Comparative RNA-Seq Analysis of Differentially Expressed Genes in the Epididymides of Yak and Cattleyak

Yak DEFB124 alleviates intestinal injury caused by Staphylococcus aureus infection

To investigate the characteristics and functions of yak β-defensin 124 (DEFB124), prokaryotic expression, analysis of gut microbiological and other methods were used in this study. The results showed that the sequence of yak DEFB124 gene was 306 bp in length and 207 bp in open reading frame, which encoded 68 amino acids. Yak DEFB124 protein was highly conserved and had the closest relationship with cattle. Yak DEFB124 protein was a secreted cationic β-defensin. The recombinant expression plasmid pET32a-DEFB124 was constructed, and an about 24 kDa protein was successfully expressed. Yak DEFB124 protein had inhibitory activity against Staphylococcus aureus (S. aureus), and its MIC value was 64 μg/mL. After treating with yak DEFB124 protein, the activities of alkaline phosphatase (AKP) and total superoxide dismutase (T-SOD) were higher (P < 0.01) in the jejunum tissue, but the activity of lysozyme (LZM) was lower (P < 0.01). The number of goblet cells in the duodenum, jejunum, and ileum of the mice in the DEFB124 group was increased (P < 0.01). Besides, the expressions of MUC2 mRNA and protein were increased (P < 0.05) after the treatment with yak DEFB124 protein. Furthermore, the relative abundance of Lactobacillus in jejunum of mice in DEFB124 group was also increased. In summary, yak DEFB124 protein could increase the number of goblet cells in mice intestine and the abundance of intestinal probiotics Lactobacillus, thereby protecting the intestinal tract and alleviating intestinal damage.

The exploration of miRNAs and mRNA profiles revealed the molecular mechanisms of cattle-yak male infertility

Cattle-yak, the first-generation offspring of cattle and yak, inherited many excellent characteristics from their parents. However, F1 male hybrid infertility restricts the utilization of heterosis greatly. In this study, we first compared the testicular tissue histological characteristics of three cattle, three yaks, and three cattle-yak. Then we explored the miRNA profiles and the target functions of nine samples with RNA-seq technology. We further analyzed the function of DE gene sets of mRNA profiles identified previously with GSEA. Testicular histology indicated that the seminiferous tubules became vacuolated and few active germ cells can be seen. RNA-seq results showed 47 up-regulated and 34 down-regulated, 16 up-regulated and 21 down-regulated miRNAs in cattle and yaks compared with cattle-yak, respectively. From the intersection of DE miRNAs, we identified that bta-miR-7 in cattle-yak is down-regulated. Target prediction indicated that the filtered genes especially MYRFL, FANCA, INSL3, USP9X, and SHF of bta-miR-7 may play crucial roles in the reproductive process. With further network analysis and GSEA, we screened such hub genes and function terms, we also found some DE gene sets that enriched in ATP binding, DNA binding, and reproduction processes. We concluded that bta-miR-7 may play an important role in influencing fecundity. Our study provides new insights for explaining the molecular mechanism of cattle-yak infertility.

Whole-Genome Profile of Greek Patients with Teratozοοspermia: Identification of Candidate Variants and Genes

Male infertility is a global health problem that affects a large number of couples worldwide. It can be categorized into specific subtypes, including teratozoospermia. The present study aimed to identify new variants associated with teratozoospermia in the Greek population and to explore the role of genes on which these were identified. For this reason, whole-genome sequencing (WGS) was performed on normozoospermic and teratozoospermic individuals, and after selecting only variants found in teratozoospermic men, these were further prioritized using a wide range of tools, functional and predictive algorithms, etc. An average of 600,000 variants were identified, and of them, 61 were characterized as high impact and 153 as moderate impact. Many of these are mapped in genes previously associated with male infertility, yet others are related for the first time to teratozoospermia. Furthermore, pathway enrichment analysis and Gene ontology (GO) analyses revealed the important role of the extracellular matrix in teratozoospermia. Therefore, the present study confirms the contribution of genes studied in the past to male infertility and sheds light on new molecular mechanisms by providing a list of variants and candidate genes associated with teratozoospermia in the Greek population.

Involvement of Porcine β-Defensin 129 in Sperm Capacitation and Rescue of Poor Sperm in Genital Tract Infection

In mammals, β-defensins have been reported to play pivotal roles in sperm protection and fertilization. However, the function and mechanism of porcine β-defensin 129 (pBD129) in the sperm remain unclear. Here, we demonstrate that pBD129 is a glycosylated protein and broadly exists in accessory sex glands and coats the sperm surface. We inhibited the pBD129 protein on the sperm surface with an anti-pBD129 antibody and found that sperm motility was not significantly affected; however, sperm acrosome integrity and tyrosine phosphorylation levels increased significantly with time (p < 0.05) during capacitation. These changes were accompanied by an increase in sperm Ca2+ influx, resulting in a significantly reduced in vitro fertilization cleavage rate (p < 0.05). Further investigation revealed that treatment with recombinant pBD129 markedly restored the sperm motility in semen contaminated with Escherichia coli. The results suggest that pBD129 is not only associated with poor sperm motility after genital tract infection but can also protect the spermatozoa from premature capacitation, which may be beneficial for semen preservation.

