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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION

Location: Cool and Cold Water Aquaculture Research

Title: Integrative Micro-Rna and Proteomic Approaches Identify Molecular Markers Predictive of Muscle Atrophy in Rainbow Trout

Authors
item Salem, Mohamed - WEST VIRGINIA UNIVERSITY
item Kenney, Brett - WEST VIRGINIA UNIVERSITY
item Rexroad, Caird
item Yao, Jainbo - WEST VIRGINIA UNIVERSITY

Submitted to: American Fisheries Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: August 28, 2009
Publication Date: August 30, 2009
Citation: Salem, M., Kenney, B., Rexroad Iii, C.E., Yao, J. 2009. INTEGRATIVE MICRO-RNA AND PROTEOMIC APPROACHES IDENTIFY MOLECULAR MARKERS PREDICTIVE OF MUSCLE ATROPHY IN RAINBOW TROUT [abstract]. American Fisheries Society Annual Meeting. Papaer No. 10

Technical Abstract: Background: MicroRNAs (miRNA) are small, highly conserved, non-coding RNAs. MiRNAs are the most significant regulators in gene expression which negatively regulate target mRNAs at the posttranscriptional levels. Recently, we have cloned and characterized a “miRNAome” in rainbow trout. In addition, we used in silico approaches to predict several miRNA -target pairs in the rainbow trout transcriptome. However, experimental validation of the in silico predicted miRNA -target pairs has been a great challenge. Reciprocal expression of miRNAs and predicted target proteins within a physiological context has been practiced as an approach to support the presence and relevance of miRNA -target pairs. Results: We analyzed the reciprocal expression of miRNAs (microarray techniques) and target proteins (proteomic techniques) using vitellogenesis-associated fish muscle degradation as a physiological context. A miRNA microarray identified 7 up-regulated and 9 down-regulated miRNAs in atrophying muscles. Using a label-free LC/MS-based protein quantification method we identified 42 more abundant and 62 less abundant proteins in the atrophying muscles. A total of 202 miRNA -target pairs were in sillico predicted (combination of the 16 differentially expressed miRNAs and sample of 41 proteins) from reciprocally differentially expressed miRNAs and proteins. Conclusion: Integrative miRNA and proteomic approaches provided molecular basis to validate miRNA-target predication and is a new tool for functional genome research in fish. This study identified novel molecular biomarkers for muscle atrophy and fillet quality in rainbow trout. MiRNAs may serve as molecular markers, predictive of specific functional and diagnostic implications which are particularly useful for fish breeding programs.

Last Modified: 8/21/2014
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