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

BMC Genomics

Research Article

Shao-Lin Wang¹  Jiong-Tang Li²  Yu-Mei Wan²  Peng Xu²  Xiao-Wen Sun²  Yan Zhang²  Jin-Tu Wang³  Wei Xue³  Ya-Ping Zhu³ 

[1] Department of Psychiatry and Neurobiology Science, University of Virginia, 22911, Charlottesville, VA, USA;The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, 100141, Beijing, China;The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, 100141, Beijing, China;College of Fisheries and Life Science, Shanghai Ocean University, 201306, Shanghai, China;

关键词: miRNAs;    Targets;    SNPs;    miRNA biogenesis;    Common carp;   

DOI  :  10.1186/1471-2164-13-413

 received in 2012-03-11, accepted in 2012-08-09,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (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.ResultsUsing 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Zhu et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.