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

Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function

Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds. Furthermore, we found 1622 co-differentially expressed genes (co-DEGs), 122 co-differentially expressed lncRNAs (co-DELs), 39 co-differentially expressed miRNAs (co-DEMs) in BMI vs introduced commercial breeds (DU and LW). Functional analysis revealed that these co-DEGs and co-DELs/co-DEMs target genes were enriched in male sexual function pathways, including MAPK, AMPK, TGF-β/Smad, Hippo, NF-kappa B, and PI3K/Akt signaling pathways. Additionally, we established 10,536 lncRNA-mRNA, 11,248 miRNA-mRNA pairs, and 62 ceRNA (lncRNA-miRNA-mRNA) networks. The ssc-miR-1343 had the most interactive factors in the ceRNA network, including 20 mRNAs and 3 lncRNAs, consisting of 56 ceRNA pairs. These factors played extremely important roles in the regulation of testis function as key nodes in the interactive regulatory network. Our results provide insight into the functional roles of lncRNAs and miRNAs in porcine testis and offer a valuable resource for understanding the differences between Chinese indigenous and introduced Western pigs.

Seasonal patterns of miRNA and mRNA expression profiles in the testes of plateau zokors (Eospalax baileyi)

The gonads of seasonal breeding animals undergo periodic annual changes in morphology, physiological hormones, and gene expression levels. To clarify the regulatory mechanism of miRNAs in the seasonal testicular development and spermatogenesis of plateau zokors, the miRNA expression profiles in their testicles during breeding and non-breeding seasons were analyzed. In total, 447 miRNAs, including 366, 81, and 167 known, novel, and differentially expressed (DE) miRNAs, respectively, were determined in the testes. Compared to the non-breeding season, 90 DE miRNAs were upregulated and 77 DE miRNAs were downregulated during the breeding season. By analysing the miRNA and mRNA expression profiles, we predicted 2096 significant target mRNAs. According to the miRNA-mRNA interaction network, target mRNAs with DE miRNAs were related to testicular development and spermatogenesis. GO indicated that target mRNAs were enriched in spermatogenesis, cell differentiation, multicellular biological development, and flagellated sperm movement and were associated with regulating testicular development and spermatogenesis. KEGG suggested that target mRNAs were enriched in lipid and fructose metabolism and provided energy and material for spermatogenesis. The target mRNA of rno-miR-24-3p was determined to be Polyubiquitin-B (UBB). Our results provide a reference for revealing the mechanism by which miRNAs regulate testicular development and spermatogenesis in plateau zokors, which has important implications for understanding the regulation of seasonal reproduction in animals.

Association between Yili goose sperm motility and expression profiles of mRNA and miRNA in testis

BACKGROUND

The study was conducted to find out the candidate microRNA (miRNA) and genes that associated with sperm motility of Yili goose through small RNA sequencing of testicular tissue of Yili goose, and provide a theoretical basis for the study of the regulation mechanism of sperm motility of Yili goose gander.

RESULTS

In this study, five male geese with high sperm motility and five male geese with low sperm motility were slaughtered to obtain their testis tissues for small RNA sequencing, and biological information methods were used for data analysis. The results showed that a total of 1575 known miRNAs and 68 novel miRNAs were identified in the testis tissue of Yili goose, and 71 differentially expressed miRNAs and 660 differentially expressed genes were screened. GO functional analysis showed that miRNAs target genes were mainly involved in the binding, kinase activity, structural constituent of cytoskeleton and intermediate filament cytoskeleton. KEGG functional analysis showed that miRNAs target genes were significantly enriched in arginine and proline metabolism, glycolysis / gluconeogenesis, fructose and mannose metabolism and beta-Alanine metabolism and other pathways. miRNAs-mRNAs interaction network suggests miR-140/miR-140-3p/miR-140-3p-NKAIN3, let-7d-BTG1 and miR-145-5p/miR -145a-5p-CLEC2E may play an important role in testis development and spermatogenesis.

CONCLUSIONS

The results of this study suggest that the sperm motility of Yili goose may be regulated by different miRNAs, and the target genes are significantly enriched in pathways related to sperm metabolism, indicating that miRNAs affect the sperm motility of Yili goose by regulating the metabolic process of sperm and the expression of related genes. This study can provide a reference for revealing the regulation mechanism of Yili goose sperm motility at the molecular level.

