Identification of the Key microRNAs and miRNA-mRNA Interaction Networks during the Ovarian Development of Hens

Transcriptome analysis of ovarian tissues highlights genes controlling energy homeostasis and oxidative stress as potential drivers of heterosis for egg number and clutch size in crossbred laying hens

Heterosis is the major benefit of crossbreeding and has been exploited in laying hens breeding for a long time. This genetic phenomenon has been linked to various modes of nonadditive gene action. However, the molecular mechanism of heterosis for egg production in laying hens has not been fully elucidated. To fill this research gap, we sequenced mRNAs and lncRNAs of the ovary stroma containing prehierarchical follicles in White Leghorn, Rhode Island Red chickens as well as their reciprocal crossbreds that demonstrated heterosis for egg number and clutch size. We further delineated the modes of mRNAs and lncRNAs expression to identify their potential functions in the observed heterosis. Results showed that dominance was the principal mode of nonadditive expression exhibited by mRNAs and lncRNAs in the prehierarchical follicles of crossbred hens. Specifically, low-parent dominance was the main mode of mRNA expression, while high-parent dominance was the predominant mode of lncRNA expression. Important pathways enriched by genes that showed higher expression in crossbreds compared to either one or both parental lines were cell adhesion molecules, tyrosine and purine metabolism. In contrast, ECM-receptor interaction, focal adhesion, PPAR signaling, and ferroptosis were enriched in genes with lower expression in the crossbred. Protein network interaction identified nonadditively expressed genes including apolipoprotein B (APOB), transferrin, acyl-CoA synthetase medium-chain family member (APOBEC) 3, APOBEC1 complementation factor, and cathepsin S as hub genes. Among these potential hub genes, APOB was the only gene with underdominance expression common to the 2 reciprocal crossbred lines, and has been linked to oxidative stress. LncRNAs with nonadditive expression in the crossbred hens targeted natriuretic peptide receptor 1, epidermal differentiation protein beta, spermatogenesis-associated gene 22, sperm-associated antigen 16, melanocortin 2 receptor, dolichol kinase, glycine amiinotransferase, and prolactin releasing hormone receptor. In conclusion, genes with nonadditive expression in the crossbred may play crucial roles in follicle growth and atresia by improving follicle competence and increasing oxidative stress, respectively. These 2 phenomena could underpin heterosis for egg production in crossbred laying hens.

microRNA transcriptome analysis of granulosa cells predicts that the Notch and insulin pathways affect follicular development in chickens

MicroRNAs (miRNAs) have been documented to play critical roles in chicken reproduction. Granulosa cell (GC) development of the follicle is closely related to hierarchical follicle ordering, making it an important factor in determining laying performance. Thus, it is meaningful to mine follicular development-related miRNAs. To identify regulatory miRNAs and the biological mechanisms by which they control follicular development, we conducted small RNA sequencing of GCs isolated from prehierarchical follicles named small yellow follicle (SYFG), the smallest hierarchical follicle (F6G), and the largest hierarchical follicle (F1G). A total of 99, 196, and 110 differentially expressed miRNAs (DEMs) were identified in SYFG.vs.F6G, SYFG.vs.F1G, and F6G.vs.F1G, respectively. Of these, 22 miRNAs, including miR-223, miR-103a, miR-449c-3p, and miR-203a, were ubiquitously identified as DEMs in three stages. Target gene prediction suggested that these miRNAs are associated with the MAPK, TGF-β, and Wnt signaling pathways, which are all associated with follicular development. The Notch and insulin signaling pathways were commonly enriched in all three comparisons. RT-qPCR analysis further indicated that the expression levels of PSEN2, which encodes an essential factor regulating Notch and insulin signaling, was significantly changed in SYFG, F6G, and F1G. The current study provides basic data and offers a new foundation for further exploration of the roles of miRNAs in follicular development in chickens.

Transcriptome Profiling of Goose Ovarian Follicle Granulosa Cells Reveals Key Regulatory Networks for Follicle Selection

The selection of follicles determines the reproductive performance of birds, but the process of follicle selection in geese is still elusive. This study focuses on Yangzhou geese during the egg-laying period and divides the follicular development process into three stages: small follicle development, follicle selection, and follicle maturation. Transcriptome sequencing was performed on granulosa cells from large white follicles, small yellow follicles, and F5 and F4 follicles. In addition, we selected the transcripts that remained unchanged during the development and maturation of small follicles but significantly changed during the follicular selection stage as the transcript collection that plays an important role in the follicular selection process. Then, we performed functional analysis on these transcripts and constructed a ceRNA network. The results showed that during the follicular selection stage, the number of differentially expressed mRNAs, miRNAs, and lncRNAs was the highest. In addition, miR-222-3p, miR-2954-3p, miR-126-5p, miR-2478, and miR-425-5p are potential key core regulatory molecules in the selection stage of goose follicles. These results can provide a reference for a better understanding of the basic mechanisms of the goose follicle selection process and potential targets for the precise regulation of goose egg production performance.

