Identification and functional annotation of novel microRNAs in the proximal sciatic nerve after sciatic nerve transection
Tóm tắt
The peripheral nervous system is able to regenerate after injury, and regeneration is associated with the expression of many genes and proteins. MicroRNAs are evolutionarily conserved, small, non-coding RNA molecules that regulate gene expression at the level of translation. In this paper, we focus on the identification and functional annotation of novel microRNAs in the proximal sciatic nerve after rat sciatic nerve transection. Using Solexa sequencing, computational analysis, and quantitative reverse transcription PCR verification, we identified 98 novel microRNAs expressed on days 0, 1, 4, 7, and 14 after nerve transection. Furthermore, we predicted the target genes of these microRNAs and analyzed the biological processes in which they were involved. The identified biological processes were consistent with the known time-frame of peripheral nerve injury and repair. Our data provide an important resource for further study of the role and regulation of microRNAs in peripheral nerve injury and regeneration.
Tài liệu tham khảo
Hama A T, Unnerstall J R, Siegan J B, et al. Modulation of NMDA receptor expression in the rat spinal cord by peripheral nerve injury and adrenal medullary grafting. Brain Res, 1995, 687: 103–113 7583294, 10.1016/0006-8993(95)00476-7, 1:CAS:528:DyaK2MXntl2ju78%3D
Zhang D, Liu M, Ding F, et al. Expression of myostatin RNA transcript and protein in gastrocnemius muscle of rats after sciatic nerve resection. J Muscle Res Cell Motil, 2006, 27: 37–44 16450055, 10.1007/s10974-005-9050-5
Angelov D N, Walther M, Streppel M, et al. Tenascin-R is antiadhesive for activated microglia that induce downregulation of the protein after peripheral nerve injury: a new role in neuronal protection. J Neurosci, 1998, 18: 6218–6229 9698315, 1:CAS:528:DyaK1cXlsVahtb4%3D
Chen K H, Yang C H, Cheng J T, et al. Altered neuronatin expression in the rat dorsal root ganglion after sciatic nerve transection. J Biomed Sci, 2010, 17: 41–47 20509861, 10.1186/1423-0127-17-41
Costigan M, Mannion R J, Kendall G, et al. Heat shock protein 27: developmental regulation and expression after peripheral nerve injury. J Neurosci, 1998, 18: 5891–5900 9671676, 1:CAS:528:DyaK1cXkvFWgurc%3D
Kloosterman W P, Plasterk R H. The diverse functions of microRNAs in animal development and disease. Dev Cell, 2006, 11: 441–450 17011485, 10.1016/j.devcel.2006.09.009, 1:CAS:528:DC%2BD28XhtFWqtLzM
Ambros V. The functions of animal microRNAs. Nature, 2004, 431: 350–355 15372042, 10.1038/nature02871, 1:CAS:528:DC%2BD2cXnsFaiu7g%3D
Hwang H W, Mendell J T. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br J Cancer, 2007, 96: R40–R44 17393584
Jovanovic M, Hengartner M O. miRNAs and apoptosis: RNAs to die for. Oncogene, 2006, 25: 6176–6187 17028597, 10.1038/sj.onc.1209912, 1:CAS:528:DC%2BD28XhtVGjsbbN
Sood P, Krek A, Zavolan M, et al. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci USA, 2006, 103: 2746–2751 16477010, 10.1073/pnas.0511045103, 1:CAS:528:DC%2BD28XksF2rt70%3D
Kim J, Krichevsky A, Grad Y, et al. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA, 2004, 101: 360–365 14691248, 10.1073/pnas.2333854100, 1:CAS:528:DC%2BD2cXjvFaltQ%3D%3D
Natera-Naranjo O, Aschrafi A, Gioio A E, et al. Identification and quantitative analyses of microRNAs located in the distal axons of sympathetic neurons. RNA, 2010, 16: 1516–1529 20584895, 10.1261/rna.1833310, 1:CAS:528:DC%2BC3cXhtVCltL3N
Fiore R, Schratt G. MicroRNAs in vertebrate synapse development. Sci World J, 2007, 7: 167–177
Schratt G. microRNAs at the synapse. Nat Rev Neurosci, 2009, 10: 842–849 19888283, 10.1038/nrn2763, 1:CAS:528:DC%2BD1MXhtlGhsbzO
Baek D, Villen J, Shin C, et al. The impact of microRNAs on protein output. Nature, 2008, 455: 64–71 18668037, 10.1038/nature07242, 1:CAS:528:DC%2BD1cXhtVKrsbjF
