A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

Gene

Volumn 533, Issue 1, 2014, Pages 261-269

  Yang, Liandong ^a,b   He, Shunping ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Comparative genomics; MicroRNAs; Rainbow trout; Targets

Indexed keywords

MICRORNA;

ARTICLE; BIOINFORMATICS; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; GENE; GENE TARGETING; GENETIC DATABASE; GENOMICS; NITROGEN METABOLISM; NONHUMAN; OXIDATIVE PHOSPHORYLATION; PRIORITY JOURNAL; PURINE METABOLISM; RAINBOW TROUT; RNA ANALYSIS; RNA METABOLISM; SEQUENCE ANALYSIS;

AGO; ARGONAUTE; BASIC LOCAL ALIGNMENT SEARCH TOOL; BLAST; COMPARATIVE GENOMICS; EST; EXPRESSED SEQUENCE TAG; GENE ONTOLOGY; GO; KEGG; KYOTO ENCYCLOPEDIA OF GENES AND GENOMES; MFE; MFEI; MICRORNA; MICRORNAS; MINIMAL FOLDING FREE ENERGY; MINIMAL FOLDING FREE ENERGY INDEX; MIRISCS; MIRNA; MIRNA PRECURSOR; MIRNA-INDUCED SILENCING COMPLEXES; NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION; NCBI; NT; NUCLEOTIDE; O. MYKISS; ONCORHYNCHUS MYKISS; PRE-MIRNA; PRI-MIRNA; PRIMARY MIRNA; RAINBOW TROUT; TARGETS; UNTRANSLATED REGIONS; UTRS;

ANIMALS; COMPUTATIONAL BIOLOGY; MICRORNAS; ONCORHYNCHUS MYKISS;

ANIMALIA; ONCORHYNCHUS MYKISS;

EID: 84887256593     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.09.060     Document Type: Article

References (70)

