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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #340500

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

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

item WANG, JIAN - University Of Delaware
item KOGANTI, PRASANTHI - West Virginia University
item YAO, JIANBO - West Virginia University
item Cleveland, Beth

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2017
Publication Date: 9/18/2017
Citation: Wang, J., Koganti, P., Yao, J., Cleveland, B.M. 2017. Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol [serial online]. Scientific Reports. 7:11780.

Interpretive Summary: 17-Estradiol is an estrogenic hormone that reduces rainbow trout growth and muscle mass, although the mechanisms through which estradiol exerts these effects is not fully understood. This study investigated the ability of estradiol to regulate long non-coding RNAs (lncRNA) in muscle as a potential mechanism involved in the response. LncRNAs play critical roles in numerous biological processes and regulate gene expression at both transcriptional and post-translational levels. In this study, 226 lncRNAs were identified as differentially expressed by estradiol in rainbow trout muscle. A functional lncRNA-mRNA co-expression network was also constructed to identify potential relationships between lncRNA and genes that encode proteins. These findings indicate that the estradiol regulates growth and fillet yield partially through lncRNA-mediated changes in gene expression, thereby identifying new mechanisms affecting economically important traits.

Technical Abstract: Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout, 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.