Identification of Metabolic Syndrome-Related miRNA-mRNA Regulatory Networks and Key Genes Based on Bioinformatics Analysis

Metabolic syndrome, which affects approximately one-quarter of the world's population, is a combination of multiple traits and is associated with high all-cause mortality, increased cancer risk, and other hazards. It has been shown that the epigenetic functions of miRNAs are closely related to metabolic syndrome, but epigenetic studies have not yet fully elucidated the regulatory network and key genes associated with metabolic syndrome. To perform data analysis and screening of potential differentially expressed target miRNAs, mRNAs and genes based on a bioinformatics approach using a metabolic syndrome mRNA and miRNA gene microarray, leading to further analysis and identification of metabolic syndrome-related miRNA-mRNA regulatory networks and key genes. The miRNA gene set (GSE98896) and mRNA gene set (GSE98895) of peripheral blood samples from patients with metabolic syndrome from the GEO database were screened, and set|logFC|> 1 and adjusted P < 0.05 were used to identify the differentially expressed miRNAs and mRNAs. Differentially expressed miRNA transcription factors were predicted using FunRich software and subjected to GO and KEGG enrichment analysis. Next, biological process enrichment analysis of differentially expressed mRNAs was performed with Metascape. Differentially expressed miRNAs and mRNAs were identified and visualized as miRNA-mRNA regulatory networks based on the complementary pairing principle. Data analysis of genome-wide metabolic syndrome-related mRNAs was performed using the gene set enrichment analysis (GSEA) database. Finally, further WGCNA of the set of genes most closely associated with metabolic syndrome was performed to validate the findings. A total of 217 differentially expressed mRNAs and 158 differentially expressed miRNAs were identified by screening the metabolic syndrome miRNA and mRNA gene sets, and these molecules mainly included transcription factors, such as SP1, SP4, and EGR1, that function in the IL-17 signalling pathway; cytokine-cytokine receptor interaction; proteoglycan syndecan-mediated signalling events; and the glypican pathway, which is involved in the inflammatory response and glucose and lipid metabolism. miR-34C-5P, which was identified by constructing a miRNA-mRNA regulatory network, could regulate DPYSL4 expression to influence insulin β-cells, the inflammatory response and glucose oxidative catabolism. Based on GSEA, metabolic syndrome is known to be closely related to oxidative phosphorylation, DNA repair, neuronal damage, and glycolysis. Finally, RStudio and DAVID were used to perform WGCNA of the gene sets most closely associated with metabolic syndrome, and the results further validated the conclusions. Metabolic syndrome is a common metabolic disease worldwide, and its mechanism of action is closely related to the inflammatory response, glycolipid metabolism, and impaired mitochondrial function. miR-34C-5P can regulate DPYSL4 expression and can be a potential research target. In addition, UQCRQ and NDUFA8 are core genes of oxidative phosphorylation and have also been identified as potential targets for the future treatment of metabolic syndrome.

gga-miR-449b-5p Regulates Steroid Hormone Synthesis in Laying Hen Ovarian Granulosa Cells by Targeting the IGF2BP3 Gene

MiRNAs have been found to be involved in the regulation of ovarian function as important post-transcriptional regulators, including regulators of follicular development, steroidogenesis, cell atresia, and even the development of ovarian cancer. In this study, we evaluated the regulatory role of gga-miR-449b-5p in follicular growth and steroid synthesis in ovarian granulosa cells (GCs) of laying hens through qRT-PCR, ELISAs, western blotting and dual-luciferase reporter assays, which have been described in our previous study. We demonstrated that gga-miR-449b-5p was widely expressed in granulosa and theca layers of the different-sized follicles, especially in the granulosa layer. The gga-miR-449b-5p had no significant effect on the proliferation of GCs, but could significantly regulate the expression of key steroidogenesis-related genes (StAR and CYP19A1) (p < 0.01) and the secretion of P4 and E2 (p < 0.01 and p < 0.05). Further research showed that gga-miR-449b-5p could target IGF2BP3 and downregulate the mRNA and protein expression of IGF2BP3 (p < 0.05). Therefore, this study suggests that gga-miR-449b-5p is a potent regulator of the synthesis of steroid hormones in GCs by targeting the expression of IGF2BP3 and may contribute to a better understanding of the role of functional miRNAs in laying hen ovarian development.