1. Alexiou P., Maragkakis M., Papadopoulos G.L., Reczko M., Hatzigeorgiou A.G. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 2009, 25:3049-3055.
2. Allen E., Xie Z., Gustafson A.M., Sung G.H., Spatafora J.W., Carrington J.C. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 2004, 36:1282-1290.
3. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
4. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
5. Altuvia Y., et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 2005, 33:2697-2706.
6. Ashburner M., Bergman C.M. Drosophila melanogaster: a case study of a model genomic sequence and its consequences. Genome Res. 2005, 15:1661-1667.
7. Ashburner M., et al. Gene ontology: tool for the unification of biology. Nat. Genet. 2000, 25:25-29.
8. Avesson L., Reimegard J., Wagner E.G., Soderbom F. MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs. RNA 2012, 18:1771-1782.
9. Barozai M.Y. The MicroRNAs and their targets in the channel catfish (Ictalurus punctatus). Mol. Biol. Rep. 2012, 39(9):8867-8872.
10. Barozai M.Y.K. Identification and characterization of the microRNAs and their targets in Salmo salar. Gene 2012, 499:163-168.
11. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
12. Bennasser Y., Le S.Y., Yeung M.L., Jeang K.T. HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 2004, 1:43.
13. Bentwich I., et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 2005, 37:766-770.
14. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120:21-24.
15. Betel D., Wilson M., Gabow A., Marks D.S., Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res. 2008, 36:D149-D153.
16. Betel D., Koppal A., Agius P., Sander C., Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 2010, 11.
17. Boguski L.T., Tolstoshev C.M. dbEST - database for "expressed sequence tags". Nat. Genet. 1993, 4:332-333.
18. Bonnet E., Wuyts J., Rouze P., Van de Peer Y. Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:11511-11516.
19. Brameier M. Genome-wide comparative analysis of microRNAs in three non-human primates. BMC Res. Notes 2010, 3:64.
20. Brown J.R., Sanseau P. A computational view of microRNAs and their targets. Drug Discov. Today 2005, 10:595-601.
21. Carthew R.W., Sontheimer E.J. Origins and mechanisms of miRNAs and siRNAs. Cell 2009, 136:642-655.
22. Chi W., Tong C., Gan X., He S. Characterization and comparative profiling of MiRNA transcriptomes in bighead carp and silver carp. PLoS One 2011, 6:e23549.
23. Colaiacovo M., Subacchi A., Bagnaresi P., Lamontanara A., Cattivelli L., Faccioli P. A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.). BMC Genomics 2010, 11:595.
24. Conesa A., Gotz S., Garcia-Gomez J.M., Terol J., Talon M., Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
25. Crooks G.E., Hon G., Chandonia J.M., Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188-1190.
26. Enright A.J., John B., Gaul U., Tuschl T., Sander C., Marks D.S. MicroRNA targets in Drosophila. Genome Biol. 2004, 5.
27. Gotz S., et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008, 36:3420-3435.
28. Grun D., Wang Y.L., Langenberger D., Gunsalus K.C., Rajewsky N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol. 2005, 1:e13.
29. Hagen J.W., Lai E.C. microRNA control of cell-cell signaling during development and disease. Cell Cycle 2008, 7:2327-2332.
30. Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 2003, 31:3429-3431.
31. Ivanovska I., et al. MicroRNAs in the miR-106b family regulate p21/CDKN1A and promote cell cycle progression. Mol. Cell. Biol. 2008, 28:2167-2174.
32. John B., Enright A.J., Aravin A., Tuschl T., Sander C., Marks D.S. Human MicroRNA targets. PLoS Biol. 2004, 2:e363.
33. Jones-Rhoades M.W., Bartel D.P. Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Mol. Cell 2004, 14:787-799.
34. Kanehisa M., Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000, 28:27-30.
35. Kertesz M., Iovino N., Unnerstall U., Gaul U., Segal E. The role of site accessibility in microRNA target recognition. Nat. Genet. 2007, 39:1278-1284.
36. Kim V.N. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 2005, 6:376-385.
37. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39:D152-D157.
38. Krol J., Loedige I., Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet. 2010, 11:597-610.
39. Krzyzanowski P.M., Price F.D., Muro E.M., Rudnicki M.A., Andrade-Navarro M.A. Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery. PLoS One 2011, 6.
40. Lagos-Quintana M., Rauhut R., Meyer J., Borkhardt A., Tuschl T. New microRNAs from mouse and human. RNA 2003, 9:175-179.
41. Lee Y., Jeon K., Lee J.T., Kim S., Kim V.N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 2002, 21:4663-4670.
42. Lee Y.S., et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 2004, 117:69-81.
43. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
44. Li L., Xu J.Z., Yang D.Y., Tan X.R., Wang H.F. Computational approaches for microRNA studies: a review. Mamm. Genome 2010, 21:1-12.
45. Lim L.P., Glasner M.E., Yekta S., Burge C.B., Bartel D.P. Vertebrate microRNA genes. Science 2003, 299:1540.
46. Linsley P.S., et al. Transcripts targeted by the MicroRNA-16 family cooperatively regulate cell cycle progression. Mol. Cell. Biol. 2007, 27:2240-2252.
47. Liu Z., Sall A., Yang D.C. MicroRNA: an emerging therapeutic target and intervention tool. Int. J. Mol. Sci. 2008, 9:978-999.
48. Ma H., Hostuttler M., Wei H.R., Rexroad C.E., Yao J.B. Characterization of the rainbow trout egg microRNA transcriptome. PLoS One 2012, 7.
49. Palti Y., et al. A first generation integrated map of the rainbow trout genome. BMC Genomics 2011, 12.
50. Ramachandra R.K., Salem M., Gahr S., Rexroad C.E., Yao J. Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): their expression during early embryonic development. BMC Dev. Biol. 2008, 8.
51. Reese T.A., Xia J., Johnson L.S., Zhou X., Zhang W., Virgin H.W. Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts. J. Virol. 2010, 84:10344-10353.
52. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 2002, 16:1616-1626.
53. Roux J., Gonzalez-Porta M., Robinson-Rechavi M. Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res. 2012, 40:5890-5900.
54. Salem M., Xiao C., Womack J., Rexroad C.E., Yao J. A microRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss). Mar. Biotechnol. (NY) 2010, 12:410-429.
55. Sethupathy P., Megraw M., Hatzigeorgiou A.G. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods 2006, 3:881-886.
56. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
57. Soares A.R., et al. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 2009, 10.
58. Sunkar R., Girke T., Jain P.K., Zhu J.K. Cloning and characterization of MicroRNAs from rice. Plant Cell 2005, 17:1397-1411.
59. Wang M., Wang Q.L., Wang B.M. Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). PLoS One 2012, 7.
60. Weber M.J. New human and mouse microRNA genes found by homology search. FEBS J. 2005, 272:59-73.
61. Wienholds E., Plasterk R.H. MicroRNA function in animal development. FEBS Lett. 2005, 579:5911-5922.
62. Xie X., et al. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 2005, 434:338-345.
63. Yoon S., De Micheli G. Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 2005, 21(Suppl. 2):ii93-ii100.
64. Yu J., et al. Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochem. Biophys. Res. Commun. 2006, 349:59-68.
65. Yu X.M., et al. The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PLoS One 2008, 3.
66. Zhang B.H., Pan X.P., Wang Q.L., Cobb G.P., Anderson T.A. Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 2005, 15:336-360.
67. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci. 2006, 63:246-254.
68. Zhang B.H., Wang Q.L., Pan X.P. MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol. 2007, 210:279-289.
69. Zhang Y., Zhang R., Su B. Diversity and evolution of MicroRNA gene clusters. Sci. China C Life Sci. 2009, 52:261-266.
70. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981, 9:133-148.