Integrated analyses of miRNA-mRNA expression profiles of ovaries reveal the crucial interaction networks that regulate the prolificacy of goats in the follicular phase

Abstract

Background Litter size is an important index of mammalian prolificacy and is determined by the ovulation rate. The ovary is a crucial organ for mammalian reproduction and is associated with follicular development, maturation and ovulation. However, prolificacy is influenced by multiple factors, and its molecular regulation in the follicular phase remains unclear. Methods Ten female goats with no significant differences in age and weight were randomly selected and divided into either the high-yielding group (n = 5, HF) or the low-yielding group (n = 5, LF). Ovarian tissues were collected from goats in the follicular phase and used to construct mRNA and miRNA sequencing libraries to analyze transcriptomic variation between high- and low-yield Yunshang black goats. Furthermore, integrated analysis of the differentially expressed (DE) miRNA-mRNA pairs was performed based on their correlation. The STRING database was used to construct a PPI network of the DEGs. RT–qPCR was used to validate the results of the predicted miRNA-mRNA pairs. Luciferase analysis and CCK-8 assay were used to detect the function of the miRNA-mRNA pairs and the proliferation of goat granulosa cells (GCs). Results A total of 43,779 known transcripts, 23,067 novel transcripts, 424 known miRNAs and 656 novel miRNAs were identified by RNA-seq in the ovaries from both groups. Through correlation analysis of the miRNA and mRNA expression profiles, 263 negatively correlated miRNA-mRNA pairs were identified in the LF vs. HF comparison. Annotation analysis of the DE miRNA-mRNA pairs identified targets related to biological processes such as “estrogen receptor binding (GO:0030331)”, “oogenesis (GO:0048477)”, “ovulation cycle process (GO:0022602)” and “ovarian follicle development (GO:0001541)”. Subsequently, five KEGG pathways (oocyte meiosis, progesterone-mediated oocyte maturation, GnRH signaling pathway, Notch signaling pathway and TGF-β signaling pathway) were identified in the interaction network related to follicular development, and a PPI network was also constructed. In the network, we found that CDK12, FAM91A1, PGS1, SERTM1, SPAG5, SYNE1, TMEM14A, WNT4, and CAMK2G were the key nodes, all of which were targets of the DE miRNAs. The PPI analysis showed that there was a clear interaction among the CAMK2G, SERTM1, TMEM14A, CDK12, SYNE1 and WNT4 genes. In addition, dual luciferase reporter and CCK-8 assays confirmed that miR-1271-3p suppressed the proliferation of GCs by inhibiting the expression of TXLNA. Conclusions These results increase the understanding of the molecular mechanisms underlying goat prolificacy. These results also provide a basis for studying interactions between genes and miRNAs, as well as the functions of the pathways in ovarian tissues involved in goat prolificacy in the follicular phase.

Differentially Expressed Circular RNA Profile Signatures Identified in Prolificacy Trait of Yunshang Black Goat Ovary at Estrus Cycle

“…Three duplicates per sample were analyzed, and a RocheLight Cycler ® 480 Ⅱ system (Roche Applied Science, Mannheim, Germany) was used to establish a standard curve. The following steps were applied for RT-qPCR: initial denaturation at 95 °C for 5 min, followed by 40 cycles of denaturation at 95 °C for 5 s, and annealing at 60 °C for 30 s. The data were analyzed using the 2 -∆∆Ct method ( Liu et al, 2021 ). The relative expression was calculated by a dependent sample t -test and SPSS 19.0 was used to analyze the significance of any differences.…”

Integrated Transcriptome Analysis Reveals the Crucial mRNAs and miRNAs Related to Fecundity in the Hypothalamus of Yunshang Black Goats during the Luteal Phase

“…In this study, the miRNA was highly expressed in the hypothalamus, speculating that it could regulate the reproductive performance of goats by affecting the proliferation of nerve cells. A previous study of our subject also demonstrated that miR-1271 targeting TXLNA in ovarian tissue, was a potential regulatory pathway affecting the reproductive performance of goats [ 68 ]. The interaction network in this study showed that miR-1271 targets PNN interacting serine and the arginine rich protein ( PNISR ).…”

Temporal transcriptomic changes in microRNAs involved in the host immune response and metabolism during Neospora caninum infection

“…Dysregulation of miRNA expression has been reported for several tissues/organs (e.g. ovary [ 45 ], liver [ 46 ], pituitary [ 47 ], lung [ 48 ]) and types of cells (e.g. skeletal muscle satellite cells [ 49 ], skin fibroblast cells [ 50 ], Leydig cells [ 51 ], blood leukocytes and milk somatic cells [ 52 ], intramuscular preadipocytes [ 53 ], endometrial epithelium cells [ 54 ]) in physiological and pathological processes in goats, including in response to infectious diseases.…”