The Y chromosome is a type of sex chromosome existing primarily in male mammalian species. The Y chromosome passes through the male gamete and determines male sex in humans, non-human primates, and other mammals. The mammalian Y chromosome varies from the X chromosome and the rest of the chromosomes primarily by size and its male sex-determining/spermatogenesis function. In the Y chromosome, male sex-determining function is exclusively located on the short arm, while the spermatogenesis function is distributed widely on the short and long arm. Deletions or mutations particularly in the male-specific region of Y chromosome (MSY) may cause male infertility. During the last few decades, researchers put forth an enormous effort to discover Y chromosome specific genes, and their encoded RNAs and proteins in humans, primates, and rodents. As a result, most of the genes and encoded proteins responsible for male-sex determination, testis development, and spermatogenesis have been discovered in humans, however not well established in non-human primates and rodents. Also, there might be a percent of proteins missing in human Y chromosome. The aim of this study is to annotate the proteins that encoded on the Y chromosome of humans, chimpanzee, and mouse using extensive bioinformatics tools. The human (annotation release 107), chimpanzee (annotation release 103), and mouse (annotation release 105) proteins were first retrieved from the National Center for Biotechnology Information (NCBI) eukaryotic genome annotation resource database. Then, the annotated human proteins (66 proteins) were compared with the core databases of human proteome project such as neXtProt, PeptideAtlas, and the Human Protein Atlas. The X-homologous of human Y chromosome-encoded proteins were searched using the NCBI Protein BLAST program. The cellular pathways and protein-protein interactions involving human Y chromosome-encoded proteins were searched using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping database, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the Pathway Studio software. Finally, the human Y chromosome-encoded protein homologs/orthologs in chimpanzee and mouse were analyzed using the NCBI bl2seq program. This analysis resulted a significant number of homologous/orthologous proteins between human, chimpanzee and mouse. Our findings provide the scientific community with updated information on the Y chromosome-encoded proteins in humans, chimpanzee, and mouse.

Cattle breeds were classified previously into three different haplogroups (Y1 and/or Y2 in Bos taurus and Y3 in B. indicus) based on Y chromosome-specific polymorphisms. In particular, a rapid and unambiguous classification method was reported recently. However, a haplogroup classification of Korean native cattle breeds has not been reported. In this study, 196 animal samples from four Korean native cattle breeds (Hanwoo, Chikso, Heugu, and Jeju black cattle) and six exotic breeds were used to determine the Y chromosome-specific haplogroup classification. We amplified an 81 bp indel region within intron 26 of the USP9Y gene and performed electrophoresis to classify the Y1 and Y2 haplogroups. Moreover, enzyme digestion was carried out with the SspI restriction enzyme to classify the Y2 and Y3 haplogroups. Finally, sequence variation in each haplogroup was confirmed by DNA sequencing. All animals in the four Korean native cattle and two exotic breeds (Charolais and Simmental) belonged to the Y2 haplogroup. Three other exotic breeds (Holstein, Angus, and Hereford) belonged to Y1 haplogroup. Japanese black cattle were divided into both the Y1 and Y2 haplogroups. The Y3 haplogroup corresponding to B. indicus was not found in this study. In conclusion, Korean native cattle breeds originated from B. taurus without introduction from B. indicus. In addition, they showed the same paternal heredity pattern which belonged to only Y2 haplogroup. These results can be used to investigate the origin of Korean native cattle breeds.

In mammals, the meiosis division in testes produces equal numbers of two different types of gametes: X chromosome-bearing sperm (X-spermatozoa) and Y chromosomebearing sperm (Y-spermatozoa), which have equal potential to fertilize the oocytes. Therefore, the expected 1: 1 sex ratio is observed. However, under some conditions like endocrine disruptors (EDs) exposure the sex ratio is deviated than the expected with more males or more females. And recently many hypotheses have been postulated to explain the mechanism of sex ratio deviation; however none of them introduced a proven experimental explanation. To solve this enigma, we hypothesized that the differences between X- and Y-spermatozoa survivability under specific conditions due to differences in their chromosome contents are the key leading to the sex ratio alteration. To examine our hypothesis, we combined two techniques; first, hypo-osmotic swelling (HOS) test that was applied to test viability of spermatozoa and second, fluorescence in situ hybridization that was applied on HOS-treated spermatozoa to define sex chromosome composition. In the present study, human spermatozoa were incubated with a group of EDs represent a widespread chemicals in the environment bisphenol A (BPA, 100 μM), nonylphenol (NP, 10 μg/ml), 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD, 2.5 μg/ml), genistein (Gen, 100 μM), and the following pesticides, dibromochloropropane (DBCP, 10 μg/ml), atrazine (Atraz, 500 μM), and diazinone (Diaz, 500 μM) for 6 hr at 37℃ in 5% CO2. Then, the viability of spermatozoa and their sex chromosome contents were evaluated simultaneously. Among seven chemicals studied only four chemicals (Atraz, DBCP, TCDD, and Diaz) significantly decreased Y-sperm viability when compared to those of X-spermatozoa in the same treatment group and viability of Y-spermatozoa when compared to those in the negative and positive (DMSO) control groups (p<0.05). Also, in these four treatment groups the sex ratio of live sperm population was significantly lowered compared to the control groups (p<0.05). Otherwise, Gen, BPA, and NP did not show any significant effect on viability of Yspermatozoa or decreasing sex ratio in live sperm population as compared to the control groups. It has been proven that TCDD, DBCP, and the pesticides decrease the sex ratio, but the same effect was not observed in case of Gen, BPA, and NP. From the present findings, there is no doubt that the EDs may alter sex ratio via decreasing Y-spermatozoa viability.

The purpose of this work was to examine whether X-Y chromosome dissociation in the primary spermatocytes of mice could be used as an in vivo short-term assaying system that detect environmental mutagens. Four alkylating agents(EMS, MMS, MMC and MNNG) which were known as strong mutagens were administered to BALB/c male mice 3-4 months old. In the control group, the mean frequencies of previously dissociated X and Y chromosomes and autosomes were 7.17% and 2.12%, respectively. Compared to the control group, mutagen-treated groups have no significant differences in dissociation rate of autosomes, while these groups were about 1.2-2.5 times higher in the frequencies of X-Y dissociation. Generally, X-Y dissociation frequency increased consistently with the concentration of mutagens whereas the tendency of autosome dissociation frequency was variable among several mutagens. These results suggest that X-Y dissociation in the primary spermatocytes of mice is applicable as an in vivo short-term assaying system for environmental mutagens. There were significantly distinct increase in dissociation of X-Y chromosome in both the hybrid and parents but the X-Y previous dissociation of hybrid appeared higher frequency than BALB/c and wild mice. These results indicate that the factor related to binding X-Y chromosome is specific to strains.