RNA-Seq reveals the functional specificity of epididymal caput, corpus, and cauda genes of cattleyak

The first filial generation of the cattleyaks demonstrates hybrid vigor; however, the male cattleyaks are infertile and restrict productivity and breeding. The discovery of genes in a segment-specific approach offers valuable information and understanding concerning fertility status, yet the biology of cattleyak epididymis is still progressing. Comparative transcriptome analysis was performed on segment pairs of cattleyak epididymis. The caput versus corpus epididymis provided the highest (57.8%) differentially expressed genes (DEGs), corpus versus cauda (25.1%) followed, whereas caput versus cauda pair (17.1%) had the least DEGs. The expression levels of genes coding EPHB6, TLR1, MUC20, MT3, INHBB, TRPV5, EI24, PAOX, KIF12, DEPDC5, and KRT25, which might have the potentials to regulate the homeostasis, innate immunity, differentiation, motility, transport, and sperm maturation-related function in epididymal cells, were downregulated in the distal segment of epididymis. Top enriched KEGG pathways included mTOR, axon guidance, and taste transduction signaling pathways. EIF4B, EPHB6, and TAS2R42 were enriched in the pathways, respectively. Identifying key, new, and unexplored DEGs among the epididymal segments and further analyzing them could boost cattleyak fertility by maximizing sperm quality from genetically better sires and also facilitate better understanding of the epididymal biology.

Next-generation sequencing analysis reveals segmental patterns of microRNA expression in yak epididymis

MicroRNAs (miRNAs) have emerged as potent regulators of gene expression and are widely expressed in biological systems. In reproduction, they have been shown to have a significant role in the acquisition and maintenance of male fertility, whereby deletion of Dicer in mouse germ cells leads to infertility. Evidence indicates that this role of miRNAs extends from the testis into the epididymis, controlling gene expression and contributing to regional variations in gene expression. In this study, RNA sequencing technology was used to investigate miRNA expression patterns in the yak epididymis. Region-specific miRNA expression was found in the yak epididymis. In all, 683 differentially expressed known miRNAs were obtained; 190, 186 and 307 differentially expressed miRNAs were identified for caput versus corpus, corpus versus cauda and caput versus cauda region pairs respectively. Kyoto Encyclopedia of Genes and Genomes results showed endocytosis as the most enriched pathway across region pairs, followed by protein processing in the endoplasmic reticulum, phagosome, spliceosome and biosynthesis of amino acids in region pair-specific hierarchical order. Gene ontology results showed varied enrichment in terms including cell, biogenesis, localisation, binding and locomotion across region pairs. In addition, significantly higher miR-34c expression was seen in the yak caput epididymidis relative to the corpus and cauda epididymidis.

High-throughput sequencing reveals differential expression of miRNAs in yak and cattleyak epididymis

Cattleyaks (CY) are interspecific hybrids between cattle (Bos taurus) and yak (Bos gruniens, YK) exhibiting the same prominent adaptability and higher performances than YK. MiRNAs have played an important role in the acquisition and maintenance of male fertility in reproduction, where deletion of Dicer in mice germ cells results in infertility. According to a body of evidence, the function of miRNA in the male reproductive system extends from the testis into the epididymis and, as such, regulates gene expression and contributes to regional gene expression variations. Using RNA sequencing on biological replicates, we described differentially expressed miRNAs profiles for tissue from epididymis of YK and CY. In the present study, High-throughput sequencing analysis showed that 55 differentially expressed (DE) miRNAs were identified in the epididymis of YK and CY. Among these, 43 DE miRNAs were upregulated while the remaining 12 DE miRNAs were downregulated between epididymis of YK and CY. Our results showed that the top most important DE miRNAs, bta-miR-449c, bta-miR-539, bta-miR-136, bta-miR-504, bta-miR-31 and bta-miR-222 were found to be involved in the reproductive system of CY. In addition, some targeted genes, Clusterins (CLU), Retinoic Acid Receptor a (RARa) and Hydroxy acyl glutathione Hydrolase (HAGH) and HSPH1 targeted by bta-miR-2411-3p and bta-miR-1298 were involved in the sperm motility, sperm morphology and post-testicular sperm maturation. Furthermore, GO and KEGG analyses were performed to classify the functions of target genes for DE miRNAs. In addition, RT-qPCR validation of the DE miRNAs and its targeted genes revealed that putative miRNAs are involved in the male CY infertility by altering the gene expression. Present findings may not only increase our understanding of the molecular mechanisms regulated by the miRNAs in epididymis, but also provide a valuable information to understand the male infertility mechanism of CY.

Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls

Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle.

Analysis of differentially abundant proteins related to boar fertility in seminal plasma using iTRAQ-based quantitative proteomics

Animal fertility is one of the most important characteristics for the livestock breeding industry. Conventional semen analysis provides basic information on sperm quality, but the predictive value of such analysis with regard to fertility remains questionable. Therefore, it is important to determine and predict male fertility more accurately in the clinic. To identify seminal plasma proteins involved in fertility, isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography with tandem mass spectrometry (quantitative proteomic analysis) were used to identify differentially abundant proteins (DAPs) in seminal plasma between high- and low-reproductive-efficiency Landrace boars. A total of 141 DAPs were identified, of which 125 upregulated and 16 downregulated proteins were subjected to bioinformatics analysis. These DAPs were found to be mainly involved in proteolysis, ATP binding, and energy metabolism. We investigated the relevance of three DAPs-ceruloplasmin, carboxypeptidase E (CPE), and serpin family A member 12 (SERPINA12)-in an in vitro fertility assay. This assay revealed that the inhibition of these proteins with antibodies can reduce or increase the fertilization rate. These results indicate possible biomarkers for the selection of high-fertility boars and provide a theoretical basis for the use of protein biomarkers in the livestock breeding industry. SIGNIFICANCE: Our study identified differentially abundant proteins in the seminal plasma of high-reproductive-efficiency and low-reproductive-efficiency Landrace boars. These proteins may be used as biomarkers to screen out high-fertility boars. The study can provide not only a new method for improving the effects of artificial insemination and reproductive efficiency of boars but also an important reference for boar breeding. Meanwhile, because pigs and humans have similar physiological parameters and organ sizes, our findings can also serve as a reference for human reproduction research.