Characterization and Comparative Profiling of MicroRNAs in a Sexual Dimorphism Insect, Eupolyphaga sinensis Walker

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Wu, Wei ^a   Ren, Qiuping ^a   Li, Chengjun ^a   Wang, Yanyun ^a   Sang, Ming ^a   Zhang, Yi ^a   Li, Bin ^a  

^a NANJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 100; MICRORNA 133; MICRORNA 184; MICRORNA 190; MICRORNA 263A; MICRORNA 276; MICRORNA 281; MICRORNA 3049; MICRORNA 3770; MICRORNA 4944; MICRORNA 8; MICRORNA 932; MICRORNA 993A; MICRORNA 9A; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CARABIDAE; COMPARATIVE STUDY; CONTROLLED STUDY; DOWN REGULATION; EUPOLYGRAPHA SINENSIS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE MAPPING; GENETIC CONSERVATION; HIGH THROUGHPUT SEQUENCING; LARVA; MALE; METAMORPHOSIS; MOLECULAR LIBRARY; NONHUMAN; PHENOTYPIC VARIATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEX DIFFERENCE; TRANSCRIPTION REGULATION; UPREGULATION; VALIDATION PROCESS;

ANIMALS; BASE SEQUENCE; BEETLES; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; MALE; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, RNA; SEX CHARACTERISTICS;

ANIMALIA; BLATTARIA; HEXAPODA;

EID: 84876433197     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059016     Document Type: Article

References (51)

1. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
2. Ambros V, (2004) The functions of animal microRNAs. Nature 431: 350-355.
3. Miska EA, (2005) How microRNAs control cell division, differentiation and death. Curr Opin Genet Dev 15: 563-568.
4. Wienholds E, Plasterk RH, (2005) MicroRNA function in animal development. FEBS Lett 579: 5911-5922.
5. Nohata N, Hanazawa T, Kinoshita T, Okamoto Y, Seki N (2012) MicroRNAs function as tumor suppressors or oncogenes: Aberrant expression of microRNAs in head and neck squamous cell carcinoma. Auris Nasus Larynx.
6. Campbell LI, Rota-Stabelli O, Edgecombe GD, Marchioro T, Longhorn SJ, et al. (2011) MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci U S A 108: 15920-15924.
7. 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.
8. Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, et al. (2009) The deep evolution of metazoan microRNAs. Evol Dev 11: 50-68.
9. Chen C, Deng B, Qiao M, Zheng R, Chai J, et al. (2012) Solexa sequencing identification of conserved and novel microRNAs in backfat of Large White and Chinese Meishan pigs. PLoS One 7: e31426.
10. Li C, Feng W, Qiu L, Xia C, Su X, et al. (2012) Characterization of skin ulceration syndrome associated microRNAs in sea cucumber Apostichopus japonicus by deep sequencing. Fish Shellfish Immunol 33: 436-441.
11. Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, et al. (2012) Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 13: 83.
12. Wang F, Li L, Liu L, Li H, Zhang Y, et al. (2012) High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Mol Genet Genomics 287: 555-563.
13. Ge GF, Yu CH, Yu B, Shen ZH, Zhang DL, et al. (2012) Antitumor effects and chemical compositions of Eupolyphaga sinensis Walker ethanol extract. J Ethnopharmacol 141: 178-182.
14. Jiang HL, Luo XH, Wang XZ, Yang JL, Yao XJ, et al. (2012) New isocoumarins and alkaloid from Chinese insect medicine, Eupolyphaga sinensis Walker. Fitoterapia 83: 1275-1280.
15. Li M, Liu Y, Wang T, Guan J, Luo Z, et al. (2011) Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing. Int J Biol Sci 7: 1045-1055.
16. Mishima T, Takizawa T, Luo SS, Ishibashi O, Kawahigashi Y, et al. (2008) MicroRNA (miRNA) cloning analysis reveals sex differences in miRNA expression profiles between adult mouse testis and ovary. Reproduction 136: 811-822.
17. Huang J, Ju Z, Li Q, Hou Q, Wang C, et al. (2011) Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci 7: 1016-1026.
18. Ma M, Huang Y, Gong Z, Zhuang L, Li C, et al. (2011) Discovery of DNA viruses in wild-caught mosquitoes using small RNA high throughput sequencing. PLoS One 6: e24758.
19. 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 Res 33: e179.
20. Cristino AS, Tanaka ED, Rubio M, Piulachs MD, Belles X, (2011) Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae). PLoS One 6: e19350.
21. Wei Y, Chen S, Yang P, Ma Z, Kang L, (2009) Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol 10: R6.
22. Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR, (2010) Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. BMC Genomics 11: 119.
23. Hui CU, Griffiths-Jones S, Ronshaugen M, (2009) The evolution of miR-10 family function in animal development. Mechanisms of development 126: S56-S56.
24. Liu S, Zhang L, Li Q, Zhao P, Duan J, et al. (2009) MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). BMC Genomics 10: 455.
25. Jaubert S, Mereau A, Antoniewski C, Tagu D, (2007) MicroRNAs in Drosophila: the magic wand to enter the Chamber of Secrets? Biochimie 89: 1211-1220.
26. Iovino N, Pane A, Gaul U, (2009) miR-184 has multiple roles in Drosophila female germline development. Dev Cell 17: 123-133.
27. Liu S, Li D, Li Q, Zhao P, Xiang Z, et al. (2010) MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics 11: 148.
28. Zhang X, Zheng Y, Jagadeeswaran G, Ren R, Sunkar R, et al. (2012) Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta. Insect Biochem Mol Biol 42: 381-395.
29. Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S, (2010) Functional shifts in insect microRNA evolution. Genome Biol Evol 2: 686-696.
30. de Wit E, Linsen SE, Cuppen E, Berezikov E, (2009) Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res 19: 2064-2074.
31. Toedling J, Servant N, Ciaudo C, Farinelli L, Voinnet O, et al. (2012) Deep-sequencing protocols influence the results obtained in small-RNA sequencing. PLoS One 7: e32724.
32. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, et al. (2008) The regulatory activity of microRNA* species has substantial influence on microRNA and 3′ UTR evolution. Nat Struct Mol Biol 15: 354-363.
33. Li T, Wu R, Zhang Y, Zhu D, (2011) A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs. BMC Genomics 12: 186.
34. Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A, et al. (2009) High throughput sequencing of microRNAs in chicken somites. FEBS Lett 583: 1422-1426.
35. Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese EL, et al. (2010) Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 11: 52.
36. Sun J, Zhong N, Li Q, Min Z, Zhao W, et al. (2011) MicroRNAs of rat articular cartilage at different developmental stages identified by Solexa sequencing. Osteoarthritis Cartilage 19: 1237-1245.
37. Fu Y, Shi Z, Wu M, Zhang J, Jia L, et al. (2011) Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One 6: e22957.
38. Chen Q, Lu L, Hua H, Zhou F, Lu L, et al. (2012) Characterization and comparative analysis of small RNAs in three small RNA libraries of the brown planthopper (Nilaparvata lugens). PLoS One 7: e32860.
39. Surridge AK, Lopez-Gomollon S, Moxon S, Maroja LS, Rathjen T, et al. (2011) Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics 12: 62.
40. Wei Z, Liu X, Feng T, Chang Y, (2011) Novel and conserved micrornas in Dalian purple urchin (Strongylocentrotus nudus) identified by next generation sequencing. Int J Biol Sci 7: 180-192.
41. Mishra PJ, Mishra PJ, Banerjee D, Bertino JR, (2008) MiRSNPs or MiR-polymorphisms, new players in microRNA mediated regulation of the cell: Introducing microRNA pharmacogenomics. Cell Cycle 7: 853-858.
42. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, et al. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17: 1850-1864.
43. Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, et al. (2010) A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res 20: 1398-1410.
44. Behura SK, (2007) Insect microRNAs: Structure, function and evolution. Insect Biochem Mol Biol 37: 3-9.
45. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89.
46. Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V, (2003) Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. Dev Biol 259: 9-18.
47. Zhang Y, Zhou X, Ge X, Jiang J, Li M, et al. (2009) Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori. PLoS One 4: e4677.
48. Xu P, Vernooy SY, Guo M, Hay BA, (2003) The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13: 790-795.
49. Hipfner DR, Weigmann K, Cohen SM, (2002) The bantam gene regulates Drosophila growth. Genetics 161: 1527-1537.
50. Parrish JZ, Xu P, Kim CC, Jan LY, Jan YN, (2009) The microRNA bantam functions in epithelial cells to regulate scaling growth of dendrite arbors in drosophila sensory neurons. Neuron 63: 788-802.
51. Silver SJ, Hagen JW, Okamura K, Perrimon N, Lai EC, (2007) Functional screening identifies miR-315 as a potent activator of Wingless signaling. Proc Natl Acad Sci U S A 104: 18151-18156.