Wansheng Liu

• Ph.D.
• Professor at Pennsylvania State University

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...

Multi-copy gene families are especially prevalent in the male-specific region (MSY) of the mammalian Y chromosome. Copy number variations (CNV) of these Y-linked gene families have been shown to affect human and animal fertility. The PRAMEY (Preferentially expressed antigen in melanoma, Y-linked) gene family is a newly identified, bovid-specific Y-...

Preferentially expressed antigen in melanoma (PRAME) is a cancer/testis antigen that is predominantly expressed in normal testicular tissues and a variety of tumors. The function of the PRAME family in spermatogenesis remains unknown. This study was designed to characterize the Y-linked PRAME (PRAMEY) protein during spermatogenesis in cattle. We fo...

Preferentially expressed antigen in melanoma (PRAME) is cancer/testis antigen and a transcriptional repressor, inhibiting the signaling of retinoic acid through the retinoic acid receptor (RAR) for promoting cell proliferation and preventing cell apoptosis in cancer cells. The role of PRAME in testis and germline is unknown. We report here the gene...

Spermatogenesis begins when cell-fate committed prospermatogonia migrates to the basement membrane and initiate spermatogenesis in response to retinoic acid (RA) in the neonatal testis. The underlying cellular and molecular mechanisms in this process are not fully understood. Here, we report findings on the involvement of a cancer-testis antigen, P...

Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms underlying economically and ecologically important physiological traits. This knowledge contributes to the advancement of sustainable and precision agriculture-food systems. Here, as part of the Farm anima...

Background PRAME constitutes one of the largest multi-copy gene families in Eutherians, encoding cancer-testis antigens (CTAs) with leucine-rich repeats (LRR) domains, highly expressed in cancer cells and gametogenic germ cells. This study aims to elucidate genetic interactions between two members, Pramex1 and Pramel1 , in the mouse Prame family du...

Background The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. Results...

Background It is not uncommon for some individuals to retain certain primitive characteristics even after domestication or long-term intensive selection. Wild ancestors or original varieties of animals typically possess strong adaptability to environmental preservation, a trait that is often lacking in highly artificially selected populations. In t...

Preferentially expressed antigen in melanoma (PRAME) is a cancer/testis antigen (CTA) that is predominantly expressed in normal male gonad tissues and a variety of tumors. PRAME proteins are present in the acrosome and sperm tail, but their role in sperm function is unknown. The objective of this study was to examine the function of the bovine Y-li...

Functional annotation of the bovine genome was performed by characterizing the spectrum of RNA transcription using a multi-omics approach, combining long- and short-read transcript sequencing and orthogonal data to identify promoters and enhancers and to determine boundaries of open chromatin. A total number of 171,985 unique transcripts (50% prote...

The preferentially expressed antigen in melanoma, Y-linked (PRAMEY) is a cancer/testis antigen expressed predominantly in bovine spermatogenic cells, playing an important role in germ cell formation. To better understand PRAMEY’s function during spermatogenesis, we studied the dynamics of PRAMEY isoforms by Western blotting (WB) with PRAMEY-specifi...

Background Preferentially expressed antigen in melanoma (PRAME) is a cancer/testis antigen (CTA) that is predominantly expressed in normal gametogenic tissues and a variety of tumors. Members of the PRAME gene family encode leucine-rich repeat (LRR) proteins that provide a versatile structural framework for the formation of protein–protein interact...

Localization of PRAMEY Protein in Bovine Testis by Immunoelectron Microscopy - Gang Ning, Wan-Sheng Liu

At present, based on whole genome sequencing, sequences and genes annotation of the sheep (Ovis aries) Y chromosome are still absent. The isolation of Y chromosomes followed by sequencing has been approved as an effective approach to analyze this complex chromosome in other species. In this study, we established a highly efficient synchronization m...

tRNA-derived small RNAs (tsRNAs) from spermatozoa could act as acquired epigenetic factors and contribute to offspring phenotypes. However, the roles of specific tsRNAs in early embryo development remain to be elucidated. Here, using pigs as a research model, we probed the tsRNA dynamics during spermatogenesis and sperm maturation, and demonstrate...

More than 99% of all known Holstein artificial insemination (AI) bulls in the United States can be traced through their male lineage to just 2 bulls born in the 1950s, and all Holstein bulls can be traced back to 2 bulls born in the late 1800s. As the Y chromosome is passed exclusively from sire to son, this suggests that variation is limited for m...

Background The widely observed RNA-DNA differences (RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing (i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA (ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family during the transcriptional...

The corpus luteum (CL) is essential for maintenance of pregnancy in all mammals and luteal rescue, which occurs around day 16-19 in the cow, is necessary to maintain luteal progesterone production. Transcriptomic and proteomic profiling were performed to compare the day 17 bovine CL of the estrous cycle and pregnancy. Among mRNA and proteins measur...

