Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol

Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout (Oncorhynchus mykiss), but the mechanisms directing with this response are not fully understood. To better characterize the effects of E2 in muscle, we identified differentially regulated mRNAs and lncRNAs in juvenile rainbow trout exposed to E2. Here, we performed next-generation RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in skeletal muscle of rainbow trout injected with E2. A total of 226 lncRNAs and 253 mRNAs were identified as differentially regulated. We identified crucial pathways, including several signal transduction pathways, hormone response, oxidative response and protein, carbon and fatty acid metabolism pathways. Subsequently, a functional lncRNA-mRNA co-expression network was constructed, which consisted of 681 co-expression relationships between 164 lncRNAs and 201 mRNAs. Moreover, a lncRNA-pathway network was constructed. A total of 65 key lncRNAs were identified that regulate 20 significantly enriched pathways. Overall, our analysis provides insights into mRNA and lncRNA networks in rainbow trout skeletal muscle and their regulation by E2 while understanding the molecular mechanism of lncRNAs.