A microRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss)

Marine Biotechnology

Volumn 12, Issue 4, 2010, Pages 410-429

  Salem, Mohamed ^a   Xiao, Caide ^a   Womack, Jonah ^a   Rexroad III, Caird E ^b   Yao, Jianbo ^a  

^a WEST VIRGINIA UNIVERSITY   (United States)

^b NATIONAL CENTER FOR COOL AND COLD WATER AQUACULTURE   (United States)

Author keywords

Functional genomics; MicroRNA; Non coding RNA; Rainbow trout

Indexed keywords

BREEDING PROGRAM; COMPUTATIONAL PREDICTIONS; DIAGNOSTIC IMPLICATIONS; DISEASE ECOLOGY; ECONOMIC INTERESTS; EXPRESSION PATTERNS; FUNCTIONAL GENOMES; FUNCTIONAL GENOMICS; GENETIC POLYMORPHISMS; GENOME SEQUENCES; MICRORNAS; MOLECULAR MARKER; NEW TOOLS; NON-CODING RNAS; ONCORHYNCHUS MYKISS; RAINBOW TROUT; REAL-TIME PCR; SALMONIDS; SINGLE NUCLEOTIDE POLYMORPHISMS; SOMATIC TISSUES; TARGET SITES; TISSUE-SPECIFIC EXPRESSION; TRANSCRIPTOMES; TRANSLATIONAL INHIBITION; UNIQUE SEQUENCE;

AGRICULTURE; AQUACULTURE; GENE EXPRESSION; HISTOLOGY; PLANTS (BOTANY); POLYMORPHISM; RESEARCH; RNA; TARGETS;

TISSUE;

MICRORNA;

BIOMARKER; BIOTECHNOLOGY; BREEDING; COMMERCIAL SPECIES; GENE EXPRESSION; GENETIC ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM; SALMONID;

ANIMAL; ARTICLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; RAINBOW TROUT; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CONSERVED SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME; MICRORNAS; ONCORHYNCHUS MYKISS; POLYMORPHISM, SINGLE NUCLEOTIDE;

ONCORHYNCHUS MYKISS; SALMONIDAE;

EID: 77954955227     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-009-9232-z     Document Type: Article

References (72)

1. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36: 1282-1290.
2. Allendorf FW, Thorgaard G (1984) Tetraploidy and the evolution of salmonid fishes. Evolutionary genetics of fishes. Plenum Press, New York, pp 1-45.
3. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. Rna 9: 277-279.
4. Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RH (2006) Differences in vertebrate microRNA expression. Proc Natl Acad Sci U S A 103: 14385-14389.
5. Axtell MJ, Bartel DP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 1658-1673.
6. Bailey GS, Poulter RT, Stockwell PA (1978) Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc Natl Acad Sci U S A 75: 5575-5579.
7. Barnes MR, Deharo S, Grocock RJ, Brown JR, Sanseau P (2007) The micro RNA target paradigm: a fundamental and polymorphic control layer of cellular expression. Exp Opin Biol Ther 7: 1387-1399.
8. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
9. Begemann G (2008) MicroRNAs and RNA interference in zebrafish development. Zebrafish 5: 111-119.
10. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37: 766-770.
11. Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, Cuppen E, Plasterk RH (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38: 1375-1377.
12. Beuvink I, Kolb FA, Budach W, Garnier A, Lange J, Natt F, Dengler U, Hall J, Filipowicz W, Weiler J (2007) A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs. Nucleic Acids Res 35: e52.
13. Bicker S, Schratt G (2008) MicroRNAs: Tiny regulators of synapse function in development and disease. J Cell Mol Med 12: 1466-1476.
14. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3: e85.
15. Brown JR, Sanseau P (2005) A computational view of microRNAs and their targets. Drug Discov Today 10: 595-601.
16. Chan JA, Krichevsky AM, Kosik KS (2005) MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 65: 6029-6033.
17. Chang J, Nicolas E, Marks D, Sander C, Lerro A, Buendia MA, Xu C, Mason WS, Moloshok T, Bort R, Zaret KS, Taylor JM (2004) miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol 1: 106-113.
18. Chen K, Rajewsky N (2006) Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38: 1452-1456.
19. Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19: 1288-1293.
20. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38: 228-233.
21. Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M, Wojcik SE, Aqeilan RI, Zupo S, Dono M, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM (2005) miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A 102: 13944-13949.
22. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C, Georges M (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38: 813-818.
23. Coutinho LL, Matukumalli LK, Sonstegard TS, van Tassell CP, Gasbarre LC, Capuco AV, Smith TP (2007) Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiol Genomics 29: 35-43.
24. Doench JG, Petersen CP, Sharp PA (2003) siRNAs can function as miRNAs. Genes Dev 17: 438-442.
25. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, Watts L, Booten SL, Graham M, McKay R, Subramaniam A, Propp S, Lollo BA, Freier S, Bennett CF, Bhanot S, Monia BP (2006) miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 3: 87-98.
26. Fujita S, Ito T, Mizutani T, Minoguchi S, Yamamichi N, Sakurai K, Iba H (2008) miR-21 Gene expression triggered by AP-1 is sustained through a double-negative feedback mechanism. J Mol Biol 378: 492-504.
27. Georges M, Clop A, Marcq F, Takeda H, Pirottin D, Hiard S, Tordoir X, Caiment F, Meish F, Bibe B, Bouix J, Elsen JM, Eychenne F, Laville E, Larzul C, Milenkovic D, Tobin J, Charlier AC (2006) Polymorphic microRNA-target interactions: a novel source of phenotypic variation. Cold Spring Harb Symp Quant Biol 71: 343-350.
28. Ghosh Z, Chakrabarti J, Mallick B (2007) miRNomics-The bioinformatics of microRNA genes. Biochem Biophys Res Commun 363: 6-11.
29. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235-240.
30. Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1: e13.
31. Gu Z, Eleswarapu S, Jiang H (2007) Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland. FEBS Lett 581: 981-988.
32. Ibanez-Ventoso C, Vora M, Driscoll M (2008) Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS ONE 3: e2818.
33. Jerome T, Laurie P, Louis B, Pierre C (2007) Enjoy the silence: the story of let-7 MicroRNA and cancer. Curr Genomics 8: 229-233.
34. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human microRNA targets. PLoS Biol 2: e363.
35. Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT (2006) miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics 7: 411.
36. Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J, Verheul M, Cuppen E, Plasterk RH (2006) Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res 34: 2558-2569.
37. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
38. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735-739.
39. 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: 1401-1414.
40. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
41. Lecellier CH, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, Himber C, Saib A, Voinnet O (2005) A cellular microRNA mediates antiviral defense in human cells. Science 308: 557-560.
42. 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.
43. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
44. Liang Y, Ridzon D, Wong L, Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8: 166.
45. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL (2005) Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17: 2186-2203.
46. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217.
47. Mtango NR, Potireddy S, Latham KE (2008) Expression of microRNA processing machinery genes in rhesus monkey oocytes and embryos of different developmental potentials. Mol Reprod Dev 76: 255-269.
48. Mudhasani R, Zhu Z, Hutvagner G, Eischen CM, Lyle S, Hall LL, Lawrence JB, Imbalzano AN, Jones SN (2008) Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells. J Cell Biol 181: 1055-1063.
49. Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432: 226-230.
50. Ramachandra RK, Salem M, Gahr S, Rexroad CE 3rd, Yao J (2008) Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): their expression during early embryonic development. BMC Dev Biol 8: 41.
51. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98: 15149-15154.
52. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14: 1902-1910.
53. Salem M, Silverstein J, Rexroad CE 3rd, Yao J (2007) Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss). BMC Genomics 8: 328.
54. Saunders MA, Liang H, Li WH (2007) Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A 104: 3300-3305.
55. Shingara J, Keiger K, Shelton J, Laosinchai-Wolf W, Powers P, Conrad R, Brown D, Labourier E (2005) An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11: 1461-1470.
56. Simon-Mateo C, Garcia JA (2006) MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism. J Virol 80: 2429-2436.
57. Smalheiser NR (2003) EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues. Genome Biol 4: 403.
58. Solomon A, Mian Y, Ortega-Cava C, Liu VW, Gurumurthy CB, Naramura M, Band V, Band H (2008) Upregulation of the let-7 microRNA with precocious development in lin-12/Notch hypermorphic Caenorhabditis elegans mutants. Dev Biol 316: 191-199.
59. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, Kim VN, Kim KS (2004) Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270: 488-498.
60. Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y (2002) Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 133: 609-646.
61. Watanabe T, Takeda A, Mise K, Okuno T, Suzuki T, Minami N, Imai H (2005) Stage-specific expression of microRNAs during Xenopus development. FEBS Lett 579: 318-324.
62. Whitehead A, Crawford DL (2005) Variation in tissue-specific gene expression among natural populations. Genome Biol 6: R13-R13.
63. Wienholds E, Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579: 5911-5922.
64. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
65. Yang M, Lee JE, Padgett RW, Edery I (2008) Circadian regulation of a limited set of conserved microRNAs in Drosophila. BMC Genomics 9: 83.
66. Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L). Genome Biol 8: R96.
67. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596.
68. Yin Z, Li C, Han X, Shen F (2008) Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 414: 60-66.
69. Ying SY, Lin SL (2005) Intronic microRNAs. Biochem Biophys Res Commun 326: 515-520.
70. Yoon S, De Micheli G (2005) Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 21(Suppl 2): ii93-ii100.
71. Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289: 3-16.
72. Zhang B, Wang Q, Pan X (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210: 279-289.