Mammalian sex chromosomes evolved from an ordinary pair of autosomes. The X chromosome is highly conserved, whereas the Y chromosome varies among species in size, structure, and gene content. Unlike autosomes that contain randomly mixed collections of genes, the sex chromosomes are enriched in testis-biased genes related to sexual development and r...

Background Milk yield for Holstein cows has doubled over five decades due to genetic selection and changes to management, but the molecular mechanisms that facilitated this increase are mostly unknown. Epigenetic modifications to the cattle genome are a plausible molecular mechanism to cause variation in milk yield and our objective was to describe...

Jersey cattle are the second most prominent breed in the United States and represent a growing portion of the dairy cow population in the United States. The objectives of our study were to determine the male lineages of Jersey sires with official genetic evaluations and to determine whether there are differences in sire conception rate among lineag...

The mammalian ovary is a dynamic organ. The coordination of follicle recruitment, selection, and ovulation and the timely development and regression of the corpus luteum are essential for a functional ovary and fertility. Deregulation of any of these processes results in ovarian dysfunction and potential infertility. MicroRNA (miRNA) are short nonc...

Holsteins are the most numerous dairy cattle breed in North America and the breed has undergone intensive selection for improving milk production and conformation. Theoretically, this intensive selection could lead to a reduction of the effective population size and reduced genetic diversity. The objective of this study was to investigate the effec...

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 do...

Recent transcriptomic analysis of the bovine Y chromosome revealed at least six multi-copy protein coding gene families, including TSPY, HSFY and ZNF280BY, on the male-specific region (MSY). Previous studies indicated that the copy number variations (CNVs) of the human and bovine TSPY were associated with male fertility in men and cattle. However,...

The mammalian sex chromosomes evolved from an ordinary pair of autosomes during evolution. Unlike the X chromosome that is highly conserved, the Y chromosome is poorly conserved among mammalian lineages. Several special features set the Y chromosome apart from the rest of genome: male-limited transmission, absence of recombination, abundance of Y-s...

Hughes et al. (1) claim we made unauthorized use of their unpublished data in our publications on the bovine Y chromosome (BTAY) 2–5). These accusations are troubling in their intent and unfounded. First, we carefully followed the international standards, including the Fort Lauderdale (www.genome.gov/pages/research/wellcomereport0303.pdf) and Toron...

The recent observation of vector sequences in the semen of men undergoing clinical gene therapy for hemophilia has highlighted the need to evaluate the risk of inadvertent germ-line transduction in a clinically relevant animal model. In the present study, we used three different approaches to investigate whether the germ line is at risk of inadvert...

PRAME belongs to a group of cancer/testis antigens (CTAs) that are characterized by their restricted expression in normal gametogenic tissues and a variety of tumors. The PRAME family is one of the most amplified gene families in the mouse and other mammalian genomes. Members of the PRAME gene family encode leucine-rich repeat (LRR) proteins functi...

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

The mammalian Y chromosome harbors genes essential for male reproduction and serves as a basis to understand chromosome evolution. The sheep is one of the major farmed animal species and is evolutionarily close to cattle. A high coverage sheep (ovine) genome assembly has been built. The ovine Y chromosome has not been included in this assembly due...

The objectives of this study were to quantify the relationships of various definitions of feed utilization with both fertility and productive life. Intake and body measurement data were collected monthly on 970 cows in 11 tie-stall herds for 6 consecutive months. Measures of feed utilization for this study were dry matter intake (DMI), dry matter i...

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from...

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: ABySS v. 1.2.6 Sequencing Technology :: Sanger dideoxy sequencing; Illumina ##Assembly-Data-END##

Telomere length variation may provide a quantitative measure of the effects of dairy management and selection practices on animal stress and welfare. The objective of this study was to evaluate the association between telomere length in Holstein cattle with age, herd, and survival. A multiplex quantitative PCR (qPCR) procedure was utilized to estim...

Preferentially expressed antigen in melanoma (PRAME) gene family belongs to a group of cancer/testis antigens that are characterized by their restricted expression in normal gametogenic tissues and a variety of tumors, and their functions in both immunity and reproduction. The PRAME gene family is one of the most amplified gene families in the mous...

The mammalian sex chromosomes, the X and Y, evolved from a pair of autosomes ~ 166 million years ago. Recombination suppression between these two ancestral chromosomes led to a male-specific region on the Y (MSY). Two major regions, X-degenerate and ampliconic, are usually present in MSY. The X-degenerate region contains single-copy genes evolved a...

The male-specific region (MSY) of the mammalian Y-chromosome, which is usually 95% of the entire Y, is characterized by its lack of recombination with the X-chromosome during meiosis, poorly conserved gene content among different lineages, and predominant functions of its genes in spermatogenesis and male fertility. In addition, many of the MSY-lin...

