RNA-Seq Analysis of the Key Long Noncoding RNAs and mRNAs Related to the Regulation of Hepatic Lipid Metabolism in Oreochromis niloticus

Abstract

Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalances and fatty liver disease during intensive farming. Long non-coding RNAs (lncRNAs) perform essential roles in various biological processes, including lipid metabolism. However, the lncRNAs involved in hepatic lipid metabolism in tilapia have not yet been identified. In this study, Illumina sequencing and bioinformatic analyses were performed on the liver of juvenile male GIFT fed a high-fat diet (HFD, 18.5% lipid) or a normal-fat diet (NFD, 8% lipid) for 56 days. RNA-seq analyses revealed 299 differentially expressed (DE)-mRNAs and 284 DE-lncRNAs between these two groups. The transcript profiles of 14 candidates (seven DE-mRNA and seven DE-lncRNAs) were verified by qRT-PCR, and the results were consistent with the RNA-seq results. Furthermore, 65 cis target genes and 3610 trans target genes of DE-lncRNAs were predicted. Functional analyses suggested that multiple metabolic pathways are affected by a high fat intake, including the PPAR signaling, fatty acid degradation, and fatty acid metabolism pathways. A co-expression network analysis indicated that many lncRNAs interact with numerous genes involved in lipid metabolism, and that some genes are regulated by multiple lncRNAs. The expression patterns of three lncRNAs (MSTRG.14598.1, MSTRG.6725.3, and MSTRG.13364.2) and their potential target genes (faldh, slc25a48, and fabp7a) in the PPAR signaling pathway were investigated. Our study provides new information about lncRNAs associated with lipid metabolism in tilapia.