The Human Y Chromosome: The Biological Role of a “Functional Wasteland”

Quintana-Murci, Lluı́s; Fellous, Marc

doi:10.1155/s1110724301000080

Cited by 97 publications

(74 citation statements)

References 62 publications

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“…gene amplification | evolution | transposition | expression T he genomics of the mammalian Y chromosome is poorly characterized compared with that of the X chromosome and autosomes because of the difficulties imposed by the abundance of repetitive sequences and the prevalent notion that the Y chromosome is degenerate with poor gene content and limited transcriptional potential (1). During evolution, the Y chromosome underwent progressive degeneration as a consequence of stepwise cessation of recombination that prevented exchange of sexual differentiation genes between the Y and X chromosomes.…”

Section: Immunologymentioning

confidence: 99%

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: Immunologymentioning

confidence: 99%

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 difference in Alu densities can be attributed to both duplications and deletions in GC-and AT-rich regions, respectively. Assuming that half of the difference is due to Alu duplications in GC-rich DNA, one can calculate that Ϸ15% of all genomic Alu could be added by DNA duplication over Ϸ65 Myrs, in good qualitative agreement with 5-6% of segmental duplications accumulated during the last [30][31][32][33][34][35].…”

Section: Discussionmentioning

confidence: 96%

Duplication, coclustering, and selection of human Alu retrotransposons

Jurka

Kohany

Pavlı́ček

et al. 2004

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

112

110

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Alu and L1 are families of non-LTR retrotransposons representing Ϸ30% of the human genome. Genomic distributions of young Alu and L1 elements are quite similar, but over time, Alu densities in GC-rich DNA increase in comparison with L1 densities. Here we analyze two processes that may contribute to this phenomenon. First, DNA duplications in the human genome occur more frequently in Alu-and GC-rich than in AT-rich chromosomal regions. Second, most Alu elements tend to be coclustered with each other, but recently retroposed elements are likely to be inserted outside the existing clusters. These ''stand-alone'' elements appear to be rapidly eliminated from the genome. We also report that over time, the densities of recently retroposed Alu families on chromosome Y decline rapidly, whereas Alu densities on chromosome X increase relative to autosomal densities. We propose that these changes in the chromosomal proportions of Alu densities and the elimination of stand-alone Alus represent the same process of paternal Alu selection. We also propose that long-term Alu accumulation in GC-rich DNA is associated with DNA duplication initiated by elevated recombinogenic activities in Alu clusters.A lu and L1 are families of non-LTR retrotransposons that have been actively retroposed throughout the evolutionary history of primates (1-3) and together contributed Ϸ30% of the DNA in the human genome (4). Both Alu and L1 elements are transcribed from a limited number of active source genes, reverse transcribed, and integrated to host DNA. The retroposed elements form subfamilies that share characteristic features with their source genes. The Alu source genes are Ϸ300 bp long and GC-rich, whereas L1 source genes are 6-7 kb long and AT-rich. Alu retrotransposition depends on reverse transcriptase encoded by active L1 retroelements (5-9), but the overall chromosomal distributions of Alu and L1 elements are quite different (10-12). L1s tend to be preserved in AT-rich DNA, whereas Alu are more abundant in GC-rich DNA. No standard biological mechanism has so far been able to explain this difference in the retroelement distribution (13,14).It has been shown recently that the chromosomal distributions of young Alu and L1 elements initially resemble each other but, unlike L1, the Alu distribution shifts toward GC-rich DNA over time (4). Based on this GC bias, it has been proposed that originally Alu elements are inserted relatively randomly throughout the genome but over time, they accumulate in GC-rich DNA (4, 15). The accumulation is particularly active for younger Alu, Ͻ5 million years (Myrs) old, but the mechanism of this process involving positive Alu selection in gene-rich regions appears to be controversial (4,16,17).In this paper, we discuss Alu-mediated DNA duplication and selection against young Alus as two basic processes that might have contributed to the postinsertional evolution of Alu distribution. DNA duplications, also known as segmental duplications or low copy repeats, represent Ϸ5% of the human genome and have been stu...

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“…For humans, there are many more X-linked than Y-linked traits because there are far more genes on the X-than on the Y-chromosome. Nevertheless, recent research has shown the significance of Y-linked genes in the biology of humans and other animals, see, for instance, Quintana-Murci and Fellous (2001) or www.nature.com/nature/focus/ychromosome/.…”

Section: Introductionmentioning

confidence: 99%

Limiting genotype frequencies of Y-linked genes through bisexual branching processes with blind choice

Alsmeyer

Gutiérrez

Martínez

2011

Journal of Theoretical Biology

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The limiting genotype growth rates and the limiting genotype frequencies of Y-linked genes are studied in a two-sex monogamous population. To this end, the evolution of the numbers of females, males, and mating units of each genotype is modeled by a multitype bisexual branching process in which it assumed that the gene has no influence on the mating process. It is deduced from this model that the average numbers of female and male descendants per mating unit of a genotype determine its growth rate, which does not depend on the behaviour of the other genotypes. Hence, the dominant genotype is found. Conditions for the simultaneous survival of genotypes to have positive probability are also investigated. Finally, the main results are illustrated by means of examples.

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The Human Y Chromosome: The Biological Role of a “Functional Wasteland”

Cited by 97 publications

References 62 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

Duplication, coclustering, and selection of human Alu retrotransposons

Limiting genotype frequencies of Y-linked genes through bisexual branching processes with blind choice

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