MicroRNA expression profile of chicken cecum in different stages during Histomonas meleagridis infection

Background

Histomonas meleagridis is an anaerobic, intercellular parasite, which infects gallinaceous birds such as turkeys and chickens. In recent years, the reemergence of Histomoniasis has caused serious economic losses as drugs to treat the disease have been banned. At present, H. meleagridis research focuses on virulence, gene expression analysis, and the innate immunity of the host. However, there are no studies on the differentially expressed miRNAs (DEMs) associated with the host inflammatory and immune responses induced by H. meleagridis. In this research, high-throughput sequencing was used to analyze the expression profile of cecum miRNA at 10 and 15 days post-infection (DPI) in chickens infected with Chinese JSYZ-F strain H. meleagridis.

Results

Compared with the controls, 94 and 127 DEMs were found in cecum of infected chickens at 10 DPI (CE vs CC) and 15 DPI (CEH vs CCH), respectively, of which 60 DEMs were shared at two-time points. Gene Ontology (GO) functional enrichment analysis of the target genes of DEMs indicated that 881 and 1027 GO terms were significantly enriched at 10 and 15 DPI, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG, www.kegg.jp/kegg/kegg1.html) pathway enrichment analysis of the target genes of DEMs demonstrated that 5 and 3 KEGG pathways were significantly enriched at 10 and 15 DPI, respectively. For previous uses, the Kanehisa laboratory have happily provided permission. The integrated analysis of miRNA–gene network revealed that the DEMs played important roles in the host inflammatory and immune responses to H. meleagridis infection by dynamically regulating expression levels of inflammation and immune-related cytokines.

Conclusion

This article not only suggested that host miRNA expression was dynamically altered by H. meleagridis and host but also revealed differences in the regulation of T cell involved in host responses to different times H. meleagridis infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03316-2.

The Roles of the miRNAome and Transcriptome in the Ovine Ovary Reveal Poor Efficiency in Juvenile Superovulation

Simple Summary

Using the technology of juvenile superovulation, more follicles can be acquired in juvenile animals than in adult animals. However, oocytes derived from the follicles of juvenile animals are usually of poor quality, meaning that they have lower levels of subsequent maturation and embryonic development. In the present study, we used an exogenous hormone treatment to stimulate Hu sheep in order to compare the differences in ovarian superovulation effects and serum hormone secretion in juvenile and adult sheep. Differentially expressed microRNA (miRNA) and messenger RNA (mRNA) from the ovaries of juvenile and adult Hu sheep were then investigated using high-throughput sequencing technology to reveal the formation mechanism of large numbers of follicles and poor oocyte quality in juvenile ovaries under superovulation treatment. We found that molecules of oar-miR-143 and follicle-stimulating hormone receptor (FSHR), among others, might regulate follicle formation, while oar-miR-485-3p, oar-miR-377-3p, and pentraxin 3 (PTX3), among others, may be associated with oocyte quality. The results will help us to identify miRNAs and mRNAs that could be used to predict ovarian superovulation potential and oocyte quality in the future.

Abstract

Juvenile superovulation can provide a wealth of oocyte material for embryo production, animal cloning, and genetic modification research, but embryos derived from juvenile oocytes show poor efficiency in subsequent developmental capacity. In order to reveal the formation mechanism of large numbers of follicles and poor oocyte quality in juvenile ovaries under superovulation treatment, differentially expressed microRNAs (miRNAs) and messenger RNAs (mRNAs) were characterized and investigated in the ovaries of lambs and adult sheep using high-throughput sequencing technology. The majority of differentially expressed miRNAs (337/358) were upregulated in lamb libraries. The expression levels of mRNAs related to hormone receptors (follicle-stimulating hormone receptor, FSHR; luteinizing hormone/choriogonadotropin receptor, LHCGR; estrogen receptor 1, ESR1), steroid hormone secretion (cytochrome P450 family 11 subfamily A member 1, CYP11A1; cytochrome P450 family 17 subfamily A member 1, CYP17A1; cytochrome P450 family 19 subfamily A member 1, CYP19A1), and oocyte quality (pentraxin 3, PTX3; BCL2 apoptosis regulator, BCL2; caspase 3, CASP3) were significantly different between the lamb and adult libraries. The miRNA aor-miR-143, which targets FSHR, was highly and differentially expressed, and PTX3 was predicted to be targeted by oar-miR-485-3p and oar-miR-377-3p in the ovine ovary. A considerable number of miRNAs were predicted to inhibit ESR1 expression in lamb ovaries. In conclusion, oar-miR-143 and FSHR molecules, among others, might regulate follicle formation, and oar-miR-485-3p, oar-miR-377-3p, and PTX3, among others, may be associated with oocyte quality. These identified miRNAs and mRNAs will be beneficial for the prediction of ovarian superovulation potential and screening of oocytes.