RNA-Sequencing for discovery of novel MicroRNAs
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.
A team led by researchers at West Virginia University set out to characterize the egg miRNA transcriptome and identify novel egg-predominant miRNAs in rainbow trout.
Highlights from the study:
They isolated RNA from mature unfertilized rainbow trout eggs and utilized LC Sciences’ Small RNA Sequencing Service to accomplish this goal.
- The massive sequencing produced 24,621,741 quality reads
- 266 known miRNAs were identified and 230 putatively novel miRNAs were predicted
- The most abundantly known miRNAs are let-7 and miR-21
- 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
They followed the sequencing project with real-time PCR validation.
- Used cDNAs derived from 10 different tissues
- Validated 87 out of 90 selected putative miRNAs
- Identified three novel miRNAs predominantly expressed in rainbow trout eggs.
- Each of these novel egg-predominant miRNAs is predicted to target a significant number of genes
- Demonstrated low expression of a selected number of target genes in eggs relative to liver and muscle tissues
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 egg quality and early embryogenesis in rainbow trout.
- Ma H, Hostuttler M, Wei H, Rexroad CE III, Yao J (2012) Characterization of the Rainbow Trout Egg MicroRNA Transcriptome. PLoS ONE 7(6): e39649. [article]