Identification and Characterization of MicroRNAs in Pearl Oyster Pinctada martensii by Solexa Deep Sequencing

Marine Biotechnology

Volumn 16, Issue 1, 2014, Pages 54-62

  Jiao, Yu ^a   Zheng, Zhe ^a   Du, Xiaodong ^a   Wang, Qingheng ^a   Huang, Ronglian ^a   Deng, Yuewen ^a   Shi, Shangli ^a   Zhao, Xiaoxia ^a  

^a GUANGDONG OCEAN UNIVERSITY   (China)

Author keywords

Biomineralization; MicroRNA; Pinctada martensii; Solexa deep sequencing

Indexed keywords

BIOMINERALIZATION; CLONE CELLS; GENE EXPRESSION; POLYMERASE CHAIN REACTION;

HAIRPIN STRUCTURES; MICRORNAS; NEGATIVE REGULATORS; PINCTADA MARTENSII; QUANTITATIVE REAL TIME PCR; SCALE CHARACTERIZATION; SEQUENCE SIMILARITY; SOLEXA DEEP SEQUENCING;

RNA;

AMPLIFICATION; BIOMINERALIZATION; BIOTECHNOLOGY; GENE EXPRESSION; MOLLUSC; RNA; SHELL;

CHINA; JAPAN;

PINCTADA; PINCTADA MARTENSI;

MICRORNA; PRIMER DNA; SMALL NUCLEAR RNA;

ANIMAL; ARTICLE; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PINCTADA; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

ANIMALS; CLONING, MOLECULAR; CONSERVED SEQUENCE; DNA PRIMERS; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; PINCTADA; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, SMALL NUCLEAR; SPECIES SPECIFICITY;

EID: 84892898694     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-013-9528-x     Document Type: Article

References (40)

1. Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC (2005) Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A 102(50): 18017-18022.
2. Atlan G, Balmain N, Berland S, Vidal B, Lopez E (1997) Reconstruction of human maxillary defects with nacre powder: histological evidence for bone regeneration. C R Acad Sci 320(3): 253-258.
3. Bueno MJ, Malumbres M (2011) MicroRNAs and the cell cycle. Biochim Biophys Acta 1812(5): 592-601.
4. Cao H, Wang J, Li X, Florez S, Huang Z, Venugopalan SR, Elangovan S, Skobe Z, Margolis HC, Martin JF, Amendt BA (2010) MicroRNAs play a critical role in tooth development. J Dent Res 89(8): 779-784.
5. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20): e179.
6. Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, Guo J, Zhang Y, Chen J, Guo X, Li Q, Li X, Wang W, Zhang Y, Wang J, Jiang X, Xiang Y, Xu C, Zheng P, Zhang J, Li R, Zhang H, Shang X, Gong T, Ning G, Wang J, Zen K, Zhang J, Zhang CY (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18(10): 997-1006.
7. Chen X, Li Q, Wang J, Guo X, Jiang X, Ren Z, Weng C, Sun G, Wang X, Liu Y, Ma L, Chen JY, Wang J, Zen K, Zhang J, Zhang CY (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10(7): R78.
8. Chen C, Deng B, Qiao M, Zheng R, Chai J, Ding Y, Peng J, Jiang S (2012) Solexa sequencing identification of conserved and novel microRNAs in backfat of Large White and Chinese Meishan pigs. PLoS One 7(2): e31426.
9. Fang Z, Wang Q, Cao W, Feng Q, Li C, Xie L, Zhang R (2009) Investigation of phosphorylation site responsible for CaLP (P. fucata) nucleo-cytoplasmic shuttling triggered by overexpression of p21Cip1. Mar Biotechnol (NY) 11(2): 270-279.
10. Ge X, Zhang Y, Jiang J, Zhong Y, Yang X, Li Z, Huang Y, Tan A (2012) Identification of microRNAs in Helicoverpa armigera and Spodoptera litura based on deep sequencing and homology analysis. Int J Biol Sci 9(1): 1-15.
11. Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ (2009) Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS One 4(7): e6349.
12. Gong N, Ma Z, Li Q, Li Q, Yan Z, Xie L, Zhang R (2008) Characterization of calcium deposition and shell matrix protein secretion in primary mantle tissue culture from the marine pearl oyster Pinctada fucata. Mar Biotechnol (NY) 10(4): 457-465.
13. Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Honer Zu Siederdissen C, Bort JA, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Puhler A, Borth N, Grillari J (2011) Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. J Biotechnol 153(1-2): 62-75.
14. Huang XD, Zhao M, Liu WG, Guan YY, Shi Y, Wang Q, Wu SZ, He MX (2012) Gigabase-scale transcriptome analysis on four species of pearl oysters. Mar Biotechnol (NY) 15(3): 253-264.
15. Inoue N, Ishibashi R, Ishikawa T, Atsumi T, Aoki H, Komaru A (2011) Gene expression patterns in the outer mantle epithelial cells associated with pearl sac formation. Mar Biotechnol (NY) 13(3): 474-483.
16. Iovino N, Pane A, Gaul U (2009) miR-184 has multiple roles in Drosophila female germline development. Dev Cell 17(1): 123-133.
17. Jiao Y, Wang H, Du X, Zhao X, Wang Q, Huang R, Deng Y (2012) Dermatopontin, a shell matrix protein gene from pearl oyster Pinctada martensii, participates in nacre formation. Biochem Biophys Res Commun 425(3): 679-683.
18. Kong Y, Jing G, Yan Z, Li C, Gong N, Zhu F, Li D, Zhang Y, Zheng G, Wang H, Xie L, Zhang R (2009) Cloning and characterization of Prisilkin-39, a novel matrix protein serving a dual role in the prismatic layer formation from the oyster Pinctada fucata. J Biol Chem 284(16): 10841-10854.
19. Kruger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34: W451-454, Web Server issue.
20. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7): 1401-1414.
21. Li C, Hu Y, Liang J, Kong Y, Huang J, Feng Q, Li S, Zhang G, Xie L, Zhang R (2010) Calcineurin plays an important role in the shell formation of pearl oyster (Pinctada fucata). Mar Biotechnol (NY) 12(1): 100-110.
22. Lian JB, Stein GS, van Wijnen AJ, Stein JL, Hassan MQ, Gaur T, Zhang Y (2012) MicroRNA control of bone formation and homeostasis. Nat Rev 8(4): 212-227.
23. Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q (2010) MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics 11: 148.
24. Lopez E, Vidal B, Berland S, Camprasse S, Camprasse G, Silve C (1992) Demonstration of the capacity of nacre to induce bone formation by human osteoblasts maintained in vitro. Tissue Cell 24(5): 667-679.
25. Lv S, Nie X, Wang L, Du X, Biradar SS, Jia X, Weining S (2012) Identification and characterization of MICRORNAS from barley (Hordeum vulgare L.) by high-throughput sequencing. Int J Mol Sci 13(3): 2973-2984.
26. Malumbres M (2012) miRNAs versus oncogenes: the power of social networking. Mol Syst Biol 8: 569.
27. Nomura T, Kimura M, Horii T, Morita S, Soejima H, Kudo S, Hatada I (2008) MeCP2-dependent repression of an imprinted miR-184 released by depolarization. Hum Mol Genet 17(8): 1192-1199.
28. Roush S, Slack FJ (2008) The let-7 family of microRNAs. Trends Cell Biol 18(10): 505-516.
29. Shi Y, Yu C, Gu Z, Zhan X, Wang Y, Wang A (2013) Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes. Mar Biotechnol (NY) 15(2): 175-187.
30. Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11: 431.
31. Thadani R, Tammi MT (2006) MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinforma 7(Suppl 5): S20.
32. Wang N, Kinoshita S, Nomura N, Riho C, Maeyama K, Nagai K, Watabe S (2011) The mining of pearl formation genes in pearl oyster Pinctada fucata by cDNA suppression subtractive hybridization. Marine Biotechnol (NY) 14(2): 177-188.
33. Wang C, Han J, Liu C, Kibet KN, Kayesh E, Shangguan L, Li X, Fang J (2012) Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 13: 122.
34. Westbroek P, Marin F (1998) A marriage of bone and nacre. Nature 392(6679): 861-862.
35. Xia Z, Chen C, Chen P, Xie H, Luo X (2011) MicroRNAs and their roles in osteoclast differentiation. Frontiers Med 5(4): 414-419.
36. Yu F, Jiao Y, Zhu Y, Wang Y, Zhu J, Cui X, Liu Y, He Y, Park EY, Zhang H, Lv X, Ma K, Su F, Park JH, Song E (2012) MicroRNA 34c gene down-regulation via DNA methylation promotes self-renewal and epithelial-mesenchymal transition in breast tumor-initiating cells. J Biol Chem 287(1): 465-473.
37. Zhang R, Wang YQ, Su B (2008) Molecular evolution of a primate-specific microRNA family. Mol Biol Evol 25(7): 1493-1502.
38. Zhang Y, Yu M, Yu H, Han J, Song C, Ma R, Fang J (2012) Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE. Mol Biol Rep 39(2): 1975-1987.
39. Zhao X, Wang Q, Jiao Y, Huang R, Deng Y, Wang H, Du X (2012) Identification of genes potentially related to biomineralization and immunity by transcriptome analysis of pearl sac in pearl oyster Pinctada martensii. Mar Biotechnol (NY) 14(6): 730-739.
40. Zhu YP, Xue W, Wang JT, Wan YM, Wang SL, Xu P, Zhang Y, Li JT, Sun XW (2012) Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs. BMC Genomics 13: 413.