Identification of cardiovascular microRNA targetomes

Journal of Molecular and Cellular Cardiology

Volumn 51, Issue 5, 2011, Pages 674-681

  Fiedler, J ^a   Gupta, S K ^a   Thum, T ^a,b  

^a Institute of Molecular and Translational Therapeutic Strategies (IMTTS)   (Germany)

^b IRCCS SAN RAFFAELE PISANA   (Italy)

Author keywords

Cardiac disease; MiRNA; MiRNA targetome; MRE; RISCome; RNA immunoprecipitation; Target prediction

Indexed keywords

MICRORNA; PROTEOME; RNA; RNA INDUCED SILENCING COMPLEX; TARGETOME; TRANSCRIPTOME; UNCLASSIFIED DRUG;

BIOINFORMATICS; CARDIOVASCULAR DISEASE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER INTERFACE; CROSS LINKING; GENE TARGETING; GENETIC DATABASE; HEART FAILURE; HEART MUSCLE FIBROSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; RNA SEQUENCE; TRANSCRIPTOMICS;

ANIMALS; CARDIOVASCULAR DISEASES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; IMMUNOPRECIPITATION; MICE; MICRORNAS; MYOCARDIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOMICS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION;

EID: 80053293348     PISSN: 00222828     EISSN: 10958584     Source Type: Journal    
DOI: 10.1016/j.yjmcc.2011.08.017     Document Type: Review

References (72)

1. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
2. Wightman B., Ha I., Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993, 75:855-862.
3. Pasquinelli A.E., Reinhart B.J., Slack F., Martindale M.Q., Kuroda M.I., Maller B., et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408:86-89.
4. 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.
5. Bauersachs J., Thum T. Biogenesis and regulation of cardiovascular microRNAs. Circ Res 2011, 109:334-347.
6. Esquela-Kerscher A., Slack F.J. Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 2006, 6:259-269.
7. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., Burge C.B. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
8. Fang Z., Rajewsky N. The impact of miRNA target sites in coding sequences and in 3'UTRs. PLoS One 2011, 6:e18067.
9. da Costa Martins P.A., Bourajjaj M., Gladka M., Kortland M., van Oort R.J., Pinto Y.M., et al. Conditional dicer gene deletion in the postnatal myocardium provokes spontaneous cardiac remodeling. Circulation 2008, 118:1567-1576.
10. Thum T. Cardiac dissonance without conductors: how dicer depletion provokes chaos in the heart. Circulation 2008, 118:1524-1527.
11. van Rooij E., Sutherland L.B., Liu N., Williams A.H., McAnally J., Gerard R.D., et al. A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci USA 2006, 103:18255-18260.
12. Thum T., Galuppo P., Wolf C., Fiedler J., Kneitz S., van Laake L.W., et al. MicroRNAs in the human heart: a clue to fetal gene reprogramming in heart failure. Circulation 2007, 116:258-267.
13. Callis T.E., Pandya K., Seok H.Y., Tang R.H., Tatsuguchi M., Huang Z.P., et al. MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. J Clin Invest 2009, 119:2772-2786.
14. Care A., Catalucci D., Felicetti F., Bonci D., Addario A., Gallo P., et al. MicroRNA-133 controls cardiac hypertrophy. Nat Med 2007, 13:613-618.
15. Kuehbacher A., Urbich C., Zeiher A.M., Dimmeler S. Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis. Circ Res 2007, 101:59-68.
16. van Rooij E., Sutherland L.B., Thatcher J.E., DiMaio J.M., Naseem R.H., Marshall W.S., et al. Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis. Proc Natl Acad Sci USA 2008, 105:13027-13032.
17. Thum T., Gross C., Fiedler J., Fischer T., Kissler S., Bussen M., et al. MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature 2008, 456:980-984.
18. van Rooij E., Sutherland L.B., Qi X., Richardson J.A., Hill J., Olson E.N. Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 2007, 316:575-579. (New York, N Y.
19. Small E.M., Olson E.N. Pervasive roles of microRNAs in cardiovascular biology. Nature 2011, 469:336-342.
20. Bonauer A., Carmona G., Iwasaki M., Mione M., Koyanagi M., Fischer A., et al. MicroRNA-92a controls angiogenesis and functional recovery of ischemic tissues in mice. Science 2009, 324:1710-1713. New York, N Y.
21. Krutzfeldt J., Rajewsky N., Braich R., Rajeev K.G., Tuschl T., Manoharan M., et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature 2005, 438:685-689.
22. da Costa Martins P.A., Salic K., Gladka M.M., Armand A.S., Leptidis S., el Azzouzi H., et al. MicroRNA-199b targets the nuclear kinase Dyrk1a in an auto-amplification loop promoting calcineurin/NFAT signalling. Nat Cell Biol 2010, 12:1220-1227.
23. Lanford R.E., Hildebrandt-Eriksen E.S., Petri A., Persson R., Lindow M., Munk M.E., et al. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 2010, 327:198-201. (New York, N Y.
24. Thomas M., Lieberman J., Lal A. Desperately seeking microRNA targets. Nat Struct Mol Biol 2010, 17:1169-1174.
25. Matkovich S.J., Van Booven D.J., Eschenbacher W.H., Dorn G.W. RISC RNA sequencing for context-specific identification of in vivo microRNA targets. Circ Res 2011, 108:18-26.
26. Grimson A., Farh K.K., Johnston W.K., Garrett-Engele P., Lim L.P., Bartel D.P. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27:91-105.
27. Friedman R.C., Farh K.K., Burge C.B., Bartel D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19:92-105.
28. Krek A., Grun D., Poy M.N., Wolf R., Rosenberg L., Epstein E.J., et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500.
29. 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.
30. Lall S., Grun D., Krek A., Chen K., Wang Y.L., Dewey C.N., et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 2006, 16:460-471.
31. Chen K., Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 2006, 38:1452-1456.
32. Enright A.J., John B., Gaul U., Tuschl T., Sander C., Marks D.S. MicroRNA targets in Drosophila. Genome Biol 2003, 5:R1.
33. John B., Enright A.J., Aravin A., Tuschl T., Sander C., Marks D.S. Human MicroRNA targets. PLoS Biol 2004, 2:e363.
34. 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:R90.
35. Hsu S.D., Lin F.M., Wu W.Y., Liang C., Huang W.C., Chan W.L., et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011, 39:D163-D169.
36. Dweep H., Sticht C., Pandey P., Gretz N. miRWalk - Database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 2011, [Electronic publication ahead of print].
37. Fasanaro P., Greco S., Lorenzi M., Pescatori M., Brioschi M., Kulshreshtha R., et al. An integrated approach for experimental target identification of hypoxia-induced miR-210. J Biol Chem 2009, 284:35134-35143.
38. Jayaswal V., Lutherborrow M., Ma D.D., Hwa Yang Y. Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data. Nucleic Acids Res 2009, 37:e60.
