Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/8/2009
Publication Date: 8/1/2010
Citation: Salem, M., Xiao, C., Womack, J., Rexroad Iii, C.E., Yao, J. 2010. A MicroRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss). Marine Biotechnology. 12:410-429. Interpretive Summary: Micro RNAs (MiRNAs) are endogenous, small RNA molecules that were identified in a wide range of eukaryotes. MiRNAs are known to control diverse processes including animal development and growth, cell differentiation, signal transduction, cancer disease, virus-induced immune defense, programmed cell death, insulin secretion and metabolism. About 30% of the human protein-coding genes are negatively regulated by miRNAs which suggests that they have a major role in regulating gene expression. Intensive research has revealed several aspects of miRNA functions in many eukaryotes; yet, little attention has been given to the roles of miRNAs in non-model species including fishes. Rainbow trout, Oncorhynchus mykiss (Walbaum), a member of the Salmonidae family, is the most cultivated, cold, freshwater fish in the US. The need for genetically improved germplasm for aquaculture has supported the continued development of the rainbow trout genomic resources. We previously identified and characterized a limited number of miRNAs in rainbow trout unfertilized eggs, the first report of miRNAs from a non-model fish and aquaculture species. We now have identified and characterized 54 miRNAs from rainbow trout somatic tissues and profiled their expression patterns. Our results suggest that their is great potential for miRNAs to affect biochemical processes underlying important aquaculture production traits.
Technical Abstract: Background: MicroRNAs (miRNA) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. MiRNAs are most often identified through computational prediction from genome sequences. The rainbow trout genome sequence is not available yet, which does not allow miRNA prediction for this species which is of great economic interest for aquaculture and sport fisheries, and is a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. Results: To identify miRNAs from rainbow trout, we constructed a miRNA library from a pool of nine somatic tissues. Analysis of the library identified 210 unique sequences representing 54 distinct miRNAs; 50 with conserved sequences matching previously identified miRNAs and 4 novel miRNAs. In addition, 13 miRNAs were computationally predicted from the rainbow trout transcriptome. Real-time PCR was used to measure miRNA expression patterns in adult somatic tissues and unfertilized eggs. The majority of the miRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. Potential miRNA-target interactions were computationally predicted and single nucleotide polymorphisms (SNPs) were identified in the miRNAs and their target sites in the rainbow trout transcripts. Conclusion: The rainbow trout miRNAs identified and characterized in this study provide a new tool for functional genome research in salmonids. Tissue-specific miRNAs may be evaluated to serve as molecular markers predictive of specific functional and diagnostic implications. Identification of sequence variations in the miRNA -target interactions may be particularly useful for rainbow trout breeding programs.