Hypoxia-induced m6A demethylase ALKBH5 promotes ovarian cancer tumorigenicity by decreasing methylation of the lncRNA RMRP

Ovarian cancer is one of the most lethal and drug-resistant gynecological diseases. Among the various post-transcriptional RNA modifications, N6-methyladenosine (m6A) has been implicated in several malignancies, including breast cancer. Recently, the biological significance of long noncoding RNA (lncRNA) methylation has garnered significant attention. The N6-methyladenosine (m6A) demethylase ALKBH5 (Alkylation Repair Homolog Protein 5) has been shown to promote ovarian cancer development by reducing the methylation of the lncRNA RMRP. In this study, we found that a hypoxic microenvironment induces an increase in ALKBH5 expression in ovarian cancer. Both in vitro and in vivo investigations demonstrated that ALKBH5, which is overexpressed in human ovarian cancer, promotes carcinogenesis. Furthermore, using bioinformatics analysis, we predicted interactions between ALKBH5 and lncRNAs, confirming RMRP as a potential binding lncRNA for ALKBH5. ALKBH5 was found to upregulate RMRP expression via demethylation. Knockdown of RMRP in ovarian cancer cell lines led to a decrease in cell growth and migration. Additionally, we demonstrated that the inhibition of ovarian cancer by ALKBH5 knockdown is partially mediated by RMRP suppression. In conclusion, our findings reveal a novel mechanism in which ALKBH5 promotes ovarian cancer by demethylating the lncRNA RMRP, suggesting its potential as a therapeutic target for the disease.

Connecting the Dots: N6-Methyladenosine (m6 A) Modification in Spermatogenesis

N6-methyladenosine (m6 A) is the most common RNA modification found in eukaryotes and is involved in multiple biological processes, including neuronal development, tumorigenesis, and gametogenesis. It is well known that methylation-modifying enzymes (classified into writers, erasers, and readers) mediate catalysis, clearance, and recognition of m6 A. Recent studies suggest that these genes may be associated with spermatogenesis. Numerous studies have revealed the m6 A role during spermatogenesis. However, the expression patterns and relationships of these m6 A enzymes during various stages of spermatogenesis remain unknown. In this review, it is aimed to provide an overview of m6 A enzyme functions and elucidate their potential mechanisms and regulatory relationships at a specific phase during spermatogenesis, providing new insights into the m6 A modification underlying the spermatogenesis process.

Association between Sperm Morphology and Altered Sperm microRNA Expression

Simple Summary

Sperm morphology is usually determined subjectively, and studies focused exclusively on sperm morphology are scarce. There is a global tendency to find objective markers of spermatozoa quality, including sperm morphology, as this will allow for a more personalized approach to managing and treating male infertility. MicroRNAs (miRNAs) are widely recognized as promising putative and objective biomarkers. In our study, we included 15 patients with normal sperm morphology and 13 patients with abnormal sperm morphology. We determined the expression profiles of 13 different miRNAs in the sperm of these participants and revealed that 9 miRNAs could serve as potential biomarkers of sperm morphology in spermatozoa.

Abstract

Evaluation of male infertility has been based on semen analysis for years. As this method can be subjective at times, there is a scientific tendency to discover stable and quantifiable biomarkers. This study included 28 couples who underwent an in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) cycle. The couples were assigned into two groups, according to sperm morphology. Couples where the males were normozoospermic were placed in the control group (15 participants), while couples where males had teratozoospermia were placed in the study group (13 participants). Thirteen candidate miRNAs were selected for qPCR analysis, based on our literature search. We determined significant under-expression of nine miRNAs (miR-10a-5p/-15b-5p/-26a-5p/-34b-3p/-122-5p/-125b-5p/-191-5p/-296-5p and let-7a-5p) in spermatozoa from patients with teratozoospermia compared to the controls, whereas expression levels of four miRNAs (miR-92a-3p/-93-3p/-99b-5p/-328-3p) did not significantly differ between the study and control groups. The expression levels of all 13 included miRNAs were significantly positively correlated with each other and significantly positively associated with spermatozoa morphology, excluding miR-99b-5p. There were no other significant associations between miRNA expression and sperm quality parameters. Only expression levels of miR-99b-5p were significantly positively correlated with good-quality day 3 embryo rate (ρ = 0.546; p = 0.003), while other variables of the IVF/ICSI cycle outcome showed no significant associations with miRNA expression profiles. This is one of the rare studies providing an insight directly into miRNA profiles in regard to sperm morphology. We identified nine miRNAs that could serve as biomarkers of spermatozoa quality in regard to teratozoospermia.

