MSY2: a slowly evolving minisatellite on the human Y chromosome which provides a useful polymorphic marker in Chinese populations

AZFa Y gene, DDX3Y, evolved novel testis transcript variants in primates with proximal 3´UTR polyadenylation for germ cell specific translation

Translational control is a major level of gene expression regulation in the male germ line. DDX3Y located in the AZFa region of the human Y chromosome encodes a conserved RNA helicase important for translational control at the G1-S phase of the cell cycle. In human, DDX3Y protein is expressed only in premeiotic male germ cells. In primates, DDX3Y evolved a second promoter producing novel testis-specific transcripts. Here, we show primate species-specific use of alternative polyadenylation (APA) sites for these testis-specific DDX3Y transcript variants. They have evolved subsequently in the 3´UTRs of the primates´ DDX3Y transcripts. Whereas a distal APA site (PAS4) is still used for polyadenylation of most DDX3Y testis transcripts in Callithrix jacchus; two proximal APAs (PAS1; PAS2) are used predominantly in Macaca mulatta, in Pan trogloydates and in human. This shift corresponds with a significant increase of DDX3Y protein expression in the macaque testis tissue. In chimpanzee and human, shift to predominant use of the most proximal APA site (PAS1) is associated with translation of these DDX3Y transcripts in only premeiotic male germ cells. We therefore assume evolution of a positive selection process for functional DDX3Y testis transcripts in these primates which increase their stability and translation efficiency to promote its cell cycle balancing function in the human male germ line.

Structural variation on the human Y chromosome from population-scale resequencing

AIM

To investigate the information about Y-structural variants (SVs) in the general population that could be obtained by low-coverage whole-genome sequencing.

METHODS

We investigated SVs on the male-specific portion of the Y chromosome in the 70 individuals from Africa, Europe, or East Asia sequenced as part of the 1000 Genomes Pilot project, using data from this project and from additional studies on the same samples. We applied a combination of read-depth and read-pair methods to discover candidate Y-SVs, followed by validation using information from the literature, independent sequence and single nucleotide polymorphism-chip data sets, and polymerase chain reaction experiments.

RESULTS

We validated 19 Y-SVs, 2 of which were novel. Non-reference allele counts ranged from 1 to 64. The regions richest in variation were the heterochromatic segments near the centromere or the DYZ19 locus, followed by the ampliconic regions, but some Y-SVs were also present in the X-transposed and X-degenerate regions. In all, 5 of the 27 protein-coding gene families on the Y chromosome varied in copy number.

CONCLUSIONS

We confirmed that Y-SVs were readily detected from low-coverage sequence data and were abundant on the chromosome. We also reported both common and rare Y-SVs that are novel.

Copy number variation in the human Y chromosome in the UK population

We have assessed copy number variation (CNV) in the male-specific part of the human Y chromosome discovered by array comparative genomic hybridization (array-CGH) in 411 apparently healthy UK males, and validated the findings using SNP genotype intensity data available for 149 of them. After manual curation taking account of the complex duplicated structure of Y-chromosomal sequences, we discovered 22 curated CNV events considered validated or likely, mean 0.93 (range 0–4) per individual. 16 of these were novel. Curated CNV events ranged in size from <1 kb to >3 Mb, and in frequency from 1/411 to 107/411. Of the 24 protein-coding genes or gene families tested, nine showed CNV. These included a large duplication encompassing the AMELY and TBL1Y genes that probably has no phenotypic effect, partial deletions of the TSPY cluster and AZFc region that may influence spermatogenesis, and other variants with unknown functional implications, including abundant variation in the number of RBMY genes and/or pseudogenes, and a novel complex duplication of two segments overlapping the AZFa region and including the 3′ end of the UTY gene.

Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome

During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the "complete" Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at http://www.phylotree.org/Y.

Complex transcriptional control of the AZFa gene DDX3Y in human testis

The human DEAD-box Y (DBY) RNA helicase (aka DDX3Y) gene is thought to be the major azoospermia factor a (AZFa) gene in proximal Yq11. Men with its deletion display no somatic pathologies, but suffer from complete absence of germ cells. Accordingly, DDX3Y protein is expressed only in the germline in spermatogonia, although the transcripts were found in many tissues. Here, we show the complex transcriptional control of a testis-specific DDX3Y transcript class with initiation at different sites upstream of the gene’s open reading frame (5′Untranslated Region; UTR) and with polyadenylation in their proximal 3′UTR. The most distal transcriptional start site (TSS; ∼1 kb upstream) was mapped in MSY2, a Y-specific minisatellite. As this testis-specific 5′UTR was subsequently processed by three alternative splicing events, it has been tentatively designated ‘exon-T’(estis). The MSY2 sequence unit was also found upstream of the mouse Ddx3y gene. However, only after its tandem amplification on the Y chromosome of Platyrrhini (new world monkeys) and Catarrhini (old world monkeys) did MSY2 become part of a novel distal promoter for DDX3Y expression in testis tissue and provides a second transcriptional start site (T-TSS-II) in Catarrhini. We therefore suggest that the development of a novel distal DDX3Y promoter in primates, which is activated only in testis tissue, is probably part of the gene’s germline translation control.

Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis

Mutation at most human minisatellites is driven by complex interallelic processes that give rise to a high degree of length polymorphism and internal structural variation. MSY1, the only highly variable minisatellite on the non-recombining region of the Y chromosome, is constitutively haploid and therefore precluded from interallelic interactions, yet maintains high diversity in both length and structure. To investigate the basis of its mutation processes, an unbiased structural analysis of >500 single-molecule MSY1 PCR products from matched sperm and blood samples from a single donor was undertaken. The overall mutation frequencies in sperm and blood DNAs were not significantly different, at 2.68% and 1.88%, respectively. Sperm DNA showed significantly more length mutants than blood DNA, with mutants in both tissues involving small-scale (1–3 repeat units in a 77 repeat progenitor allele) increases or decreases in repeat block lengths, with no gain or loss bias. Isometric mutations altering structure but not length were found in both tissues, and involved either the apparent shift of a boundary between repeat unit blocks (a ‘boundary switch’) or the conversion of a repeat within a block to a different repeat type (‘modular structure’ mutant). There was a significant excess of boundary switch mutants and deficit of modular structure mutants in sperm. A comparison of mutant structures with phylogenetically matched alleles in population samples showed that alleles with structures resembling the blood mutants were unlikely to arise in populations. Mutation seems likely to involve gene conversion via synthesis-dependent strand annealing, and the blood-sperm differences may reflect more relaxed constraint on sister chromatid alignment in blood.

Origin and evolution of two Yugur sub-clans in Northwest China: a case study in paternal genetic landscape

BACKGROUND

Yugur is an ethnic group that was officially identified by the Chinese Government in 1953. Within the population there are two sub-clans distinctly identified as the Eastern Yugur and Western Yugur, partly because they have different local languages.

AIM

A parentage comparison was conducted between the two sub-clans to investigate their genetic relationship.

SUBJECTS AND METHODS

Male subjects were chosen from the two clans to investigate their paternal genetic landscape through typing 14 single nucleotide polymorphisms (SNP) and 12 short tandem repeats (STR) of the Y chromosome.

RESULTS

Significant differences were revealed between the sub-clans at the haplogroup level. Genetic divergence was also observed by analyses of multidimensional scaling (MDS) and principal components (PC). Genetically, the Eastern Yugur are closer to the Han Chinese and Mongolian people than the Western Yugur. The Uygur people, who share a common ancestor (ancient Huihu) with the Yugur, were genetically separate from both sub-clans of Yugur. Moreover, the constructed phylogenetic network for haplogroup O provided further evidence that the two Yugur sub-groups present an underlying genetic difference.

CONCLUSION

Overall, the diffusion of Mongolians during the Mongol Period has affected the Eastern Yugur more than the Western Yugur. The genetic contribution of the Han people to the Eastern Yugur seems to be more pronounced than to the Western Yugur. Besides the two different contributions referred to above, small population size and genetic drift have resulted in the genetic differentiation of the current sub-clans of Yugur.

Testing the hypothesis of an ancient Roman soldier origin of the Liqian people in northwest China: a Y-chromosome perspective

The Liqian people in north China are well known because of the controversial hypothesis of an ancient Roman mercenary origin. To test this hypothesis, 227 male individuals representing four Chinese populations were analyzed at 12 short tandem repeat (STR) loci and 12 single nucleotide polymorphisms (SNP). At the haplogroup levels, 77% Liqian Y chromosomes were restricted to East Asia. Principal component (PC) and multidimensional scaling (MDS) analysis suggests that the Liqians are closely related to Chinese populations, especially Han Chinese populations, whereas they greatly deviate from Central Asian and Western Eurasian populations. Further phylogenetic and admixture analysis confirmed that the Han Chinese contributed greatly to the Liqian gene pool. The Liqian and the Yugur people, regarded as kindred populations with common origins, present an underlying genetic difference in a median-joining network. Overall, a Roman mercenary origin could not be accepted as true according to paternal genetic variation, and the current Liqian population is more likely to be a subgroup of the Chinese majority Han.

