Profiling kidney microRNAs from juvenile grass carp (Ctenopharyngodon idella) after 56 days of oral exposure to decabromodiphenyl ethane

Grass carp (Ctenopharyngodon idella) is one of the most important species in China. Decabromodiphenyl ethane (DBDPE) is a brominated flame retardant that has been used widely in industry, and has been observed to accumulate in the tissues of fish from South China. Evidence has shown that DBDPE is toxic to aquatic animals, but the molecular response has been unclear. MicroRNAs (miRNAs) are small noncoding and negative regulatory RNAs that are 20–24 nucleotides in length, which are involved in a wide range of biological processes. We took advantage of deep-sequencing techniques to accurately and comprehensively profile the kidney miRNA expression of grass carp after 8 weeks of oral exposure to DBDPE. After mapping sequencing data to the genome and Expressed Sequence Tags (ESTs) of grass carp, we identified 493 miRNAs in the sequenced grass carp samples, which included 51 new miRNAs. The results indicated that 5 miRNAs were significantly down-regulated and 36 miRNAs were significantly up-regulated (FDR < 0.001, 1.5-fold change) after DBDPE exposure. Real-time quantitative PCR (RT-qPCR) was performed on 4 miRNAs from the two samples, and the sequencing and RT-qPCR data were consistent. This study provides the first comprehensive identification of grass carp miRNAs, and the first expression analysis of grass carp miRNAs following DBDPE exposure. The results indicated that miRNAs have potential for use as biomarkers.