Identification and Characterization of MicroRNAs in Channel Catfish (Ictalurus punctatus) by Using Solexa Sequencing Technology

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Xu, Zhiqiang ^a,b   Chen, Jiaping ^c   Li, Xuguang ^b   Ge, Jiachun ^b   Pan, Jianlin ^b   Xu, Xiaofeng ^a  

^a NANJING NORMAL UNIVERSITY   (China)

^b Freshwater Fisheries Research Institute of Jiangsu Province   (China)

^c NANJING MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

IPU MIR 129B; IPU MIR 203C; IPU MIR 7147; IPU MIR 7553; IPU MIR 7556; IPU MIR 7557; IPU MIR 7558A; IPU MIR 7558B; IPU MIR 7559; IPU MIR 7560; IPU MIR 7561; IPU MIR 7562; IPU MIR 7563A; IPU MIR 7563B; IPU MIR 7563C; IPU MIR 7564; IPU MIR 7565; IPU MIR 7566; IPU MIR 7567; IPU MIR 7568; IPU MIR 7569; IPU MIR 7570; IPU MIR 7571; IPU MIR 7572; IPU MIR 7573; IPU MIR 7574; IPU MIR 7575; IPU MIR 7576; MICRORNA; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CHANNEL CATFISH; DNA LIBRARY; GENE EXPRESSION; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SOLEXA SEQUENCING; TISSUE DISTRIBUTION; TISSUE SPECIFICITY; ZEBRA FISH;

ANIMALS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; ICTALURIDAE; MICRORNAS;

DANIO RERIO; EUKARYOTA; ICTALURUS; ICTALURUS PUNCTATUS; VERTEBRATA;

EID: 84872469598     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054174     Document Type: Article

References (47)

