The history of the Y chromosome in man

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

eXclusionarY: 10 years later, where are the sex chromosomes in GWASs?

10 years ago, a detailed analysis showed that only 33% of genome-wide association study (GWAS) results included the X chromosome. Multiple recommendations were made to combat such exclusion. Here, we re-surveyed the research landscape to determine whether these earlier recommendations had been translated. Unfortunately, among the genome-wide summary statistics reported in 2021 in the NHGRI-EBI GWAS Catalog, only 25% provided results for the X chromosome and 3% for the Y chromosome, suggesting that the exclusion phenomenon not only persists but has also expanded into an exclusionary problem. Normalizing by physical length of the chromosome, the average number of studies published through November 2022 with genome-wide-significant findings on the X chromosome is ∼1 study/Mb. By contrast, it ranges from ∼6 to ∼16 studies/Mb for chromosomes 4 and 19, respectively. Compared with the autosomal growth rate of ∼0.086 studies/Mb/year over the last decade, studies of the X chromosome grew at less than one-seventh that rate, only ∼0.012 studies/Mb/year. Among the studies that reported significant associations on the X chromosome, we noted extreme heterogeneities in data analysis and reporting of results, suggesting the need for clear guidelines. Unsurprisingly, among the 430 scores sampled from the PolyGenic Score Catalog, 0% contained weights for sex chromosomal SNPs. To overcome the dearth of sex chromosome analyses, we provide five sets of recommendations and future directions. Finally, until the sex chromosomes are included in a whole-genome study, instead of GWASs, we propose such studies would more properly be referred to as "AWASs," meaning "autosome-wide scans."

Genetics, sex, and gender

This review aims to give an overview of what has been discovered so far and what still needs to be analyzed about how sex and gender affect the disease development. These two terms are often confused and indifferently used. In principle, the term "sex" refers to biological differences between males and females, specifically reproductive organs and their functions, while the term "gender" refers to the social context in which people live and which contributes to a subjective sexual identity, masculine or feminine. This dichotomy, however, is not so rigid and both sex and gender influence different aspects of human health, such as brain, health and aging and drug treatment and pharmacokinetics. In particular, we want to focus on genetic differences between men and women: indeed, the expression of the genes mapped on X chromosome or Y chromosome and all epigenetic interactions affect the diseases development. Finally, we will briefly outline sex and gender differences in clinical manifestations of three neurological diseases: Alzheimer's disease, Parkinson's disease, and obsessive compulsive disorder. In the era of personalized medicine, we must not forget the importance of gender medicine to promote personalized care for any kind of patients.

Y Chromosome Genes May Play Roles in the Development of Neural Rosettes from Human Embryonic Stem Cells

BACKGROUND

The human Y chromosome harbors genes that are mainly involved in the growth, development, sexual dimorphism, and spermatogenesis process. Despite many studies, the function of the male-specific region of the Y chromosome (MSY) awaits further clarification, and a cell-based approach can help in this regard.

RESULTS

In this study, we have developed four stable transgenic male embryonic stem cell (ESCs) lines that can overexpress male-specific genes HSFY1, RBMY1A1, RPS4Y1, and SRY. As a proof of principle, we differentiated one of these cell lines (RPS4Y1 over-expressing ESCs) to the neural stem cell (rosette structure) and characterized them based on the expression level of lineage markers. RPS4Y1 expression in the Doxycycline-treated group was significantly higher than control groups at transcript and protein levels. Furthermore, we found Doxycycline-treated group had a higher differentiation efficiency than the untreated control groups.

CONCLUSIONS

Our results suggest that the RPS4Y1 gene may play a critical role in neurogenesis. Also, the generated transgenic ESC lines can be widely employed in basic and preclinical studies, such as sexual dimorphism of neural and cardiac functions, the development of cancerous and non-cancerous disease models, and drug screening.

Sex and Liver Disease: The Necessity of an Overarching Theory to Explain the Effect of Sex on Nonreproductive Functions

The number of studies illuminating major sex differences in liver metabolic activities is growing, but we still lack a theory to explain the origin of the functional differences we are identifying. In the animal kingdom, energy metabolism is tightly associated with reproduction; conceivably, the major evolutionary step that occurred about 200 million years ago with placentation determined a significant change in female physiology, as females had to create new energy strategies to allow the growth of the embryo in the womb and the lactation of the newborn. In vertebrates the liver is the metabolic organ most tuned to gonadal functions because the liver synthesizes and transports of all the components necessary for the maturation of the egg upon estrogenic stimulation. Thus, in mammals, evolution must have worked on the already strict gonad-liver relationship fostering these novel reproductive needs. As a consequence, the functions of mammalian liver in females diverged from that in males to acquire the flexibility necessary to tailor metabolism according to reproductive status and to ensure the parsimonious exploitation and storage of energy for the continuation of gestation in case of food scarcity. Indeed, several studies show that male and female livers adopt very different strategies when confronted with nutritional stress of varied origins. Considering the role of liver and energy metabolism in most pathologies, a better focus on liver functions in the 2 sexes might be of considerable help in personalizing medicine and pharmacology for male and female needs.

Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs

Maoming is located in the southwest region of Guangdong Province and is the cradle of Gaoliang culture, which is the representative branch of Lingnan cultures. Historical records showed that the amalgamations between Gaoliang aborigines and distinct ethnic minorities had some influences on the shaping of Gaoliang culture, especially for the local Tai-kadai language-speaking Baiyue and Han Chinese from Central China. However, there is still no exact genetic evidence for the influences on the genetic pool of Maoming Han, and the genetic relationships between Maoming Han and other Chinese populations are still unclear. Hence, in order to get a better understanding of the paternal genetic structures and characterize the forensic features of 27 Y-chromosomal short tandem repeats (Y-STRs) in Han Chinese from Guangdong Maoming, we firstly applied the AmpFLSTR® Yfiler® Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA, United States) to genotype the haplotypes in 431 Han males residing in Maoming. A total of 263 different alleles were determined across all 27 Y-STRs with the corresponding allelic frequencies from 0.0004 to 0.7401, and the range of genetic diversity (GD) was 0.4027 (DYS391) to 0.9596 (DYS385a/b). In the first batch of 27 Yfiler data in Maoming Han, 417 distinct haplotypes were discovered, and nine off-ladder alleles were identified at six Y-STRs; in addition, no copy number variant or null allele was detected. The overall haplotype diversity (HD) and discrimination capacity (DC) of 27 Yfiler were 0.9997 and 0.9675, respectively, which demonstrated that the 6-dye and 27-plex system has sufficient system effectiveness for forensic applications in Maoming Han. What is more, the phylogenetic analyses indicated that Maoming Han, which is a Southern Han Chinese population, has a close relationship with Meizhou Kejia, which uncovered that the role of the gene flows from surrounding Han populations in shaping the genetic pool of Maoming Han cannot be ignored. From the perspectives of genetics, linguistics, and geographies, the genetic structures of Han populations correspond to the patterns of the geographical-scale spatial distributions and the relationships of language families. Nevertheless, no exact genetic evidence supports the intimate relationships between Maoming Han and Tai-Kadai language-speaking populations and Han populations of Central Plains in the present study.

The Y-STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics

The Y-STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y-STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA-confirmed father-son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off-ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y-STR mutation rate was 4.85 × 10^-3 (95% CI, 4.4 × 10^-3 -5.4 × 10^-3 ). The Spearman correlation analyses indicated that GD values (R² = 0.6548) and average allele sizes (R² = 0.5989) have positive correlations with Y-STR mutation rates. Our RM Y-STR set including 8 candidate RM Y-STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father-son pairs. This study also clarified the population structures of CSEH which isolated in population-mixed South China relatively. The strategy, SM Y-STRs for familial searching and RM Y-STRs for individual identification regionally, could be applicable based on enough knowledge of the Y-STR mutability of different populations.

Y chromosome in health and diseases

Sex differences are prevalent in normal development, physiology and disease pathogeneses. Recent studies have demonstrated that mosaic loss of Y chromosome and aberrant activation of its genes could modify the disease processes in male biased manners. This mini review discusses the nature of the genes on the human Y chromosome and identifies two general categories of genes: those sharing dosage-sensitivity functions with their X homologues and those with testis-specific expression and functions. Mosaic loss of the former disrupts the homeostasis important for the maintenance of health while aberrant activation of the latter promotes pathogenesis in non-gonadal tissues, thereby contributing to genetic predispositions to diseases in men.

The eXceptional nature of the X chromosome

The X chromosome is unique in the genome. In this review we discuss recent advances in our understanding of the genetics and epigenetics of the X chromosome. The X chromosome shares limited conservation with its ancestral homologue the Y chromosome and the resulting difference in X-chromosome dosage between males and females is largely compensated for by X-chromosome inactivation. The process of inactivation is initiated by the long non-coding RNA X-inactive specific transcript (XIST) and achieved through interaction with multiple synergistic silencing pathways. Identification of Xist-interacting proteins has given insight into these processes yet the cascade of events from initiation to maintenance have still to be resolved. In particular, the initiation of inactivation in humans has been challenging to study as: it occurs very early in development; most human embryonic stem cell lines already have an inactive X; and the process seems to differ from mouse. Another difference between human and mouse X inactivation is the larger number of human genes that escape silencing. In humans over 20% of X-linked genes continue to be expressed from the otherwise inactive X chromosome. We are only beginning to understand how such escape occurs but there is growing recognition that escapees contribute to sexually dimorphic traits. The unique biology and epigenetics of the X chromosome have often led to its exclusion from disease studies, yet the X constitutes 5% of the genome and is an important contributor to disease, often in a sex-specific manner.

Battle of the sexes: contrasting roles of testis-specific protein Y-encoded (TSPY) and TSPX in human oncogenesis

The Y-located testis-specific protein Y-encoded (TSPY) and its X-homologue TSPX originated from the same ancestral gene, but act as a proto-oncogene and a tumor suppressor gene, respectively. TSPY has specialized in male-specific functions, while TSPX has assumed the functions of the ancestral gene. Both TSPY and TSPX harbor a conserved SET/NAP domain, but are divergent at flanking structures. Specifically, TSPX contains a C-terminal acidic domain, absent in TSPY. They possess contrasting properties, in which TSPY and TSPX, respectively, accelerate and arrest cell proliferation, stimulate and inhibit cyclin B-CDK1 phosphorylation activities, have no effect and promote proteosomal degradation of the viral HBx oncoprotein, and exacerbate and repress androgen receptor (AR) and constitutively active AR variant, such as AR-V7, gene transactivation. The inhibitory domain has been mapped to the carboxyl acidic domain in TSPX, truncation of which results in an abbreviated TSPX exerting positive actions as TSPY. Transposition of the acidic domain to the C-terminus of TSPY results in an inhibitory protein as intact TSPX. Hence, genomic mutations/aberrant splicing events could generate TSPX proteins with truncated acidic domain and oncogenic properties as those for TSPY. Further, TSPY is upregulated by AR and AR-V7 in ligand-dependent and ligand-independent manners, respectively, suggesting the existence of a positive feedback loop between a Y-located proto-oncogene and male sex hormone/receptors, thereby amplifying the respective male oncogenic actions in human cancers and diseases. TSPX counteracts such positive feedback loop. Hence, TSPY and TSPX are homologues on the sex chromosomes that function at the two extremes of the human oncogenic spectrum.

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.