseudogenes, the genomic primers used in this study were designed in regions of low sequence similarity between TSPY-C and TSPY . The sex-determining region, SRY , was selected as a single copy Ychromosomal reference gene [Chandler et al, 2007], using primer sets SRY-1 [Hamilton et al, 2009] and SRY-2 [Wang et al, 2010] for trials #1 and #2, respectively.…”

Section: Gene Selection and Primer Designmentioning

confidence: 99%

Testis-Specific Protein Y-Encoded Copy Number Is Correlated to Its Expression and the Field Fertility of Canadian Holstein Bulls

Hamilton

Verduzco-Gomez

Favetta

et al. 2012

Sex Dev

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Testis-specific protein Y-encoded (TSPY) is present in varying copy number in both human (20–76 copies) and cattle (37–200 copies), and some studies have linked this variation to semen quality in men. The purpose of this study was to determine if TSPY copy number is associated with fertility in bulls by using adjusted non-return rates, a commonly used measure of field fertility in Canada. In addition, we investigated the associations between TSPY copy number and its expression as well as specific semen parameters, such as average sperm concentration, sperm count, ejaculate volume, and motility. In 2 independent trials, TSPY copy number was shown to be positively correlated to adjusted non-return rates (trial #1: Spearman r = 0.34, p < 0.05; trial #2: Spearman r = 0.77, p < 0.01). Furthermore, TSPY copy number was inversely correlated to TSPY mRNA expression in the testis (Pearson r = –0.71, p < 0.0001). There were no correlations of TSPY copy number or expression with the semen parameters measured. Therefore, TSPY copy number might represent a potential marker of bull fertility, but its mechanism does not appear to be directly related to the semen characteristics analyzed as part of this study.

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Organization and concerted evolution of the ampliconic Y-chromosomal TSPY genes from cattle

Cited by 19 publications

References 33 publications

Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development

Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development

Copy Number Variation of Testis-Specific Protein, Y-Encoded <i>(TSPY)</i> in 14 Different Breeds of Cattle <i>(Bos taurus)</i>

Testis-Specific Protein Y-Encoded Copy Number Is Correlated to Its Expression and the Field Fertility of Canadian Holstein Bulls

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