Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Takane, Kahori ^a   Fujishima, Kosuke ^a   Watanabe, Yuka ^a   Sato, Asako ^a   Saito, Nobuto ^a   Tomita, Masaru ^a   Kanai, Akio ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PROTEIN LET 7; PROTEIN LIN 4; PROTEIN MIR 1; PROTEIN MIR 124; PROTEIN MIR 125; PROTEIN MIR 34; REGULATOR PROTEIN; UNCLASSIFIED DRUG; MIRN1 MICRORNA, HUMAN; MIRN124 MICRORNA, HUMAN; MIRNLET7 MICRORNA, HUMAN;

ARTICLE; CELL ADHESION; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE TARGETING; GENETIC CONSERVATION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HELA CELL; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; MUSCLE DEVELOPMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PREDICTION; REPORTER GENE; RNA ANALYSIS; VALIDATION STUDY; 3' UNTRANSLATED REGION; ANIMAL; BIOLOGY; GENETICS; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ANIMALIA; BILATERIA; EUKARYOTA;

3' UNTRANSLATED REGIONS; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DOWN-REGULATION; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MICRORNAS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 77950289112     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-101     Document Type: Article

References (44)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
2. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408(6808):86-89. 10.1038/35040556, 11081512.
3. Shivdasani RA. MicroRNAs: regulators of gene expression and cell differentiation. Blood 2006, 108(12):3646-3653. 10.1182/blood-2006-01-030015, 1895474, 16882713.
4. Wienholds E, Plasterk RH. MicroRNA function in animal development. FEBS Lett 2005, 579(26):5911-5922. 10.1016/j.febslet.2005.07.070, 16111679.
5. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, et al. A microRNA polycistron as a potential human oncogene. Nature 2005, 435(7043):828-833. 10.1038/nature03552, 15944707.
6. Johnson CD, Esquela-Kerscher A, Stefani G, Byrom M, Kelnar K, Ovcharenko D, Wilson M, Wang X, Shelton J, Shingara J, et al. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res 2007, 67(16):7713-7722. 10.1158/0008-5472.CAN-07-1083, 17699775.
7. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403(6772):901-906. 10.1038/35002607, 10706289.
8. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2006, 38(2):228-233. 10.1038/ng1725, 2538576, 16380711.
9. Yu JY, Chung KH, Deo M, Thompson RC, Turner DL. MicroRNA miR-124 regulates neurite outgrowth during neuronal differentiation. Exp Cell Res 2008, 314(14):2618-2633. 10.1016/j.yexcr.2008.06.002, 2702206, 18619591.
10. Caygill EE, Johnston LA. Temporal regulation of metamorphic processes in Drosophila by the let-7 and miR-125 heterochronic microRNAs. Curr Biol 2008, 18(13):943-950. 10.1016/j.cub.2008.06.020, 2736146, 18571409.
11. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ. RAS is regulated by the let-7 microRNA family. Cell 2005, 120(5):635-647. 10.1016/j.cell.2005.01.014, 15766527.
12. He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, et al. A microRNA component of the p53 tumour suppressor network. Nature 2007, 447(7148):1130-1134. 10.1038/nature05939, 17554337.
13. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-158. 2238936, 17991681.
14. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19(1):92-105. 10.1101/gr.082701.108, 2612969, 18955434.
15. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004, 10(10):1507-1517. 10.1261/rna.5248604, 1370637, 15383676.
16. Thadani R, Tammi MT. MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformatics 2006, 7(Suppl 5):S20. 10.1186/1471-2105-7-S5-S20, 1764477, 17254305.
17. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39(10):1278-1284. 10.1038/ng2135, 17893677.
18. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004, 2(11):e363. 10.1371/journal.pbio.0020363, 521178, 15502875.
19. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37(5):495-500. 10.1038/ng1536, 15806104.
20. Watanabe Y, Tomita M, Kanai A. Computational methods for microRNA target prediction. Methods Enzymol 2007, 427:65-86. 10.1016/S0076-6879(07)27004-1, 17720479.
21. Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 2007, 8:69. 10.1186/1471-2105-8-69, 1838429, 17331257.
22. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115(7):787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
23. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004, (32 Database):D109-111. 10.1093/nar/gkh023, 308757, 14681370.
24. Huang Y, Gu X. A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs. BMC Genomics 2007, 8:66. 10.1186/1471-2164-8-66, 1832191, 17341314.
25. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 2008, 455(7217):1193-1197. 10.1038/nature07415, 18830242.
26. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27(1):91-105. 10.1016/j.molcel.2007.06.017, 17612493.
27. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433(7027):769-773. 10.1038/nature03315, 15685193.
28. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455(7209):58-63. 10.1038/nature07228, 18668040.
29. Smyth N, Vatansever HS, Murray P, Meyer M, Frie C, Paulsson M, Edgar D. Absence of basement membranes after targeting the LAMC1 gene results in embryonic lethality due to failure of endoderm differentiation. J Cell Biol 1999, 144(1):151-160. 10.1083/jcb.144.1.151, 2148127, 9885251.
30. Liu J, Bang AG, Kintner C, Orth AP, Chanda SK, Ding S, Schultz PG. Identification of the Wnt signaling activator leucine-rich repeat in Flightless interaction protein 2 by a genome-wide functional analysis. Proc Natl Acad Sci USA 2005, 102(6):1927-1932. 10.1073/pnas.0409472102, 548559, 15677333.
31. Toyofuku T, Zhang H, Kumanogoh A, Takegahara N, Suto F, Kamei J, Aoki K, Yabuki M, Hori M, Fujisawa H, et al. Dual roles of Sema6D in cardiac morphogenesis through region-specific association of its receptor, Plexin-A1, with off-track and vascular endothelial growth factor receptor type 2. Genes Dev 2004, 18(4):435-447. 10.1101/gad.1167304, 359397, 14977921.
32. Moss EG, Lee RC, Ambros V. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 1997, 88(5):637-646. 10.1016/S0092-8674(00)81906-6, 9054503.
33. Wu L, Belasco JG. Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells. Mol Cell Biol 2005, 25(21):9198-9208. 10.1128/MCB.25.21.9198-9208.2005, 1265813, 16227573.
34. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 2004, 18(10):1165-1178. 10.1101/gad.1184704, 415641, 15131085.
35. Shields JM, Rogers-Graham K, Der CJ. Loss of transgelin in breast and colon tumors and in RIE-1 cells by Ras deregulation of gene expression through Raf-independent pathways. J Biol Chem 2002, 277(12):9790-9799. 10.1074/jbc.M110086200, 11773051.
36. Haag J, Aigner T. Identification of calponin 3 as a novel Smad-binding modulator of BMP signaling expressed in cartilage. Exp Cell Res 2007, 313(16):3386-3394. 10.1016/j.yexcr.2007.08.003, 17825283.
37. Oki T, Yamazaki K, Kuromitsu J, Okada M, Tanaka I. cDNA cloning and mapping of a novel subtype of glutamine:fructose-6-phosphate amidotransferase (GFAT2) in human and mouse. Genomics 1999, 57(2):227-234. 10.1006/geno.1999.5785, 10198162.
38. Rick M, Ramos SI, Herr C, Thal DR, Noegel AA, Clemen CS. Nuclear localization of Annexin A7 during murine brain development. BMC Neurosci 2005, 6:25. 10.1186/1471-2202-6-25, 1087847, 15819996.
39. Vaucheret H, Vazquez F, Crete P, Bartel DP. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 2004, 18(10):1187-1197. 10.1101/gad.1201404, 415643, 15131082.
40. Bousquet-Antonelli C, Deragon JM. A comprehensive analysis of the La-motif protein superfamily. RNA 2009, 15(5):750-764. 10.1261/rna.1478709, 2673062, 19299548.
41. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 2004, 14(1):160-169. 10.1101/gr.1645104, 314293, 14707178.
42. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, (37 Database):D155-158. 10.1093/nar/gkn809, 2686456, 18957447.
43. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
44. Lai EC. miRNAs: whys and wherefores of miRNA-mediated regulation. Curr Biol 2005, 15(12):R458-460. 10.1016/j.cub.2005.06.015, 15964265.