Protamine-1 represents a sperm specific gene transcript: a study in Callithrix jacchus and Bos taurus

Extensive Variation in Gene Expression is Revealed in 13 Fertility-Related Genes Using RNA-Seq, ISO-Seq, and CAGE-Seq From Brahman Cattle

Fertility is a key driver of economic profitability in cattle production. A number of studies have identified genes associated with fertility using genome wide association studies and differential gene expression analysis; however, the genes themselves are poorly characterized in cattle. Here, we selected 13 genes from the literature which have previously been shown to have strong evidence for an association with fertility in Brahman cattle (Bos taurus indicus) or closely related breeds. We examine the expression variation of the 13 genes that are associated with cattle fertility using RNA-seq, CAGE-seq, and ISO-seq data from 11 different tissue samples from an adult Brahman cow and a Brahman fetus. Tissues examined include blood, liver, lung, kidney, muscle, spleen, ovary, and uterus from the cow and liver and lung from the fetus. The analysis revealed several novel isoforms, including seven from SERPINA7. The use of three expression characterization methodologies (5′ cap selected ISO-seq, CAGE-seq, and RNA-seq) allowed the identification of isoforms that varied in their length of 5′ and 3′ untranslated regions, variation otherwise undetectable (collapsed as degraded RNA) in generic isoform identification pipelines. The combinations of different sequencing technologies allowed us to overcome the limitations of relatively low sequence depth in the ISO-seq data. The lower sequence depth of the ISO-seq data was also reflected in the lack of observed expression of some genes that were observed in the CAGE-seq and RNA-seq data from the same tissue. We identified allele specific expression that was tissue-specific in AR, IGF1, SOX9, STAT3, and TAF9B. Finally, we characterized an exon of TAF9B as partially nested within the neighboring gene phosphoglycerate kinase 1. As this study only examined two animals, even more transcriptional variation may be present in a genetically diverse population. This analysis reveals the large amount of transcriptional variation within mammalian fertility genes and illuminates the fact that the transcriptional landscape cannot be fully characterized using a single technology alone.

Cryopreservation and its effects on motility and gene expression patterns and fertilizing potential of bovine epididymal sperm

Despite encountering new challenges in using epididymal sperm recovered from cauda epididymides, this accessible and, in some species, worthwhile sample makes inevitable the further development of a suitable cryopreservation protocol. In this study, sperm was recovered from the epididymis of 4°C overnight stored slaughtered bulls' testes and the effects of cryopreservation on the bovine epididymal sperm motility (with CASA) and gene expression patterns (with quantitative Real time-PCR) were evaluated. Moreover the fertilizing potential of cryopreserved epididymal sperm was used in in vitro fertilization (IVF). After freezing and thawing of epididymal sperm, total and slow progressive sperm motility, VCL, VAP, MAD, ALH and BCF were significantly decreased (p < .05), while in the parameters of fast progressive motility, VSL, LIN, WOB and STR there were not any significant variations in the frozen sperm compared to fresh (non-frozen) counterpart. The assessment of abundance of transcripts encoding motility (TSSK6) and fertility (PRM1 and PRM2)-related genes in epididymal sperm, showed that these transcripts were affected by freezing especially in slow progressive motility status (p < .01). Furthermore, cleavage and blastocyst rate did not present any significant differences between bovine embryos produced in vitro by fresh or frozen-thawed epididymal sperm. It can be concluded that epididymal sperm has enough freezability after overnight testes storage, and cryopreservation could not affect the percentage of in vitro produced embryos in spite of the changes of relative abundance of some transcripts and direction progressive motility pattern of sperm.

Sub-fertility in crossbred bulls: deciphering testicular level transcriptomic alterations between zebu (Bos indicus) and crossbred (Bos taurus x Bos indicus) bulls

BACKGROUND

The incidence of poor semen quality and sub-fertility/infertility is higher in crossbred as compared to Zebu males. Several attempts have been made to understand the possible reasons for higher incidence of fertility problems in crossbred males, at sperm phenotype, proteome and genome level but with variable results. Since the quality of the ejaculated spermatozoa is determined by the testicular environment, assessing the testicular transcriptome between these breeds would help in identifying the possible mechanisms associated with infertility in crossbred bulls. However, such information is not available. We performed global transcriptomic profiling of testicular tissue from crossbred and Zebu bulls using Agilent Bos taurus GXP 8X60k AMADID: 29411 array. To the best of our knowledge, this is the first study comparing the testicular mRNAs between crossbred and Zebu bulls.

RESULTS

Out of the 14,419 transcripts detected in bovine testis, 1466 were differentially expressed between crossbred and Zebu bulls, in which 1038 were upregulated and 428 were downregulated in crossbred bulls. PI4KB and DPY19L2 genes, reported to be involved in sperm capacitation and acrosome formation respectively, were among the top 10 downregulated transcripts in crossbred testis. Genes involved in ubiquitination and proteolysis were upregulated, while genes involved in cell proliferation, stem cell differentiation, stem cell population maintenance, steroidogenesis, WNT signalling, protein localization to plasma membrane, endocannabinoid signalling, heparin binding, cAMP metabolism and GABA receptor activity were downregulated in crossbred testis. Among the 10 genes validated using qPCR, expression of CCNYL, SOX2, MSMB, SPATA7, TNP1, TNP2 and CRISP2 followed the same trend as observed in microarray analysis with SPATA7 being significantly downregulated and transition proteins (TNP1, TNP2) being significantly upregulated in crossbred bulls.

CONCLUSIONS

Abundant proteolysis by ubiquitination and downregulation of WNT signaling, cell proliferation, differentiation and steroidogenesis might be associated with higher incidence of poor semen quality and/or sub-fertility/infertility in crossbred bulls as compared to Zebu bulls. Downregulation of SPATA7 (Spermatogenesis Associated 7) and upregulation of transition proteins (TNP1 and TNP2) in crossbred bull testis might be associated with impaired spermatogenesis processes including improper chromatin compaction in crossbred bulls.