A Deep Sequencing Approach to Uncover the miRNOME in the Human Heart

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Leptidis, Stefanos ^a   el Azzouzi, Hamid ^a   Lok, Sjoukje I ^b   de Weger, Roel ^b   Olieslagers, Serv ^a   Kisters, Natasja ^a   Silva, Gustavo J ^a   Heymans, Stephane ^a   Cuppen, Edwin ^c   Berezikov, Eugene ^c   de Windt, Leon J ^a   da Costa Martins, Paula ^a  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c HUBRECHT INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 1; MICRORNA 103; MICRORNA 125A; MICRORNA 126; MICRORNA 133A; MICRORNA 143; MICRORNA 145; MICRORNA 195; MICRORNA 199A; MICRORNA 199B; MICRORNA 23B; MICRORNA 24; MICRORNA 30B; MICRORNA 30C; MICRORNA 30D; MICRORNA LET 7; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CLINICAL ARTICLE; CONGESTIVE CARDIOMYOPATHY; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; GENE LOCATION; HEART FAILURE; HUMAN; HUMAN TISSUE; HYPERTROPHIC CARDIOMYOPATHY; NUCLEOTIDE SEQUENCE; PATHOPHYSIOLOGY; QUANTITATIVE STUDY; RNA ANALYSIS; RNA GENE; RNA SEQUENCE; TISSUE DISTRIBUTION; UPREGULATION;

CARDIOMYOPATHY, DILATED; CARDIOMYOPATHY, HYPERTROPHIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HEART FAILURE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; MYOCARDIUM;

EID: 84874536359     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057800     Document Type: Article

References (57)

