Mechanistic insights into regulatory roles of long non-coding RNAs during ovarian development in heat-stressed Nile Tilapia (Oreochromis niloticus).

Abstract

High temperatures adversely affect ovarian development in teleosts, manifested as elevated follicular atresia rates and reduced egg quality. However, the transcriptional and post-transcriptional regulatory mechanisms underlying heat stress-induced ovary syndrome in teleosts are poorly understood. In this study, RNA-Seq analyses were conducted to identify long non-coding RNAs (lncRNAs) and mRNAs showing differential expression in the ovary of reproductively active Nile tilapia (Oreochromis niloticus) between heat-stressed (34.5 ± 0.5 °C) and control (27.5 ± 0.5 °C) groups. By analyzing RNA-Seq data, we identified 681 differentially expressed (DE)-lncRNAs and 1764 DE-mRNAs after 12 days of heat exposure. Six randomly selected DE-lncRNAs and six DE-mRNAs were validated by RT-qPCR, including MSTRG.8300.1, elovl5, and others. The DE-lncRNAs were predicted to regulate 99 cis and 453 trans DE-mRNA targets. Pathway enrichment analyses indicated that these potential targets were involved in controlling the ovarian state and in the stimulus response, including the ErbB signaling pathway, endocytosis, apoptosis, and oocyte meiosis. A protein-protein interaction network analysis of DE-lncRNA predicted targets revealed six hub genes and four functional modules involved in ovarian responses to thermal stress. By combining the previously reported heat stress-responsive DE-miRNAs and the putative lncRNAs and mRNA targets predicted in this study, we constructed a predicted competing endogenous RNA (ceRNA) network that may be involved in the regulation of ovarian development under high temperatures. This predicted ceRNA network comprised 213 DE-mRNAs, 216 DE-lncRNAs, and 23 DE-miRNAs. Overall, our findings provide a foundational framework for elucidating heat stress-induced ovarian dysfunction in Nile tilapia via the lncRNA-associated regulatory network, but all predicted interactions in this study require further experimental functional validation.