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| 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, |
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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.
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.
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Received: 23 August 2010
Accepted:
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| Fund: This work was supported by grants from the National Natural Science Foundation of China (30771607). |
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Corresponding Authors:
Correspondence ZHANG Yan-ming, Professor, Tel: +86-29-87092040, Fax: +86-29-87091032, E-mail: ylzhangym@sohu.com
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| About author: DAI Chen, Ph D, E-mail: ddc_moon@163.com |
Cite this article:
DAI Chen, ZHANG Yan-ming, ZHANG Qian, WU Zong-song, DENG Wen, ZHANG Xu, GUO Kang-kang, TANG Qing-hai , HOU Bo.
2011.
A MicroRNA Catalog of Swine Umbilical Vein Endothelial Cells Identified by Deep Sequencing. Journal of Integrative Agriculture, 10(9): 1467-1474.
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| [1]Adams B D, Cowee D M, White B A. 2009. The role of miR-206in the epidermal growth factor (EGF) induced repression ofestrogen receptor-??(ER?) signaling and a luminal phenotypein MCF-7 breast cancer cells. Molecular Endocrinology, 23,1215-1230.[2]Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, AravinA, Brownstein M J, Tuschl T, Margalit H. 2005. Clusteringand conservation patterns of human microRNAs. NucleicAcids Research, 33, 2697-2706.[3]Antonini D, Russo M T, de Rosa L, Gorrese M, del Vecchio L,Missero C. 2010. Transcriptional repression of miR-34family contributes to p63-mediated cell cycle progression inepidermal cells. Journal of Investigative Dermatology, 130,1249-1257.[4]Bartel D P. 2004. MicroRNAs: genomics, biogenesis, mechanism,and function. Cell, 116, 281-297.[5]Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O,Barzilai A, Einat P, Einav U, Meiri E, et al. 2005. Identificationof hundreds of conserved and nonconserved humanmicroRNAs. Nature Genetics, 37, 766-770.[6]Berezikov E, Cuppen E, Plasterk R H. 2006a. Approaches tomicroRNA discovery. Nature Genetics, 38, 2-7.[7]Berezikov E, Thuemmler F, van Laake L W, Kondova I, BontropR, Cuppen E, Plasterk R H. 2006b. Diversity of microRNAsin human and chimpanzee brain. Nature Genetics, 38, 1375-1377.[8]Browne E P, Li J, Chong M, Littman D R. 2005. Virus-hostinteractions: new insights from the small RNA world. GenomeBiology, 6, 238-242.[9]Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, MeyersB C, Green P J, Markis M, Isaacs G, Huang E, Morgan R W.2008. Deep sequencing of chicken microRNAs. BMCGenomics, 9, 185-194.[10]Cheng Y, Zhang C. 2010. MicroRNA-21 in cardiovascular disease.Journal of Cardiovascular Translational Research, 3, 251-255.[11]Cho I S, Kim J, Seo H Y, Lim D H, Hong J S, Park Y H, Park DC, Hong K C, Whang K Y, Lee Y S. 2010. Cloning andcharacterization of microRNAs from porcine skeletal muscleand adipose tissue. Molecular Biology Reports, 37, 3567-3574.[12]Cullen B R. 2006. Viruses and microRNAs. Nature Genetics, 38,25-23.[13]Griffiths-Jones S, Grocock R J, van Dongen S, Bateman A, EnrightA J. 2006. miRBase: microRNA sequences, targets and genenomenclature. Nucleic Acids Research, 34, 140-144.[14]Griffiths-Jones S, Saini H K, van Dongen S, Enright A J. 2008.miRBase: tools for microRNA genomics. Nucleic AcidsResearch, 36, 154-158.[15]Grimson A, Farh K K, Johnston W K, Garrett-Engele P, Lim LP, Bartel D P. 2007. MicroRNA targeting specificity inmammals: determinants beyond seed pairing. Molecules andCells, 27, 91-105.[16]He L, Hannon G J. 2004. MicroRNAs: small RNAs with a bigrole in gene regulation. Nature Reviews Genetics, 5, 522-531.[17]Hong H X, Zhang Y M, Xu H, Su Z Y, Sun P. 2007.Immortalization of swine umbilical vein endothelial cells withhuman telomerase reverse transcriptase. Nature ReviewsGenetics, 24, 358-363.