The alterations of MicroRNAs(miRNAs) in host cell after foot-and-mouth disease virus (FMDV) infection is still obscure. To increase our understanding of the pathogenesis of FMDV at the post-transcriptional regulation level, Solexa high-throu MicroRNAs (miRNAs) play an important role both in the post-transcriptional regulation of gene expression and host-virus interactions. Despite investigations of miRNA expression ghput sequencing and bioinformatic tools were used to identify differentially expressed miRNAs and analyze their functions during FMDV infection of PK-15cells. Results indicated that 9,165,674 and 9,230,378 clean reads were obtained, with 172 known and 72 novel miRNAs differently expressed in infected and uninfected groups respectively. Some of differently expressed miRNAs were validated using stem-loop real-time quantitative RT-PCR. The GO annotation and KEGG pathway analysis for target genes revealed that differently expressed miRNAs were involved in immune response and cell death pathways.
Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS (2005) Post-transcriptional gene silencing by siRNAs and miRNAs. Current opinion in structural biology 15: 331–341. doi: 10.1016/j.sbi.2005.05.006
[3]
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854. doi: 10.1016/0092-8674(93)90529-y
[4]
Ghosh Z, Mallick B, Chakrabarti J (2009) Cellular versus viral microRNAs in host-virus interaction. Nucleic acids research 37: 1035–1048. doi: 10.1093/nar/gkn1004
[5]
Zhang R, Su B (2008) MicroRNA regulation and the variability of human cortical gene expression. Nucleic acids research 36: 4621–4628. doi: 10.1093/nar/gkn431
[6]
Esau C, Kang X, Peralta E, Hanson E, Marcusson EG, et al. (2004) MicroRNA-143 regulates adipocyte differentiation. The Journal of biological chemistry 279: 52361–52365. doi: 10.1074/jbc.c400438200
[7]
Inoue K (2007) [MicroRNA function in animal development]. Tanpakushitsu kakusan koso Protein, nucleic acid, enzyme 52: 197–204.
[8]
Ye L, Su X, Wu Z, Zheng X, Wang J, et al. (2012) Analysis of differential miRNA expression in the duodenum of Escherichia coli F18-sensitive and -resistant weaned piglets. Plos One 7: e43741. doi: 10.1371/journal.pone.0043741
[9]
Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK (2006) Host-virus interaction: a new role for microRNAs. Retrovirology 3: 68. doi: 10.1186/1742-4690-3-68
[10]
Gottwein E, Cullen BR (2008) Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe 3: 375–387. doi: 10.1016/j.chom.2008.05.002
[11]
Boss IW, Plaisance KB, Renne R (2009) Role of virus-encoded microRNAs in herpesvirus biology. Trends in microbiology 17: 544–553. doi: 10.1016/j.tim.2009.09.002
[12]
Singh CP, Singh J, Nagaraju J (2012) A baculovirus-encoded MicroRNA (miRNA) suppresses its host miRNA biogenesis by regulating the exportin-5 cofactor Ran. Journal of virology 86: 7867–7879. doi: 10.1128/jvi.00064-12
[13]
Ho BC, Yu SL, Chen JJ, Chang SY, Yan BS, et al. (2011) Enterovirus-induced miR-141 contributes to shutoff of host protein translation by targeting the translation initiation factor eIF4E. Cell Host Microbe 9: 58–69. doi: 10.1016/j.chom.2010.12.001
[14]
Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309: 1577–1581. doi: 10.1126/science.1113329
[15]
Zheng Z, Ke X, Wang M, He S, Li Q, et al. (2013) Human microRNA hsa-miR-296-5p suppresses enterovirus 71 replication by targeting the viral genome. Journal of virology 87: 5645–5656. doi: 10.1128/jvi.02655-12
[16]
Huang J, Wang F, Argyris E, Chen K, Liang Z, et al. (2007) Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med 13: 1241–1247. doi: 10.1038/nm1639
[17]
Sung TL, Rice AP (2009) miR-198 inhibits HIV-1 gene expression and replication in monocytes and its mechanism of action appears to involve repression of cyclin T1. Plos Pathog 5: e1000263. doi: 10.1371/journal.ppat.1000263
[18]
Umbach JL, Kramer MF, Jurak I, Karnowski HW, Coen DM, et al. (2008) MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454: 780–783. doi: 10.1038/nature07103
[19]
Wu Q, Luo Y, Lu R, Lau N, Lai EC, et al. (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A 107: 1606–1611. doi: 10.1073/pnas.0911353107
[20]
Reese TA, Xia J, Johnson LS, Zhou X, Zhang W, et al. (2010) Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts. Journal of virology 84: 10344–10353. doi: 10.1128/jvi.00707-10
[21]
Metzker ML (2010) Sequencing technologies - the next generation. Nature reviews Genetics 11: 31–46. doi: 10.1038/nrg2626
[22]
Parameswaran P, Sklan E, Wilkins C, Burgon T, Samuel MA, et al. (2010) Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. Plos Pathog 6: e1000764. doi: 10.1371/journal.ppat.1000764
[23]
