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Open Access Highly Accessed Research article

Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs

Ya-Ping Zhu12, Wei Xue12, Jin-Tu Wang12, Yu-Mei Wan1, Shao-Lin Wang3, Peng Xu1, Yan Zhang1, Jiong-Tang Li1* and Xiao-Wen Sun1*

Author Affiliations

1 The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China

2 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China

3 Department of Psychiatry and Neurobiology Science, University of Virginia, Charlottesville, VA, 22911, USA

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BMC Genomics 2012, 13:413  doi:10.1186/1471-2164-13-413

Published: 21 August 2012

Abstract

Background

MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis. SNPs are often associated with diseases or traits. To date, no studies into the effects of SNPs on miRNA biogenesis and regulation in the common carp have been reported.

Results

Using homology-based prediction combined with small RNA sequencing, we have identified 113 common carp mature miRNAs, including 92 conserved miRNAs and 21 common carp specific miRNAs. The conserved miRNAs had significantly higher expression levels than the specific miRNAs. The miRNAs were clustered into three phylogenetic groups. Totally 394 potential miRNA binding sites in 206 target mRNAs were predicted for 83 miRNAs. We identified 13 SNPs in the miRNA precursors. Among them, nine SNPs had the potential to either increase or decrease the energy of the predicted secondary structures of the precursors. Further, two SNPs in the 3’ untranslated regions of target genes were predicted to either disturb or create miRNA-target interactions.

Conclusions

The common carp miRNAs and their target genes reported here will help further our understanding of the role of miRNAs in gene regulation. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The resource data generated in this study will help advance the study of miRNA function and phenotype-associated miRNA identification.

Keywords:
miRNAs; Targets; SNPs; miRNA biogenesis; Common carp