Preferentially expressed antigen in melanoma (PRAME) gene family is one of the cancer-testis antigen (CTA) families, whose expressions are restricted to testis and a variety of tumors. In tumor cells, PRAME functions in transcriptional regulation either as an inhibitor or an activator in different pathways. However, the function of PRAME in normal...

Cytogenetic Analysis of Bovine Sex Chromosomes X and Y Chromosome Genetic and Physical Maps The Pseudoautosomal Region Pseudoautosomal Boundary The MSY Region Bovine Y-Chromosome Phylogeny Sex Chromosome Abnormalities Sex Chromosomes QTLs References

Data from 879 Holstein cows from 11 tie-stall herds in Pennsylvania were analyzed to determine the effects of nutritional management practices on the level of genetic expression for milk, fat, and protein yields. Environments were defined according to the amount of dry matter refusals at the end of 24h for the average cow (DMR), diet crude protein...

3D structure of the OFD1X and the positively selected residues. Eight sites were detected to be positively selected on the branch leading to eutherians. The sites were mapped to the 3D structure of the human OFD1X protein. The coiled-coil region involved in mediating homo-oligomerization is highlighted in green. Red: posterior possibility (pp) > 0....

The genomic structure of the bovine OFD1Y . (DOC)

Sequences of primers designed for PCR and RT-PCR. (DOC)

Positively selected branches and sites in the mammalian OFD1 homologs. (DOC)

Sliding window Ka/Ks analysis for pairs of the X-linked, Y-linked or autosomal OFD1 in cattle and primates. The analysis was performed by comparing pairs of OFD1 genes in the bovine, macaque, orangutan, chimpanzee (300 bp window, 50 bp slide). Ka/Ks ratio is plotted against the length of the coding region of the mRNAs. (TIF)

The genomic structure of the bovine OFD1X . (DOC)

The OFD1 (oral-facial-digital, type 1) gene is implicated in several developmental disorders in humans. The X-linked OFD1 (OFD1X) is conserved in Eutheria. Knowledge about the Y-linked paralog (OFD1Y) is limited. In this study, we identified an OFD1Y on the bovine Y chromosome, which is expressed differentially from the bovine OFD1X. Phylogenetic a...

We used the IMNpRH2(12,000-rad) RH and IMpRH(7,000-rad) panels to integrate 2019 transcriptome (RNA-seq)-generated contigs with markers from the porcine genetic and radiation hybrid (RH) maps and bacterial artificial chromosome finger-printed contigs, into 1) parallel framework maps (LOD ≥ 10) on both panels for swine chromosome (SSC) 4, and 2) a h...

Preferentially expressed antigen in melanoma (PRAME) belongs to a group of cancer-testis (CT) antigens that are predominantly expressed in normal testis and a variety of tumors, and is associated with immunity and reproduction. Members of the PRAME gene family encode leucine-rich proteins, which have been shown to function as a dominant repressor o...

The bovine corpus luteum (CL) is a transient organ in the ovary whose function is to produce progesterone. In the early stage, the CL rapidly grows and becomes fully functional by midcycle. During midcycle, the function and structure of the CL in cyclic cows are maintained until luteal regression is initiated by prostaglandin F2 alpha (PGF2α). The...

Autosome-to-Y transposition of male fertility genes is a recurrent theme in mammalian Y-chromosome evolution. As the transposition events occurred separately in different lineages, Y-chromosome genes have been accumulated in the male-specific region (MSY) in a lineage-dependent manner. We have recently discovered two bovid-specific Y-chromosome gen...

The objectives of this study were to calculate the heritability of feed efficiency and residual feed intake, and examine the relationships between feed efficiency and other traits of productive and economic importance. Intake and body measurement data were collected monthly on 970 cows in 11 tie-stall herds for 6 consecutive mo. Measures of efficie...

A list of BACs containing homologous PRAMEY. (DOC)

PRAME/PRAMEY homologs in the phylogenetic tree. (DOC)

Primers for (RT-) PCR and strand-specific qRT-PCR. (DOC)

Alignment of the ZNF280B/ZNF280A/PRAME gene block across 17 species. The ZNF280B/ZNF280A/PRAME gene blocks are conserved in the syntenic regions in most mammals except the rodents where the block was rearranged in two different chromosomes (MMU4/10 and RNO5/20). This plot was generated based on the HSA22 assembly (hg19, Feb. 2009). The boxes repres...

Positively selected sites detected from branch-site model tests. (DOC)

Motif alignment between the bovine PRAMEY and the human PRAME on HSA22. The aliphatic sites of LXXLL motifs observed on the human PRAME on HSA22 [16], [12] are conserved in the bovine PRAME(Y). These motif modifications are restricted to the aliphatic group, including the leucine to valine in the third and seventh motifs and leucine to isoleucine i...

Site-specific selection tests on the homologs in Clade I and Clade IIa. (DOC)

Probes for in situ hybridization. (DOC)