Pig StAR: mRNA expression and alternative splicing in testis and Leydig cells, and association analyses with testicular morphology traits

Prolonged exposure to dexamethasone alters the proteome and cellular phenotype of human testicular peritubular cells

Human testicular peritubular cells (HTPCs) are smooth muscle cells, which in the testis form a small compartment surrounding the seminiferous tubules. Contractions of HTPCs are responsible for sperm transport, HTPCs contribute to spermatogenesis, have immunological roles and are a site of glucocorticoid receptor expression. Importantly, HTPCs maintain their characteristics in vitro, and thus can serve as an experimental window into the male gonad. Previously we reported consequences of 3-day treatment with Dexamethasone (Dex), a synthetic glucocorticoid and multi-purpose anti-inflammatory drug. However, as glucocorticoid therapies in man often last longer, we now studied consequences of a prolonged 7-day exposure to 1 µM Dex. Combining live cell imaging with quantative proteomics of samples taken from men, we confirmed our recent findings but more importantly, found numerous novel proteomic alterations induced by prolonged Dex treatment. The comparison of the 7-day treatment with the 3-day treatment dataset revealed that extracellular matrix- and focal adhesion-related proteins become more prominent after 7 days of treatment. In contrast, extended stimulation is, for example, associated with a decrease of proteins related to cholesterol and steroid metabolism. Our dataset, which describes phenotypic and proteomic alterations, is a valuable resource for further research projects investigating effects of Dex on human testicular cells.

Identification and Analysis of Genes Related to Testicular Size in 14-Day-Old Piglets

The RNA-Seq technology was used to screen the key genes that affect the early development of the testes of Duroc × Landrace × Yorkshire piglets, to determine the regulatory pathway and provide reference for subsequent reproductive performance research, breeding, and other production practices. This study selected 14-day-old Duroc × Landrace × Yorkshire piglets as the trial animals. Testes from piglets with similar weights and no pathological changes were divided into small testis (ST) and large testis (LT) groups, and the RNA-Seq screening of differentially expressed genes (DEGs) was performed to find candidate genes and regulatory pathways related to early testicular development. The results show that 570 DEGs were found in the ST and LT groups, with 281 upregulated and 289 downregulated. The DEGs were mainly enriched on 47 gene ontology (GO) functional items. The Kyoto encyclopedia of genes and genotypes (KEGG) enrichment analysis found that there were 44 significantly enriched KEGG signal pathways, and the regulation of testicular development mainly focused on the arachidonic acid metabolism, Wnt signaling pathway and GnRH secretion pathways. The PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes were found to be as closely related to the testicular development of these Duroc × Landrace × Yorkshire piglets, and the differential gene expression was consistent with the real-time quantitative reverse transcription PCR (real-time qRT-PCR) validation results. This study was validated by high-throughput sequencing analysis and real-time qRT-PCR, and showed that the PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes may be involved in the regulation of germ cell development, spermatogenesis and semen traits. These should be further studied as candidate genes for early testicular development and reproductive trait regulation in boars.

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

Background

In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells.

Methods

Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells' transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR.

Results

The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.

Comparison of miRNA and mRNA Expression in Sika Deer Testes With Age

To elucidate the complex physiological process of testis development and spermatogenesis in Sika deer, this study evaluated the changes of miRNA and mRNA profiles in the four developmental stages of testis in the juvenile (1-year-old), adolescence (3-year-old), adult (5-year-old), and aged (10-year-old) stages. The results showed that a total of 198 mature, 66 novel miRNAs, and 23,558 differentially expressed (DE) unigenes were obtained; 14,918 (8,413 up and 6,505 down), 4,988 (2,453 up and 2,535 down), and 5,681 (2,929 up and 2,752 down) DE unigenes, as well as 88 (43 up and 45 down), 102 (44 up and 58 down), and 54 (18 up and 36 down) DE miRNAs were identified in 3- vs. 1-, 5- vs. 3-, and 10- vs. 5-year-old testes, respectively. By integrating miRNA and mRNA expression profiles, we predicted 10,790 mRNA-mRNA and 69,883 miRNA-mRNA interaction sites. The target genes were enriched by GO and KEGG pathways to obtain DE mRNA (IGF1R, ALKBH5, Piwil, HIF1A, BRDT, etc.) and DE miRNA (miR-140, miR-145, miR-7, miR-26a, etc.), which play an important role in testis development and spermatogenesis. The data show that DE miRNAs could regulate testis developmental and spermatogenesis through signaling pathways, including the MAPK signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, etc. miR-140 was confirmed to directly target mutant IGF1R-3'UTR by the Luciferase reporter assays. This study provides a useful resource for future studies on the role of miRNA regulation in testis development and spermatogenesis.