The combination of SMRT sequencing and Illumina sequencing highlights organ-specific and age-specific expression patterns of miRNAs in Sika Deer

Due to the lack of high-quality Sika Deer (Cervus nippon) transcriptome and sRNAome across multiple organs or development stages, it is impossible to comprehensively analyze the mRNA and miRNA regulatory networks related to growth, development and immunity response. In this study, we used single molecule-real time sequencing (SMRT-seq) and Illumina sequencing methods to generate transcriptome and sRNAome from ten tissues and four age groups of Sika Deer to help us understand molecular characteristics and global miRNA expression profiles. The results showed that a total of 240,846 consensus transcripts were generated with an average length of 2,784 bp. 4,329 Transcription factors (TFs), 109,000 Simple Sequence Repeats (SSRs) and 18,987 Long non-coding RNAs (LncRNAs) were identified. Meanwhile, 306 known miRNAs and 143 novel miRNAs were obtained. A large number of miRNAs showed organ-specific and age-specific differential expression patterns. In particular, we found that the organ-specific miRNAs were enriched in the brain, some of which shared only between the brain and adrenal. These miRNAs were involved in maintaining specific functions within the brain and adrenal. By constructing miRNA96mRNA interaction networks associated with Sika Deer immunity, we found that miRNAs (miR-148a, miR-26a, miR-214, let-7b, etc.) and mRNAs (CD6, TRIM38, C3, CD163, etc.) might play an important role in the immune response of Sika Deer spleen. Together, our study generated an improved transcript annotation for Sika Deer by SMRT-seq and revealed the role of miRNA in regulating the growth, development and immunity response of Sika Deer.

Transcriptome sequencing reveals differences between leydig cells and sertoli cells of yak

In this study, we detected the expression of mRNAs, lncRNAs, and miRNAs in primary cultured leydig cells (LCs) and sertoli cells (SCs) of yak by RNA sequencing technology. A total of 84 differently expression mRNAs (DEmRNAs) (LCs vs. SCs: 15 up and 69 down), 172 differently expression lncRNAs (DElncRNAs) (LCs vs. SCs: 36 up and 136 down), and 90 differently expression miRNAs (DEmiRNAs) (LCs vs. SCs: 72 up and 18 down) were obtained between the two types of cells. GO enrichment and KEGG analysis indicated that the differential expression genes (DEGs) were more enriched in the regulation of actin cytoskeleton, Rap1/MAPK signaling pathway, steroid biosynthesis, focal adhesion, and pathways associated with metabolism. Targeted regulation relationship pairs of 3β-HSD and MSTRG.54630.1, CNTLN and MSTRG.19058.1, BRCA2 and MSTRG.28299.4, CA2 and novel-miR-148, and ceRNA network of LAMC3-MSTRG.68870.1- bta-miR-7862/novel-miR-151/novel-miR-148 were constructed by Cytoscape software. In conclusion, the differences between LCs and SCs were mainly reflected in steroid hormone synthesis, cell proliferation and metabolism, and blood-testicular barrier (BTB) dynamic regulation, and 3β-HSD, CNTLN, BRCA2, CA2, and LAMC3 may be the key factors causing these differences, which may be regulated by ncRNAs. This study provides a basic direction for exploring the differential regulation of LCs and SCs by ncRNAs.

Small RNA perspective of physical exercise-related improvement of male reproductive dysfunction due to obesity

PURPOSE

To study whether physical exercise can effectively ameliorate obesity-induced abnormalities in male fertility and provide a new perspective on the role of small noncoding RNAs in spermatogenesis in obese male mice.

METHODS

In this study, four-week-old C57/Bl6 male mice were randomly allocated to receive a control diet, a high-fat diet or physical exercise intervention for 40 weeks. Purified round spermatids and spermatozoa were obtained after intervention. Sperm motility, concentration, the ability of the sperm to undergo capacitation and acrosome reaction were assessed. Small RNA sequencing was conducted on round spermatids and spermatozoa. The small noncoding RNAs expression pattern was systematically analyzed.

RESULTS

The spermatozoa concentration and percentage of motile spermatozoa, the capacitation and acrosome reaction, and the reproductive success rate, including mating success and pregnancy success, were decreased or delayed in the obesity group compared with controls. Physical exercise was able to restore the parameters to normal levels. Three microRNAs were consistently upregulated and 5 were downregulated in round spermatids and epididymal spermatozoa between the obesity and control groups.

CONCLUSIONS

This report provides evidence that the adverse effects of obesity could be offset after physical exercise. small noncoding RNAs, especially microRNAs in germ cells, may play an important role in the effects of obesity and physical exercise on spermatozoa.