Lack of association between Y chromosome haplogroups and male infertility in Japanese men

The Y chromosome carries several genes involved in spermatogenesis, which are distributed in three regions in the euchromatic part of the long arm, called AZFa (azoospermia factor a), AZFb, and AZFc. Microdeletions in these regions have been seen in 10-15% of sterile males with azoospermia or severe oligozoospermia. The relatively high de novo occurrence of these microdeletion events might be due to particular chromosome arrangements associated with certain Y chromosome haplogroups. To test whether there is any association between Y chromosome types and male infertility, we studied a sample of 84 Japanese oligozoospermic or azoospermic males. The patients were analyzed for the presence of Yq microdeletions and also typed with a battery of unique event polymorphisms (UEPs) to define their Y haplogroups. Six of the infertile patients presented likely pathological microdeletions detectable with the sequence tagged sites (STS) markers used. There was no significant association between Y chromosome haplogroups and the microdeletions. We also compared the Y haplogroup frequencies in our subset sample of 51 idiopathic azoospermia patients with 57 fertile control Japanese males, and did not observe any significant differences. Contrary to previous reports, our data suggest that Y microdeletions and other molecular events causally associated with male infertility in Japan occur independently of the Y chromosome background.

Relationship between Y-chromosomal DNA haplotype and sperm count in Italy

Forty Italian individuals with sperm counts in the range 20-130x10(6)/ml were typed with eleven Y-specific binary markers. Five Y haplogroups (1, 2, 3, 9 and 21) were present in the sample. In Italy, in contrast to Denmark, sperm counts were similar in the different haplogroups.

A genetic landscape reshaped by recent events: Y-chromosomal insights into central Asia

Sixteen Y-chromosomal microsatellites and 16 binary markers have been used to analyze DNA variation in 408 male subjects from 15 populations in Central Asia. Large genetic differences were found between populations, but these did not display an obvious geographical or linguistic pattern like that usually seen for Y-chromosomal variation. Nevertheless, an underlying east-west clinal pattern could be detected by the Autocorrelation Index for DNA Analysis and admixture analysis, and this pattern was interpreted as being derived from the ancient peopling of the area, reinforced by subsequent migrations. Two particularly striking features were seen: an extremely high level of Y-chromosomal differentiation between geographically close populations, accompanied by low diversity within some populations. These were due to the presence of high-frequency population-specific lineages and suggested the occurrence of several recent bottlenecks or founder events. Such events could account for the lack of a clear overall pattern and emphasize the importance of multiple recent events in reshaping this genetic landscape.

A nomenclature system for the tree of human Y-chromosomal binary haplogroups

The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.

Hierarchical patterns of global human Y-chromosome diversity

We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.

The human Y chromosome: function, evolution and disease

The human Y chromosome is strictly paternally inherited and, in most of its length, does not recombine during male meiosis. These features make the Y a very useful genetic marker for different purposes. In the last decade, the Y has been increasingly used to investigate the evolution, migrations and range expansions of modern humans. The possibility to construct highly informative Y chromosome haplotypes has also had a significant impact in forensic studies and paternity testing. All these studies assume that the Y chromosome markers used are selectively neutral. However, recent experimental and statistical analyses suggest that both positive and negative selection are acting on the Y chromosome and, consequently, may influence Y chromosome haplotype distribution in the general population. Current data suggest that the effects of selection on patterns of Y chromosome distribution are minimal, however as interest focuses on biological functions of the Y chromosome which have a major impact on male fitness such as fertility, these assumptions may be challenged. This review briefly describes the genes and biological functions of the human Y chromosome and its use in disentangling the origin and history of human populations. An overview of the role of selection acting on the Y chromosome from the perspective of human population histories and disease is given.

Y-chromosomal DNA haplotypes in infertile European males carrying Y-microdeletions

We have determined Y-chromosomal DNA haplotypes in 73 infertile European males carrying Y microdeletions and compared them with the haplotypes of 299 infertile males lacking microdeletions. Chromosomes were typed with a set of 11 binary Y markers, which identified 8 haplogroups in the sample. Haplogroup frequencies were compared between 3 microdeletion classes and the non-deleted infertile males. Deletions arise on many different haplotypic backgrounds. No statistically significant differences in frequency were seen, although the small number of AZFa deletions lay predominantly on one branch of the Y haplotype tree.