Selbach M, Schwanhausser B, Thierfelder N, et al. Widespread changes in protein synthesis induced by microRNAs. Nature, 2008, 455: 58–63 18668040, 10.1038/nature07228, 1:CAS:528:DC%2BD1cXhtVKrsbnK
Liu N K, Wang X F, Lu Q B, et al. Altered microRNA expression following traumatic spinal cord injury. Exp Neurol, 2009, 219: 424–429 19576215, 10.1016/j.expneurol.2009.06.015, 1:CAS:528:DC%2BD1MXhtFajs7rP
Nakanishi K, Nakasa T, Tanaka N, et al. Responses of microRNAs 124a and 223 following spinal cord injury in mice. Spinal Cord, 2010, 48: 192–196 19621023, 10.1038/sc.2009.89, 1:STN:280:DC%2BC3c7ltlOhtw%3D%3D
Chen X, Li Q, Wang J, et al. Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol, 2009, 10: R78 19615057, 10.1186/gb-2009-10-7-r78
Li R, Li Y, Kristiansen K, et al. SOAP: short oligonucleotide alignment program. Bioinformatics, 2008, 24: 713–714 18227114, 10.1093/bioinformatics/btn025, 1:CAS:528:DC%2BD1cXislKlt7Y%3D
Liu S, Li D, Li Q, et al. MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics, 2010, 11: 148 20199675, 10.1186/1471-2164-11-148
Wang X, Zhang J, Li F, et al. MicroRNA identification based on sequence and structure alignment. Bioinformatics, 2005, 21: 3610–3614 15994192, 10.1093/bioinformatics/bti562, 1:CAS:528:DC%2BD2MXpvFGqsbw%3D
Griffiths-Jones S, Grocock R J, van Dongen S, et al. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res, 2006, 34: D140–D144 16381832, 10.1093/nar/gkj112, 1:CAS:528:DC%2BD28XisFyhtw%3D%3D
Griffiths-Jones S, Saini H K, van Dongen S, et al. miRBase: tools for microRNA genomics. Nucleic Acids Res, 2008, 36: D154–D158 17991681, 10.1093/nar/gkm952, 1:CAS:528:DC%2BD1cXhtVWjsb8%3D
Wang X, Zhang J, Li F, et al. MicroRNA identification based on sequence and structure alignment. Bioinformatics, 2005, 21: 3610–3614 15994192, 10.1093/bioinformatics/bti562, 1:CAS:528:DC%2BD2MXpvFGqsbw%3D
Jiang P, Wu H, Wang W, et al. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res, 2007, 35: W339–W344 17553836, 10.1093/nar/gkm368
Pillai R S. MicroRNA function: multiple mechanisms for a tiny RNA? RNA, 2005, 11: 1753–1761 16314451, 10.1261/rna.2248605, 1:CAS:528:DC%2BD2MXhtlWnu73M
Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics, 2006, 7: 191 16597342, 10.1186/1471-2105-7-191
Ng K L, Mishra S K. De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 2007, 23: 1321–1330 17267435, 10.1093/bioinformatics/btm026, 1:CAS:528:DC%2BD2sXns1Olu7w%3D
Chen C, Ridzon D A, Broomer A J, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res, 2005, 33: e179 16314309, 10.1093/nar/gni178
Lewis B P, Shih I H, Jones-Rhoades M W, et al. Prediction of mammalian microRNA targets. Cell, 2003, 115: 787–798 14697198, 10.1016/S0092-8674(03)01018-3, 1:CAS:528:DC%2BD2cXhsFCnsw%3D%3D
Lewis B P, Burge C B, Bartel D P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 2005, 120: 15–20 15652477, 10.1016/j.cell.2004.12.035, 1:CAS:528:DC%2BD2MXot1ChsA%3D%3D
Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004, 116: 281–297 14744438, 10.1016/S0092-8674(04)00045-5, 1:CAS:528:DC%2BD2cXhtVals7o%3D
Schratt G. Fine-tuning neural gene expression with microRNAs. Curr Opin Neurobiol, 2009, 19: 213–219 19539460, 10.1016/j.conb.2009.05.015, 1:CAS:528:DC%2BD1MXptVGktbg%3D
Vogelaar C F, Hoekman M F, Brakkee J H, et al. Developmental regulation of homeobox gene expression in dorsal root ganglion neurons is not recapitulated during regeneration of the crushed sciatic nerve. Neuroscience, 2004, 125: 645–650 15099678, 10.1016/j.neuroscience.2004.02.006, 1:CAS:528:DC%2BD2cXjt1antbs%3D
Yekta S, Shih I H, Bartel D P. MicroRNA-directed cleavage of HOXB8 mRNA. Science, 2004, 304: 594–596 15105502, 10.1126/science.1097434, 1:CAS:528:DC%2BD2cXjt1Crsr0%3D
Stefani G, Slack F J. Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol, 2008, 9: 219–230 18270516, 10.1038/nrm2347, 1:CAS:528:DC%2BD1cXitlGnurY%3D