Identification of three new microsatellites and their effects on body measurement traits in pigs using time of flight-mass spectrometry (TOF-MS)

The body status of livestock affects their physiological function and productive performances. Microsatellites, one of the most used DNA markers, have been found to be associated with pig productive traits. However, their identifications and effects on body measurement traits of the Chinese Qinghai Bamei pig still uncovered. According to our previous sequencing data, in this study, three novel microsatellites were found in this breed. Using time of flight-mass spectrometry (TOF-MS) method, these microsatellites were further identified in a large Bamei pig population. TOF-MS spectra showed that there are three microsatellites loci, named P1, P2 and P3. These microsatellites were linkage equilibrium based on the values of D' and r² tests. Association results demonstrated that P1 locus was associated with the body length, body height and chest width and the beneficial genotype was 150-/150-bp (p < 0.05); and P2 locus was associated with the body height (p < 0.05), and the 145-/145-bp, 145-/147-bp and 145-/149-bp were claimed as favorable genotypes and 145-bp allele was considered as the favorable allele. These findings suggested that P1 and P2 microsatellites might be considered as the candidate genetic markers to select pigs with superior body sizes, especially in local breed.

Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation

Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA sequencing of 34 different tissues in Duroc pigs. In total, 138,403 AS events and 29,270 expressed genes were identified. An alternative donor site was the most common AS form and accounted for 44% of the total AS events. The percentage of the other three AS forms (exon skipping, alternative acceptor site, and intron retention) was approximately 19%. The results showed that the most common AS events involving alternative donor sites could produce different transcripts or proteins that affect the biological processes. The expression of genes with tissue-specific AS events showed that gene functions were consistent with tissue functions. AS increased proteome diversity and resulted in novel proteins that gained or lost important functional domains. In summary, these findings extend porcine genome annotation and highlight roles that AS could play in determining tissue identity.

Aquatic hypoxia disturbs oriental river prawn (Macrobrachium nipponense) testicular development: A cross-generational study

Recently, we reported that hypoxia disrupts the endocrine system and causes metabolic abnormalities in prawns. Although transgenerational impairment effects of hypoxia have become a hot topic in vertebrate, it is unknown whether hypoxia could exert cross-generational effects on testicular function crustaceans. The present study aimed to investigate hypoxia's toxic effects on the testicular function of oriental river prawns (Macrobrachium nipponense) and offspring development. Hypoxia disrupted testicular germ cells quality, caused sex hormone imbalance (testosterone and estradiol), and delayed testicular development. The F1 generation derived from male prawns exposed to hypoxia showed retarded embryonic development, and reduced hatching success and larval development, despite not being exposed to hypoxia. Analysis of the transcriptome the F0 generation (exposed to hypoxia) showed that the impaired testicular functions were associated with changes to mitochondrial oxidative phosphorylation, apoptosis, and steroid biosynthesis. Interestingly, quantitative real-time PCR confirmed that hypoxia could significantly suppress the expression of antioxidant and gonad development-related genes in the testis of the F1 generations, with and without continued hypoxia exposures. In addition, paternal exposure to hypoxia could result in a higher production of reactive oxygen species in offspring testis tissue compared with those without hypoxia exposure. The cross-generational effects of testicular function implied that the sustainability of natural freshwater prawn populations would be threatened by chronic hypoxia.