1. 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.
2. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
3. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Ambros V, (2004) The functions of animal microRNAs. Nature 431: 350-355.
5. Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
6. Hwang HW, Mendell JT, (2006) MicroRNAs in cell proliferation, cell death, and tumorigenesis. British journal of cancer 94: 776-780.
7. Cheng AM, Byrom MW, Shelton J, Ford LP, (2005) Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic acids research 33: 1290-1297.
8. Small EM, Frost RJ, Olson EN, (2010) MicroRNAs add a new dimension to cardiovascular disease. Circulation 121: 1022-1032.
9. Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC, (2007) Mammalian mirtron genes. Molecular cell 28: 328-336.
10. Barringhaus KG, Zamore PD, (2009) MicroRNAs: regulating a change of heart. Circulation 119: 2217-2224.
11. Dorn GW, 2nd (2011) MicroRNAs in cardiac disease. Transl Res 157: 226-235.
12. Hata A (2012) Functions of MicroRNAs in Cardiovascular Biology and Disease. Annu Rev Physiol.
13. van Empel VP, De Windt LJ, da Costa Martins PA, (2012) Circulating miRNAs: Reflecting or Affecting Cardiovascular Disease? Current hypertension reports 14: 498-509.
14. Sayed D, Hong C, Chen IY, Lypowy J, Abdellatif M, (2007) MicroRNAs play an essential role in the development of cardiac hypertrophy. Circulation research 100: 416-424.
15. van Rooij E, Sutherland LB, Liu N, Williams AH, McAnally J, et al. (2006) A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proceedings of the National Academy of Sciences of the United States of America 103: 18255-18260.
16. Cheng Y, Ji R, Yue J, Yang J, Liu X, et al. (2007) MicroRNAs are aberrantly expressed in hypertrophic heart: do they play a role in cardiac hypertrophy? The American journal of pathology 170: 1831-1840.
17. Tatsuguchi M, Seok HY, Callis TE, Thomson JM, Chen JF, et al. (2007) Expression of microRNAs is dynamically regulated during cardiomyocyte hypertrophy. Journal of molecular and cellular cardiology 42: 1137-1141.
18. van Rooij E, Sutherland LB, Thatcher JE, DiMaio JM, Naseem RH, et al. (2008) Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis. Proceedings of the National Academy of Sciences of the United States of America 105: 13027-13032.
19. Ikeda S, Kong SW, Lu J, Bisping E, Zhang H, et al. (2007) Altered microRNA expression in human heart disease. Physiol Genomics 31: 367-373.
20. Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, et al. (2008) Serum microRNAs are promising novel biomarkers. PloS one 3: e3148.
21. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, et al. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.
22. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nature genetics 37: 766-770.
23. Matkovich SJ, Zhang Y, Van Booven DJ, Dorn GW, 2nd (2010) Deep mRNA sequencing for in vivo functional analysis of cardiac transcriptional regulators: application to Galphaq. Circulation research 106: 1459-1467.
24. Lee JH, Gao C, Peng G, Greer C, Ren S, et al. (2011) Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circulation research 109: 1332-1341.
25. Krichevsky AM, King KS, Donahue CP, Khrapko K, Kosik KS, (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9: 1274-1281.
26. Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, et al. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America 101: 9740-9744.
27. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, et al. (2005) Elucidation of the small RNA component of the transcriptome. Science 309: 1567-1569.
28. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
29. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, et al. (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome research 18: 1602-1609.
30. 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: 2496-2505.
31. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, et al. (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome research 18: 957-964.
32. Gommans WM, Berezikov E, (2012) Sample preparation for small RNA massive parallel sequencing. Methods in molecular biology 786: 167-178.
33. Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, et al. (2006) Diversity of microRNAs in human and chimpanzee brain. Nature genetics 38: 1375-1377.
34. Zhang Z, Berman P, Miller W, (1998) Alignments without low-scoring regions. Journal of computational biology: a journal of computational molecular cell biology 5: 197-210.
35. Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R, (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 22: 500-503.
36. van Loosdregt J, van Oosterhout MF, Bruggink AH, van Wichen DF, van Kuik J, et al. (2006) The chemokine and chemokine receptor profile of infiltrating cells in the wall of arteries with cardiac allograft vasculopathy is indicative of a memory T-helper 1 response. Circulation 114: 1599-1607.
37. de Wit E, Linsen SE, Cuppen E, Berezikov E, (2009) Repertoire and evolution of miRNA genes in four divergent nematode species. Genome research 19: 2064-2074.
38. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, et al. (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313: 320-324.
39. Aravin A, Tuschl T, (2005) Identification and characterization of small RNAs involved in RNA silencing. FEBS letters 579: 5830-5840.
40. Bonauer A, Carmona G, Iwasaki M, Mione M, Koyanagi M, et al. (2009) MicroRNA-92a controls angiogenesis and functional recovery of ischemic tissues in mice. Science 324: 1710-1713.
41. Fiedler J, Jazbutyte V, Kirchmaier BC, Gupta SK, Lorenzen J, et al. (2011) MicroRNA-24 regulates vascularity after myocardial infarction. Circulation 124: 720-730.
42. Elia L, Contu R, Quintavalle M, Varrone F, Chimenti C, et al. (2009) Reciprocal regulation of microRNA-1 and insulin-like growth factor-1 signal transduction cascade in cardiac and skeletal muscle in physiological and pathological conditions. Circulation 120: 2377-2385.
43. Care A, Catalucci D, Felicetti F, Bonci D, Addario A, et al. (2007) MicroRNA-133 controls cardiac hypertrophy. Nat Med 13: 613-618.
44. Matkovich SJ, Wang W, Tu Y, Eschenbacher WH, Dorn LE, et al. (2010) MicroRNA-133a protects against myocardial fibrosis and modulates electrical repolarization without affecting hypertrophy in pressure-overloaded adult hearts. Circulation research 106: 166-175.
45. Callis TE, Pandya K, Seok HY, Tang RH, Tatsuguchi M, et al. (2009) MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. J Clin Invest 119: 2772-2786.
46. van Rooij E, Sutherland LB, Qi X, Richardson JA, Hill J, et al. (2007) Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 316: 575-579.
47. Shieh JT, Huang Y, Gilmore J, Srivastava D, (2011) Elevated miR-499 levels blunt the cardiac stress response. PloS one 6: e19481.
48. Wang JX, Jiao JQ, Li Q, Long B, Wang K, et al. (2011) miR-499 regulates mitochondrial dynamics by targeting calcineurin and dynamin-related protein-1. Nat Med 17: 71-78.
49. da Costa Martins PA, Salic K, Gladka MM, Armand AS, Leptidis S, et al. (2010) MicroRNA-199b targets the nuclear kinase Dyrk1a in an auto-amplification loop promoting calcineurin/NFAT signalling. Nat Cell Biol 12: 1220-1227.
50. Thum T, Gross C, Fiedler J, Fischer T, Kissler S, et al. (2008) MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature 456: 980-984.
51. Thum T, Galuppo P, Wolf C, Fiedler J, Kneitz S, et al. (2007) MicroRNAs in the human heart: a clue to fetal gene reprogramming in heart failure. Circulation 116: 258-267.
52. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, et al. (2009) miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460: 705-710.
53. Mayorga ME, Penn MS, (2012) miR-145 is differentially regulated by TGF-beta1 and ischaemia and targets Disabled-2 expression and wnt/beta-catenin activity. J Cell Mol Med 16: 1106-1113.
54. Caruso P, Dempsie Y, Stevens HC, McDonald RA, Long L, et al. (2012) A role for miR-145 in pulmonary arterial hypertension: evidence from mouse models and patient samples. Circulation research 111: 290-300.
55. 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 research 18: 610-621.
56. Ryu S, Joshi N, McDonnell K, Woo J, Choi H, et al. (2011) Discovery of novel human breast cancer microRNAs from deep sequencing data by analysis of pri-microRNA secondary structures. PloS one 6: e16403.
57. Meiri E, Levy A, Benjamin H, Ben-David M, Cohen L, et al. (2010) Discovery of microRNAs and other small RNAs in solid tumors. Nucleic acids research 38: 6234-6246.