39. Jayaswal V., Lutherborrow M., Ma D.D., Yang Y.H. Identification of microRNA-mRNA modules using microarray data. BMC Genomics 2011, 12:138.
40. Bang-Berthelsen C.H., Pedersen L., Floyel T., Hagedorn P.H., Gylvin T., Pociot F. Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes. BMC Genomics 2011, 12:97.
41. Baek D., Villen J., Shin C., Camargo F.D., Gygi S.P., Bartel D.P. The impact of microRNAs on protein output. Nature 2008, 455:64-71.
42. Selbach M., Schwanhausser B., Thierfelder N., Fang Z., Khanin R., Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455:58-63.
43. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
44. Yang Y., Chaerkady R., Kandasamy K., Huang T.C., Selvan L.D., Dwivedi S.B., et al. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst 2010, 6:1873-1882.
45. Yan G.R., Xu S.H., Tan Z.L., Liu L., He Q.Y. Global identification of miR-373-regulated genes in breast cancer by quantitative proteomics. Proteomics 2011, 11:912-920.
46. Elkan-Miller T., Ulitsky I., Hertzano R., Rudnicki A., Dror A.A., Lenz D.R., et al. Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PLoS One 2011, 6:e18195.
47. Yang Y., Chaerkady R., Beer M.A., Mendell J.T., Pandey A. Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics 2009, 9:1374-1384.
48. Leivonen S.K., Rokka A., Ostling P., Kohonen P., Corthals G.L., Kallioniemi O., et al. Identification of miR-193b targets in breast cancer cells and systems biological analysis of their functional impact. Mol Cell Proteomics 2011, 10. :M110.005322.
49. Fleissner F., Jazbutyte V., Fiedler J., Gupta S.K., Yin X., Xu Q., et al. Short communication: asymmetric dimethylarginine impairs angiogenic progenitor cell function in patients with coronary artery disease through a microRNA-21-dependent mechanism. Circ Res 2010, 107:138-143.
50. Brandes R.P. A miR-thless perspective: how asymmetric dimethylarginine impairs the functions of angiogenic progenitor cells. Circ Res 2010, 107:12-14.
51. Huang Y., Qi Y., Ruan Q., Ma Y., He R., Ji Y., et al. A rapid method to screen putative mRNA targets of any known microRNA. Virol J 2011, 8:8.
52. Li J., Xia W., Huang B., Chen L., Su X., Li S., et al. A strategy to rapidly identify the functional targets of microRNAs by combining bioinformatics and mRNA cytoplasmic/nucleic ratios in culture cells. FEBS Lett 2010, 584:3198-3202.
53. Orom U.A., Lund A.H. Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods 2007, 43:162-165.
54. Fiedler J., Jazbutyte V., Kirchmaier B.C., Gupta S.K., Lorenzen J., Hartmann D., et al. MicroRNA-24 regulates vascularity after myocardial infarction. Circulation 2011.
55. Vo N.K., Dalton R.P., Liu N., Olson E.N., Goodman R.H. Affinity purification of microRNA-133a with the cardiac transcription factor, Hand2. Proc Natl Acad Sci USA 2010, 107:19231-19236.
56. Jain R., Devine T., George A.D., Chittur S.V., Baroni T.E., Penalva L.O., et al. RIP-Chip analysis: RNA-binding protein immunoprecipitation-microarray (Chip) profiling. Methods Mol Biol 2011, 703:247-263.
57. Tan L.P., Seinen E., Duns G., de Jong D., Sibon O.C., Poppema S., et al. A high throughput experimental approach to identify miRNA targets in human cells. Nucleic Acids Res 2009, 37:e137.
58. Zhang L., Ding L., Cheung T.H., Dong M.Q., Chen J., Sewell A.K., et al. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 2007, 28:598-613.
59. Landthaler M., Gaidatzis D., Rothballer A., Chen P.Y., Soll S.J., Dinic L., et al. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA 2008, 14:2580-2596.
60. Keene J.D., Komisarow J.M., Friedersdorf M.B. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 2006, 1:302-307.
61. Prokopi M., Mayr M. Proteomics: a reality-check for putative stem cells. Circ Res 2011, 108:499-511.
62. Nelson P.T., Wang W.X., Mao G., Wilfred B.R., Xie K., Jennings M.H., et al. Specific sequence determinants of miR-15/107 microRNA gene group targets. Nucleic Acids Res 2011.
63. Nonne N., Ameyar-Zazoua M., Souidi M., Harel-Bellan A. Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res 2010, 38:e20.
64. Chi S.W., Zang J.B., Mele A., Darnell R.B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486.
65. Leung A.K., Young A.G., Bhutkar A., Zheng G.X., Bosson A.D., Nielsen C.B., et al. Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol 2011, 18:237-244.
66. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
67. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., et al. PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 2010, (41). pii: 2034. 10.3791/2034.
68. Fichtlscherer S., De Rosa S., Fox H., Schwietz T., Fischer A., Liebetrau C., et al. Circulating microRNAs in patients with coronary artery disease. Circ Res 2010, 107:677-684.
69. Zampetaki A., Kiechl S., Drozdov I., Willeit P., Mayr U., Prokopi M., et al. Plasma microRNA profiling reveals loss of endothelial miR-126 and other microRNAs in type 2 diabetes. Circ Res 2010, 107:810-817.
70. Barrey E., Saint-Auret G., Bonnamy B., Damas D., Boyer O., Gidrol X. Pre-microRNA and mature microRNA in human mitochondria. PLoS One 2011, 6:e20220.
71. Yeom K.H., Heo I., Lee J., Hohng S., Kim V.N., Joo C. Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation. EMBO Rep 2011, 12:690-696.
72. Ponting C.P., Oliver P.L., Reik W. Evolution and functions of long noncoding RNAs. Cell 2009, 136:629-641.