Pig Hsd17b3: Alternative splice variants expression, insertion/deletion (indel) in promoter region and their associations with male reproductive traits

Hydroxysteroid 17-Beta Dehydrogenase 3 (Hsd17b3), primarily expressed in Leydig cells (LCs) of the mammalian testes, is essential for testosterone biosynthesis and male fertility. The aim of our study was to profile the expression, splice variants (SV) and novel insertion/deletion (indel) of Hsd17b3 in boars. Quantitative analysis showed that the expression level of Hsd17b3 in the testis was significantly highest. Among different testicular cell types, the Hsd17b3 mRNA expression level of LCs was significantly higher than that of SSCs (spermatogonial stem cells) and SCs (Sertoli cells). Furthermore, the SV was firstly identified in pigs and it was highly expressed in LCs comparing with SSCs and SCs. In addition, two mutations were identified in pig Hsd17b3 gene promotor and intron, respectively, which were associated with male reproductive traits (P <  0.05). In conclusion, both transcripts of Hsd17b3 gene were highly expressed in pig testes and LCs; the two novel indel variants of Hsd17b3 gene can be used as potential DNA makers for the marker-assisted selection in pigs. All these findings would enrich the study of Hsd17b3 gene in pig genetic breeding.

Relationship between SNPs of POU1F1 Gene and Litter Size and Growth Traits in Shaanbei White Cashmere Goats

POU (Pit-Oct-Unc) class 1 homeobox 1 (POU1F1, or Pit-1) is a transcription factor that directly regulates pituitary hormone-related genes, as well as affects the reproduction and growth in mammals. Thus, POU1F1 gene was investigated as a candidate gene for litter size and growth performance in goats. In the current study, using direct DNA sequencing, c.682G > T, c.723T > G and c.837T > C loci were genotyped in Shaanbei white cashmere (SBWC) goats (n = 609), but c.876 + 110T > C was monomorphic. Besides, the c.682G > T locus was first identified by HinfI (Haemophilus influenzae Rf) restriction endonuclease. Association analysis results showed that the c.682G > T, c.837T > C loci and diplotypes were significantly associated with goat litter size (p < 0.05). The positive genotypes were GT and TT for the two SNPs, respectively, and the optimal diplotype was H3H7 (GTTT-TTTT). On the other hand, the c.682G > T, c.723T > G and c.837T > C strongly affected growth traits and body measurement indexes in SBWC goats (p < 0.05). The positive genotypes or allele of these SNPs were GT, G and TT, respectively. Additionally, the goats with H3H7 diplotype also had a greater growth status than others (p < 0.05). Here, individuals with same genotype had both a better litter size and growth traits, showing a positive correlation between these economic traits. Meanwhile, the positive genotypes of four SNPs were combined to obtain the optimal diplotype, which was also H3H7. These SNPs, especially the diplotype, could be used for the genomic selection of excellent individuals with a greater litter size and better growth status in goat breeding.

The novel 22 bp insertion mutation in a promoter region of the <i>PITX2</i> gene is associated with litter size and growth traits in goats

Abstract. The paired-like homeodomain 2 (PITX2) gene plays a critical role in regulating development, reproduction, and growth traits in ruminants. Hence, the objective of this study was to explore the polymorphisms of this gene and to evaluate their associations with quantitative traits. Herein, a novel insertion in the promoter region of the PITX2 gene was reported in Shaanbei white cashmere (SBWC) goats (n=1012). The genotype distributions between mothers of single-kid and multi-kid groups within SBWC goats were significantly different (P<0.01), implying that this indel mutation might affect the litter size. Furthermore, association analysis found that this indel mutation was significantly associated with litter size (P=0.001). Individuals with genotype DD had a significantly smaller litter size than those with other genotypes (P<0.01). Besides, this indel was significantly associated with the body length (P=0.042) and the chest width (P=0.031). Especially, the individuals with genotype DD had a significantly lower body length than those with genotype II (P<0.05), which was consistent with the trend in litter size. These findings suggested that the new 22 bp indel mutation within the PITX2 gene is significantly associated with litter size and growth traits; this can be utilized as a functional molecular marker in goat breeding.