Schopman NC, Willemsen M, Liu YP, Bradley T, van Kampen A, et al. (2012) Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs. Nucleic acids research 40: 414–427. doi: 10.1093/nar/gkr719
[24]
Wu YQ, Chen DJ, He HB, Chen DS, Chen LL, et al. (2012) Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs. Plos One 7: e30988. doi: 10.1371/journal.pone.0030988
[25]
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic acids research 33: e179. doi: 10.1093/nar/gni178
Sellers R, Gloster J (2008) Foot-and-mouth disease: a review of intranasal infection of cattle, sheep and pigs. Vet J 177: 159–168. doi: 10.1016/j.tvjl.2007.03.009
[28]
Davies G (2002) Foot and mouth disease. Research in veterinary science 73: 195–199. doi: 10.1016/s0034-5288(02)00105-4
[29]
Song QX, Liu YF, Hu XY, Zhang WK, Ma B, et al. (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC plant biology 11: 5. doi: 10.1186/1471-2229-11-5
[30]
Li B, Qin Y, Duan H, Yin W, Xia X (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. Journal of experimental botany 62: 3765–3779. doi: 10.1093/jxb/err051
[31]
Mahajan VS, Drake A, Chen J (2009) Virus-specific host miRNAs: antiviral defenses or promoters of persistent infection. Trends in immunology 30: 1–7. doi: 10.1016/j.it.2008.08.009
[32]
Zhou Y, Tang X, Song Q, Ji Y, Wang H, et al. (2013) Identification and characterization of pig embryo microRNAs by Solexa sequencing. Reproduction in domestic animals 48: 112–120. doi: 10.1111/j.1439-0531.2012.02040.x
[33]
Aldridge JR Jr, Moseley CE, Boltz DA, Negovetich NJ, Reynolds C, et al. (2009) TNF/iNOS-producing dendritic cells are the necessary evil of lethal influenza virus infection. Proc Natl Acad Sci U S A 106: 5306–5311. doi: 10.1073/pnas.0900655106
[34]
Li Y, Chan EY, Li J, Ni C, Peng X, et al. (2010) MicroRNA expression and virulence in pandemic influenza virus-infected mice. Journal of virology 84: 3023–3032. doi: 10.1128/jvi.02203-09
Grinberg M, Gilad S, Meiri E, Levy A, Isakov O, et al. (2012) Vaccinia virus infection suppresses the cell microRNA machinery. Archives of virology 157: 1719–1727. doi: 10.1007/s00705-012-1366-z
[37]
Matskevich AA, Moelling K (2007) Dicer is involved in protection against influenza A virus infection. The Journal of general virology 88: 2627–2635. doi: 10.1099/vir.0.83103-0
[38]
Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207–221. doi: 10.1016/j.cell.2005.04.004
[39]
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, et al. (2005) Specific effects of microRNAs on the plant transcriptome. Developmental cell 8: 517–527. doi: 10.1016/j.devcel.2005.01.018
[40]
Coll RC, O'Neill LA (2010) New insights into the regulation of signalling by toll-like receptors and nod-like receptors. J Innate Immun 2: 406–421. doi: 10.1159/000315469
[41]
Huang B, Zhao J, Lei Z, Shen S, Li D, et al. (2009) miR-142-3p restricts cAMP production in CD4+CD25- T cells and CD4+CD25+ TREG cells by targeting AC9 mRNA. EMBO reports 10: 180–185. doi: 10.1038/embor.2008.224
[42]
Tang X, Muniappan L, Tang G, Ozcan S (2009) Identification of glucose-regulated miRNAs from pancreatic {Nabetani, #896} cells reveals a role for miR-30d in insulin transcription. RNA 15: 287–293. doi: 10.1261/rna.1211209
[43]
Lerner M, Lundgren J, Akhoondi S, Jahn A, Ng HF, et al. (2011) MiRNA-27a controls FBW7/hCDC4-dependent cyclin E degradation and cell cycle progression. Cell cycle 10: 2172–2183. doi: 10.4161/cc.10.13.16248
[44]
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713–714. doi: 10.1093/bioinformatics/btn025
[45]
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic acids research 31: 3406–3415. doi: 10.1093/nar/gkg595
[46]
Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, et al. (2012) Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic acids research 40: 4298–4305. doi: 10.1093/nar/gks043
[47]
Zuker M, Jacobson AB (1998) Using reliability information to annotate RNA secondary structures. RNA 4: 669–679. doi: 10.1017/s1355838298980116
[48]
Ji Z, Wang G, Xie Z, Wang J, Zhang C, et al. (2012) Identification of novel and differentially expressed MicroRNAs of dairy goat mammary gland tissues using solexa sequencing and bioinformatics. Plos One 7: e49463. doi: 10.1371/journal.pone.0049463
[49]
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. (2005) InterProScan: protein domains identifier. Nucleic acids research 33: W116–120. doi: 10.1093/nar/gki442
[50]
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674–3676. doi: 10.1093/bioinformatics/bti610
[51]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic acids research 40: D109–114. doi: 10.1093/nar/gkr988
[52]
Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nature protocols 3: 1101–1108. doi: 10.1038/nprot.2008.73
