MicroRNA Expression Profiling and Functional Analysis of CDH3 during Oogenesis in the Chinese Alligator (Alligator sinensis)

MicroRNAs (miRNAs), noncoding RNAs that regulate the expression of target mRNAs, have gained attention. Nevertheless, the biological mechanism underlying oogenesis in crocodiles remains unclear. In this study, RNA sequencing was utilized to analyses miRNA expression at 1-, 15-, and 90-days post hatching (dph) in Alligator sinensis. We identified 92 differentially expressed known miRNAs. Among these genes, 17, 1, and 5 had specific expression patterns at 1, 15, and 90-dph, respectively. GO and KEGG analyses of the predicted miRNA targets revealed enrichment in cell adhesion molecule pathways. The expression of CDH3 was significantly higher than that of other family members and was high during the embryonic stage, which coincided with the commencement of mammalian oogenesis. Our prediction indicated the presence of three Ca2+ binding sites, two cadherin domains, and a cadherin cytoplasmic region in the CDH3 amino acid sequence. This finding suggests a similar cell adhesion function to that of mammalian CAM family genes. IHC analysis revealed minimal CDH3 expression in the germ cell nests at 1-dph. Elevated CDH3 expression was observed in primordial follicles formed via Nest breakdown at 15-dph. Notably, CDH3 expression decreased significantly at 90-dph, but positive signals remained in thecal epithelia of the medullary cavities. The results of lentivirus experiments revealed that CDH3 downregulation suppressed the expression of oogenesis genes (FSHR, CYP19A1, BMP15, and BCL2). Our research highlights the function of miRNAs in crocodilian oogenesis, and CDH3 is proposed to be crucial for reproductive developmental mechanisms.