1. Food and Agriculture Organization (FAO) (2010) Yearbook of Fishery Statistics Summary tables. FAO website, Available: ftp://ftp.fao.org/fi/stat/summary/default.htm. Accessed 2012 Aug 8.
2. Arias CR, Cai W, Peatman E, Bullard SA, (2012) Catfish hybrid Ictalurus punctatus × I. furcatus exhibits higher resistance to columnaris disease than the parental species. Dis Aquat Organ 100(1): 77-81.
3. Pohlenz C, Buentello A, Criscitiello MF, Mwangi W, Smith R, et al. (2012) Synergies between vaccination and dietary arginine and glutamine supplementation improve the immune response of channel catfish against Edwardsiella ictaluri. Fish Shellfish Immunol 33(3): 543-51.
4. Li C, Zhang Y, Wang R, Lu J, Nandi S, et al. (2012) RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol 32(5): 816-27.
5. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2): 281-297.
6. 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(5): 843-854.
7. Li SC, Chan WC, Hu LY, Lai CH, Hsu CN, et al. (2010) Identification of homologous microRNAs in 56 animal genomes. Genomics 96(1): 1-9.
8. Chen SJ, Chen GH, Chen YH, Liu CY, Chang KP, et al. (2010) Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing. PLoS One 5(9): e12745.
9. Annibali D, Gioia U, Savino M, Laneve P, Caffarelli E, et al. (2012) A New Module in Neural Differentiation Control: Two MicroRNAs Upregulated by Retinoic Acid, miR-9 and-103, Target the Differentiation Inhibitor ID2. PLoS One 7(7): e40269.
10. Wu Y, Liu GL, Liu SH, Wang CX, Xu YL, et al. (2012) MicroRNA-148b enhances the radiosensitivity of non-Hodgkin's Lymphoma cells by promoting radiation-induced apoptosis. J Radiat Res 53(4): 516-25.
11. Salem M, Xiao C, Womack J, Rexroad CE, Yao J, (2010) A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout (Oncorhynchus mykiss). Mar Biotechnol 12(4): 410-429.
12. Jones-Rhoades MW, Bartel DP, (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14(6): 787-799.
13. Barozai MY, (2012) The MicroRNAs and their targets in the channel catfish (Ictalurus punctatus). Mol Biol Rep 39(9): 8867-72.
14. Bhardwaj J, Mohammad H, Yadav SK, (2010) Computational identification of microRNAs and their targets from the expressed sequence tags of horsegram (Macrotyloma uniflorum (Lam.) Verdc.). J Struct Funct Genomics 11(4): 233-240.
15. Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, et al. (2008) MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 26(10): 2496-2505.
16. Chi W, Tong C, Gan X, He S, (2011) Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp. PLoS One 6(8): e23549.
17. 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(7): e22957.
18. Yan X, Ding L, Li Y, Zhang X, Liang Y, et al. (2012) Identification and Profiling of MicroRNAs from Skeletal Muscle of the Common Carp. PLoS One 7(1): e30925.
19. Ou J, Meng Q, Li Y, Xiu Y, Du J, et al. (2011) Identification and comparative analysis of the Eriocheir sinensis microRNA transcriptome response to Spiroplasma eriocheiris infection using a deep sequencing approach. Fish Shellfish Immunol 32(2): 345-52.
20. Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J, et al. (2006) Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res 34(9): 2558-2569.
21. Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, et al. (2009) Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 10: 195.
22. Tani S, Kusakabe R, Naruse K, Sakamoto H, Inoue K, (2010) Genomic organization and embryonic expression of miR-430 in medaka (Oryzias latipes): insights into the post-transcriptional gene regulation in early development. Gene 449(1-2): 41-9.
23. Wang Y, Aker WG, Hwang HM, Yedjou CG, Yu H, et al. (2011) A study of the mechanism of in vitro cytotoxicity of metal oxide nanoparticles using catfish primary hepatocytes and human HepG2 cells. Sci Total Environ. 409(22): 4753-62.
24. Saunders HL, Oko AL, Scott AN, Fan CW, Magor BG, (2010) The cellular context of AID expressing cells in fish lymphoid tissues. Dev Comp Immunol. 34(6): 669-76.
25. Chen C, Ridzon DZ, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
26. Kruger J, Rehmsmeier M, (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucl Acids Res 34: W451-454.
27. Lu J, Peatman E, Yang Q, Wang S, Hu Z, et al. (2010) The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Res 39: D815-821.
28. Li QJ, Chau J, Ebert PJ, Sylvester G, Min H, et al. (2007) miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 129(1): 147-61.
29. Cichocki F, Felices M, McCullar V, Presnell SR, Al-Attar A, et al. (2011) Cutting edge: microRNA-181 promotes human NK cell development by regulating Notch signaling. J Immunol 187(12): 6171-5.
30. 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(6808): 86-89.
31. Mondol V, Pasquinelli AE, (2012) Let's make it happen: the role of let-7 microRNA in development. Curr Top Dev Biol 99: 1-30.
32. Wang X, Cao L, Wang Y, Wang X, Liu N, et al. (2012) Regulation of let-7 and its target oncogenes (Review). Oncol Lett. 3(5): 955-960.
33. Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, et al. (2006) Differences in vertebrate microRNA expression. Proc Natl Acad Sci USA 103(39): 14385-14389.
34. Leucht C, Stigloher C, Wizenmann A, Klafke R, Folchert A, et al. (2008) MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary. Nat Neurosci 11(6): 641-648.
35. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 18(4): 610-21.
36. Li SC, Liao YL, Chan WC, Ho MR, Tsai KW, et al. (2011) Interrogation of rabbit miRNAs and their isomiRs. Genomics 98(6): 453-9.
37. Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, et al. (2009) Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 37(8): 2461-70.
38. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, et al. (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Research 18(11): 1787-1797.
39. Guo L, Yang Q, Lu J, Li H, Ge Q, et al. (2011) A Comprehensive Survey of miRNA Repertoire and 3′Addition Events in the Placentas of Patients with Pre-Eclampsia from High-Throughput Sequencing. PLoS ONE 6(6): e21072.
40. Fernandez-Valverde SL, Taft RJ, Mattick JS, (2010) Dynamic isomiR regulation in Drosophila development. RNA 16(10): 1881-1888.
41. Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, et al. (2010) A comprehensive survey of 39 animal miRNA modification events and a possible role for 39 adenylation in modulating miRNA targeting effectiveness. Genome Research 20(10): 1398-1410.
42. Guo L, Lu Z, (2010) The Fate of miRNA* Strand through Evolutionary Analysis: Implication for Degradation As Merely Carrier Strand or Potential Regulatory Molecule? PLoS ONE 5(6): e11387.
43. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, et al. (2008) The regulatory activity of microRNA star species has substantial influence on micro- RNA and 3 ' UTR evolution. Nature Structural & Molecular Biology 15(4): 354-363.
44. Whitehead A, Crawford DL, (2005) Variation in tissue-specific gene expression among natural populations. Genome Biol 6(2): R13.
45. Assel Issabekova, Olga Berillo, Mireille Regnier, Ivashchenko Anatoliy, (2012) Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis. Bioinformation 8(11): 513-8.
46. Fang Z, Rajewsky N, (2011) The Impact of miRNA Target Sites in Coding Sequences and in 3′UTRs. PLoS ONE 6(3): e18067.
47. Bilodeau-Bourgeois L, Bosworth BG, Peterson BC, (2008) Differences in mortality, growth, lysozyme, and toll-like receptor gene expression among genetic groups of catfish exposed to virulent Edwardsiella ictaluri. Fish Shellfish Immunol 24(1): 82-9.