A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing

doi:10.1016/S1671-2927(11)60140-5

Journal of Integrative Agriculture ›› 2011, Vol. 10 ›› Issue (9): 1467-1474.DOI: 10.1016/S1671-2927(11)60140-5

A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing

DAI Chen, ZHANG Yan-ming, ZHANG Qian, WU Zong-song, DENG Wen, ZHANG Xu, GUO Kang-kang, TANG Qing-hai , HOU Bo

College of Veterinary Medicine, Northwest A&F University,

收稿日期:2010-08-23 出版日期:2011-09-01 发布日期:2011-09-09
通讯作者: Correspondence ZHANG Yan-ming, Professor, Tel: +86-29-87092040, Fax: +86-29-87091032, E-mail: ylzhangym@sohu.com
作者简介:DAI Chen, Ph D, E-mail: ddc_moon@163.com
基金资助:
This work was supported by grants from the National Natural Science Foundation of China (30771607).

A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing

DAI Chen, ZHANG Yan-ming, ZHANG Qian, WU Zong-song, DENG Wen, ZHANG Xu, GUO Kang-kang, TANG Qing-hai , HOU Bo

College of Veterinary Medicine, Northwest A&F University,

Received:2010-08-23 Online:2011-09-01 Published:2011-09-09
Contact: Correspondence ZHANG Yan-ming, Professor, Tel: +86-29-87092040, Fax: +86-29-87091032, E-mail: ylzhangym@sohu.com
About author:DAI Chen, Ph D, E-mail: ddc_moon@163.com
Supported by:
This work was supported by grants from the National Natural Science Foundation of China (30771607).

摘要/Abstract

摘要： 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.

关键词: microRNA, sequencing, Solexa, pig, umbilical vein endothelial cells

Abstract: 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.

Key words: microRNA, sequencing, Solexa, pig, umbilical vein endothelial cells

DAI Chen, ZHANG Yan-ming, ZHANG Qian, WU Zong-song, DENG Wen, ZHANG Xu, GUO Kang-kang, TANG Qing-hai , HOU Bo. A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing[J]. Journal of Integrative Agriculture, 2011, 10(9): 1467-1474.

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A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing

A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing

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