[18]Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z. 2007. MiPred:classification of real and pseudo microRNA precursors usingrandom forest prediction model with combined features.Nucleic Acids Research, 35, 339-344.[19]Jopling C L, Yi M, Lancaster A M, Lemon S M, Sarnow P. 2005.Modulation of hepatitis C virus RNA abundance by a liverspecificmicroRNA. Science, 309, 1577-1581.[20]Kim H J, Cui X S, Kim E J, Kim W J, Kim N H. 2006. Newporcine microRNA genes found by homology search.Genome, 49, 1283-1286.[21]Kim J, Cho I S, Hong J S, Choi Y K, Kim H, Lee Y S. 2008.Identification and characterization of new microRNAs frompig. Mammalian Genome, 19, 570-580.[22]Kloosterman W P, Plasterk R H. 2006. The diverse functions ofmicroRNAs in animal development and disease.Developmental Cell, 11, 441-450.[23]Kuehbacher A, Urbich C, Zeiher A M, Dimmeler S. 2007. Role ofDicer and Drosha for endothelial microRNA expression andangiogenesis. Circulation Research, 101, 59-68.[24]Lee D Y, Deng Z, Wang C H, Yang B B. 2007. MicroRNA-378promotes cell survival, tumor growth, and angiogenesis bytargeting SuFu and Fus-1 expression. Proceedings of theNational Academy of Sciences of the USA, 104, 20350-20355.[25]Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: shortoligonucleotide alignment program. Bioinformatics, 24, 713-714.[26]Liu X, Wang T, Wakita T, Yang W. 2010. Systematic identificationof microRNA and messenger RNA profiles in hepatitis Cvirus-infected human hepatoma cells. Virology, 398, 57-67.[27]McDaneld T G, Smith T P, Doumit M E, Miles J R, Coutinho LL, Sonstegard T S, Matukumalli L K, Nonneman D J,Wiedmann R T. 2009. MicroRNA transcriptome profilesduring swine skeletal muscle development. BMC Genomics,10, 77-88.[28]Moxon S, Moulton V, Kim J T. 2008. A scoring matrix approachto detecting miRNA target sites. Algorithms for MolecularBiology, 3, 3-12.[29]Nielsen M, Hansen J H, Hedegaard J, Nielsen R O, Panitz F,Bendixen C, Thomsen B. 2010. MicroRNA identity andabundance in porcine skeletal muscles determined by deepsequencing. Animal Genetics, 41, 159-168.[30]Niwa R, Slack F J. 2007. The evolution of animal microRNAfunction. Current Opinion in Genetics & Development, 17,145-150.[31]Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A,Dalmay T. 2009. High throughput sequencing of microRNAs in chicken somites. FEBS Letters, 583, 1422-1426.[32]Reddy A M, Zheng Y, Jagadeeswaran G, Macmil S L, Graham WB, Roe B A, Desilva U, Zhang W, Sunkar R. 2009. Cloning,characterization and expression analysis of porcinemicroRNAs. BMC Genomics, 10, 65-85.[33]Sawera M, Gorodkin J, Cirera S, Fredholm M. 2005. Mappingand expression studies of the mir17-92 cluster on pigchromosome 11. Mammalian Genome, 16, 594-598.[34]Shan Z X, Lin Q X, Fu Y H, Deng C Y, Zhou Z L, Zhu J N, LiuX Y, Zhang Y Y, Li Y, Lin S G, et al. 2009. Upregulatedexpression of miR-1/miR-206 in a rat model of myocardialinfarction. Biochemical and Biophysical ResearchCommunications, 4, 597-561.[35]Sharbati S, Friedlander M R, Sharbati J, Hoeke L, Chen W, KellerA, Stahler P F, Rajewsky N, Einspanier R. 2010. Decipheringthe porcine intestinal microRNA transcriptome. BMCGenomics, 11, 275-289.[36]Weber M, Baker M B, Moore J P, Searles C D. 2010. MiR-21 isinduced in endothelial cells by shear stress and modulatesapoptosis and eNOS activity. Biochemical and BiophysicalResearch Communications, 393, 643-648.[37]Wernersson R, Schierup M H, Jorgensen F G, Gorodkin J, PanitzF, Staerfeldt H H, Christensen O F, Mailund T, Hornshoj H,Klein A, et al. 2005. Pigs in sequence space: a 0.66X coveragepig genome survey based on shotgun sequencing. BMCGenomics, 6, 70-77.[38]Zuker M. 2003. Mfold web server for nucleic acid folding andhybridization prediction. Nucleic Acids Research, 31, 3406-3415. |
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