A microrna catalog of swine umbilical vein endothelial cells identified by deep sequencing
2011
Dai Chen, Northwest Agricuture and Forestry University, Yangling (China), College of Veterinary Medicine | Zhang Yanming, Northwest Agricuture and Forestry University, Yangling (China), College of Veterinary Medicine | Zhang Qian, Northwest Agricuture and Forestry University, Yangling (China), College of Veterinary Medicine
MicroRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in targeting mRNAs for cleavageor translational repression. Despite the discovery of increasing numbers of human and mouse miRNAs, little is knownabout miRNAs from pig. In this study, we sought to extend the repertoire of porcine small regulatory RNAs using Solexasequencing. We sequenced a library of small RNAs prepared from immortalized swine umbilical vein endothelial cells(SUVECs). We produced over 13.6 million short sequence reads, of which 8 547 658 perfectly mapped to the pig genome.A bioinformatics pipeline was used to identify authentic mature miRNA sequences. We identified 154 porcine miRNAgenes, among which 146 were conserved across species, and 8 were pig-specific miRNA genes. The 146 miRNA genesencoded 116 conserved mature miRNAs and 66 miRNA*. The 8 pig-specific miRNA genes encoded 4 mature miRNAs.Four potential novel miRNAs were identified. The secondary structures of the 154 miRNA genes were predicted; 13miRNAs have 2 structures, and miR-9 and miR-199 have 4 and 3 structures, respectively. 36 miRNAs were organized into19 compact clusters. miR-206, miR-21 and miR-378 were the relatively highly expressed miRNAs. In conclusion, Solexasequencing allowed the successful discovery of known and novel porcine miRNAs with high accuracy and efficiency.Furthermore, our results supply new data to the somewhat insufficient pig miRBase, and are useful for investigatingfeatures of the blood-brain barrier, vascular diseases and inflammation.
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