Non-coding RNA in control of gene regulatory programs in cardiac development and disease

Journal of Molecular and Cellular Cardiology

Volumn 89, Issue , 2015, Pages 51-58

  Philippen, Leonne E ^a   Dirkx, Ellen ^a,b   da Costa Martins, Paula A ^a   De Windt, Leon J ^a  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

Gene expression; LncRNA; MicroRNA; Non coding RNA

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA 1; MICRORNA 133; MICRORNA 15; MICRORNA 17 92; MICRORNA 208A; MICRORNA 208B; MICRORNA 499; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

CARDIAC GENE; CISTRON; EMBRYO DEVELOPMENT; GENE; GENE CLUSTER; GENE FUNCTION; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC REGULATION; HEART DEVELOPMENT; HEART DISEASE; HEART FUNCTION; HEART MUSCLE; HEART VENTRICLE HYPERTROPHY; HUMAN; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; REVIEW; ANIMAL; CARDIOVASCULAR DISEASE; EMBRYOLOGY; GENE EXPRESSION REGULATION; GENETICS; HEART; METABOLISM;

ANIMALS; CARDIOVASCULAR DISEASES; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; HEART; HUMANS; RNA, LONG NONCODING;

EID: 84952716495     PISSN: 00222828     EISSN: 10958584     Source Type: Journal    
DOI: 10.1016/j.yjmcc.2015.03.014     Document Type: Review

References (55)

