ARS | Publication request: Characterization of the rainbow trout oocyte microRNA transcriptome

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 24, 2012
Publication Date: June 25, 2012
Citation: Ma, H., Hostuttler, M.A., Wei, H., Rexroad III, C.E., Yao, J. 2012. Characterization of the rainbow trout oocyte microRNA transcriptome. PLoS One. 7(6):1-8.

Interpretive Summary: Maintaining a high degree of egg quality from rainbow trout brooders is critical so that fertilization and embryonic development lead to successful growth through to the fingerling stage. Identification of biomarkers that could serve as indicators of egg quality would provide the capability to better predict reproductive success. To this end we used high-throughput DNA sequencing technologies to identify microRNAs (miRNAs) from trout eggs. MiRNAs are small RNA molecules known to affect biological processes; therefore those identified in developing eggs may impact egg quality. In total 492 were identified, 262 which are known based on comparison to other species and 230 putatively novel which were predicted by sequence analysis. Our results represent the first characterization of miRNAs in fish eggs and provides a starting point for understanding their roles in controlling reproductive success in rainbow trout.

Technical Abstract: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNA molecules that regulate post-transcriptional expression of target genes and play important roles in animal development. The objectives of this study were to characterize the egg miRNA transcriptome and identify novel egg-specific miRNAs in rainbow trout. Small RNAs isolated from mature unfertilized rainbow trout eggs were subjected to deep sequencing using an Illumina Genome Analyzer. The massive sequencing produced 24,621,741 quality reads, among which, 262 known miRNAs were identified and 230 putatively novel miRNAs were predicted. The most abundantly known miRNAs are miR-7 and miR-21, accounting for 24.01% and 18.71% of the known miRNAs, respectively. Other known miRNAs which are abundantly present in eggs include miR-24, miR-202, miR-148, miR-30, miR-10, miR-146, miR-25 and miR-143. Real time PCR analysis using cDNAs derived from 12 tissues validated 87 out of 90 selected putative miRNAs and identified four novel miRNAs predominantly expressed in rainbow trout eggs. Each of these novel miRNAs is predicted to target a significant number of genes, most of which are significantly down-regulated in naturally ovulated rainbow trout eggs based on analysis of publicly available microarray data sets. This study represents the first complete survey of miRNAs in fish eggs and provides a starting point for future studies aimed at understanding the roles of miRNAs in controlling ovarian folliculogenesis and early embryogenesis in rainbow trout.