1. 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.
2. Srivastava D. Making or breaking the heart: from lineage determination to morphogenesis. Cell 2006, 126:1037-1048.
3. Buckingham M., Meilhac S., Zaffran S. Building the mammalian heart from two sources of myocardial cells. Nat Rev Genet 2005, 6:826-835.
4. Kirby M.L., Waldo K.L. Neural crest and cardiovascular patterning. Circ Res 1995, 77:211-215.
5. Olson E.N. Gene regulatory networks in the evolution and development of the heart. Science 2006, 313:1922-1927.
6. Pashmforoush M., Lu J.T., Chen H., Amand T.S., Kondo R., Pradervand S., et al. Nkx2-5 pathways and congenital heart disease; loss of ventricular myocyte lineage specification leads to progressive cardiomyopathy and complete heart block. Cell 2004, 117:373-386.
7. Lin C.Y., Lin C.J., Chen C.H., Chen R.M., Zhou B., Chang C.P. The secondary heart field is a new site of calcineurin/Nfatc1 signaling for semilunar valve development. J Mol Cell Cardiol 2012, 52:1096-1102.
8. Dirkx E., da Costa Martins P.A., De Windt L.J. Regulation of fetal gene expression in heart failure. Biochim Biophys Acta 1832, 2013:2414-2424.
9. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
10. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
11. Consortium E.P. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
12. Bernstein E., Kim S.Y., Carmell M.A., Murchison E.P., Alcorn H., Li M.Z., et al. Dicer is essential for mouse development. Nat Genet 2003, 35:215-217.
13. Wang Y., Medvid R., Melton C., Jaenisch R., Blelloch R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet 2007, 39:380-385.
14. Fukuda T., Yamagata K., Fujiyama S., Matsumoto T., Koshida I., Yoshimura K., et al. DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol 2007, 9:604-611.
15. Morita S., Horii T., Kimura M., Goto Y., Ochiya T., Hatada I. One Argonaute family member, Eif2c2 (Ago2), is essential for development and appears not to be involved in DNA methylation. Genomics 2007, 89:687-696.
16. Zhao Y., Ransom J.F., Li A., Vedantham V., von Drehle M., Muth A.N., et al. Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 2007, 129:303-317.
17. Chapnik E., Sasson V., Blelloch R., Hornstein E. Dgcr8 controls neural crest cells survival in cardiovascular development. Dev Biol 2012, 362:50-56.
18. 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.
19. Chen J.F., Mandel E.M., Thomson J.M., Wu Q., Callis T.E., Hammond S.M., et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2006, 38:228-233.
20. Zhao Y., Samal E., Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436:214-220.
21. Srivastava D., Thomas T., Lin Q., Kirby M.L., Brown D., Olson E.N. Regulation of cardiac mesodermal and neural crest development by the bHLH transcription factor, dHAND. Nat Genet 1997, 16:154-160.
22. Liu N., Bezprozvannaya S., Williams A.H., Qi X., Richardson J.A., Bassel-Duby R., et al. microRNA-133a regulates cardiomyocyte proliferation and suppresses smooth muscle gene expression in the heart. Genes Dev 2008, 22:3242-3254.
23. 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.
24. Karakikes I., Chaanine A.H., Kang S., Mukete B.N., Jeong D., Zhang S., et al. Therapeutic cardiac-targeted delivery of miR-1 reverses pressure overload-induced cardiac hypertrophy and attenuates pathological remodeling. J.Am. Heart Assoc. 2013, 2:e000078.
25. Kumarswamy R., Lyon A.R., Volkmann I., Mills A.M., Bretthauer J., Pahuja A., et al. SERCA2a gene therapy restores microRNA-1 expression in heart failure via an Akt/FoxO3A-dependent pathway. Eur Heart J 2012, 33:1067-1075.
26. Castaldi A., Zaglia T., Di Mauro V., Carullo P., Viggiani G., Borile G., et al. MicroRNA-133 modulates the beta1-adrenergic receptor transduction cascade. Circ Res 2014, 115:273-283.
27. Elia L., Contu R., Quintavalle M., Varrone F., Chimenti C., Russo M.A., et al. 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 2009, 120:2377-2385.
28. Lompre A.M., Nadal-Ginard B., Mahdavi V. Expression of the cardiac ventricular alpha- and beta-myosin heavy chain genes is developmentally and hormonally regulated. J Biol Chem 1984, 259:6437-6446.
29. Weiss A., Leinwand L.A. The mammalian myosin heavy chain gene family. Annu Rev Cell Dev Biol 1996, 12:417-439.
30. van Rooij E., Quiat D., Johnson B.A., Sutherland L.B., Qi X., Richardson J.A., et al. A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance. Dev Cell 2009, 17:662-673.
31. 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.
32. Montgomery R.L., Hullinger T.G., Semus H.M., Dickinson B.A., Seto A.G., Lynch J.M., et al. Therapeutic inhibition of miR-208a improves cardiac function and survival during heart failure. Circulation 2011, 124:1537-1547.
33. Ventura A., Young A.G., Winslow M.M., Lintault L., Meissner A., Erkeland S.J., et al. Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 2008, 132:875-886.
34. Wang J., Greene S.B., Bonilla-Claudio M., Tao Y., Zhang J., Bai Y., et al. Bmp signaling regulates myocardial differentiation from cardiac progenitors through a MicroRNA-mediated mechanism. Dev Cell 2010, 19:903-912.
35. Chen J., Huang Z.P., Seok H.Y., Ding J., Kataoka M., Zhang Z., et al. miR-17-92 cluster is required for and sufficient to induce cardiomyocyte proliferation in postnatal and adult hearts. Circ Res 2013, 112:1557-1566.
36. Dirkx E., Gladka M.M., Philippen L.E., Armand A.S., Kinet V., Leptidis S., et al. Nfat and miR-25 cooperate to reactivate the transcription factor Hand2 in heart failure. Nat Cell Biol 2013, 15:1282-1293.
37. Wahlquist C., Jeong D., Rojas-Munoz A., Kho C., Lee A., Mitsuyama S., et al. Inhibition of miR-25 improves cardiac contractility in the failing heart. Nature 2014, 508:531-535.
38. Porrello E.R., Johnson B.A., Aurora A.B., Simpson E., Nam Y.J., Matkovich S.J., et al. MiR-15 family regulates postnatal mitotic arrest of cardiomyocytes. Circ Res 2011, 109:670-679.
39. Porrello E.R., Mahmoud A.I., Simpson E., Johnson B.A., Grinsfelder D., Canseco D., et al. Regulation of neonatal and adult mammalian heart regeneration by the miR-15 family. Proc Natl Acad Sci U S A 2013, 110:187-192.
40. Cesana M., Cacchiarelli D., Legnini I., Santini T., Sthandier O., Chinappi M., et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011, 147:358-369.
41. Lee J.T. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev 2009, 23:1831-1842.
42. Maurano M.T., Humbert R., Rynes E., Thurman R.E., Haugen E., Wang H., et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012, 337:1190-1195.
43. Klattenhoff C.A., Scheuermann J.C., Surface L.E., Bradley R.K., Fields P.A., Steinhauser M.L., et al. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 2013, 152:570-583.
44. Grote P., Wittler L., Hendrix D., Koch F., Wahrisch S., Beisaw A., et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 2013, 24:206-214.
45. Colley S.M., Leedman P.J. Steroid receptor RNA activator-a nuclear receptor coregulator with multiple partners: insights and challenges. Biochimie 2011, 93:1966-1972.
46. Caretti G., Schiltz R.L., Dilworth F.J., Di Padova M., Zhao P., Ogryzko V., et al. The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell 2006, 11:547-560.
47. Friedrichs F., Zugck C., Rauch G.J., Ivandic B., Weichenhan D., Muller-Bardorff M., et al. HBEGF, SRA1, and IK: three cosegregating genes as determinants of cardiomyopathy. Genome Res 2009, 19:395-403.
48. Han P., Li W., Lin C.H., Yang J., Shang C., Nurnberg S.T., et al. A long noncoding RNA protects the heart from pathological hypertrophy. Nature 2014, 514:102-106.
49. Hang C.T., Yang J., Han P., Cheng H.L., Shang C., Ashley E., et al. Chromatin regulation by Brg1 underlies heart muscle development and disease. Nature 2010, 466:62-67.
50. Ounzain S., Micheletti R., Beckmann T., Schroen B., Alexanian M., Pezzuto I., et al. Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J 2015, 36:353-368.
51. Ishii N., Ozaki K., Sato H., Mizuno H., Saito S., Takahashi A., et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 2006, 51:1087-1099.
52. Matkovich S.J., Edwards J.R., Grossenheider T.C., de Guzman Strong C., Dorn G.W. Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs. Proc Natl Acad Sci U S A 2014, 111:12264-12269.
53. Liu Y., Li G., Lu H., Li W., Li X., Liu H., et al. Expression profiling and ontology analysis of long noncoding RNAs in post-ischemic heart and their implied roles in ischemia/reperfusion injury. Gene 2014, 543:15-21.
54. Yang K.C., Yamada K.A., Patel A.Y., Topkara V.K., George I., Cheema F.H., et al. Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support. Circulation 2014, 129:1009-1021.
55. Wang K., Liu F., Zhou L.Y., Long B., Yuan S.M., Wang Y., et al. The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 2014, 114:1377-1388.