Small RNAs have a big impact on regeneration

RNA Biology

Volumn 7, Issue 3, 2010, Pages

  Thatcher, Elizabeth J ^a   Patton, James G ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

MicroRNAs; Regeneration; Stem cells; Zebrafish

Indexed keywords

EID: 85011942158     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.7.3.12085     Document Type: Review

References (77)

1. Flynt A, Li N, Thatcher E, Solnica-Krezel L, Patton J. Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet 2007; 39:259-63.
2. Flynt A, Thatcher E, Burkewitz K, Li N, Liu Y, Patton J. miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos. J Cell Biol 2009; 185:115-27.
3. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 2006; 3:87-98.
4. Plasterk RH. Micro RNAs in animal development. Cell 2006; 124:877-81.
5. Bartel D. MicroRNAs: genomics, biogenesis, mechanism and function. Cell 2004; 116:281-97.
6. Hobert O. Common logic of transcription factor and microRNA action. Trends Biochem Sci 2004; 29:462-8.
7. Carthew RW. Gene regulation by microRNAs. Curr Opin Genet Dev 2006; 16:203-8.
8. Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, Ruohola-Baker H. Stem cell division is regulated by the microRNA pathway. Nature 2005; 435:974.
9. Slack FJ, Weidhaas JB. MicroRNAs as a potential magic bullet in cancer. Future Oncol 2006; 2:73-82.
10. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 2005; 435:839-43.
11. Voorhoeve PM, le Sage C, Schrier M, Gillis AJ, Stoop H, Nagel R, et al. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 2006; 124:1169-81.
12. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U. Nuclear export of microRNA precursors. Science 2004; 303:95-8.
13. Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003; 17:3011-6.
14. Bernstein E, Ahmet M. Denli, Gregory J. Hannon. The rest is silence. RNA 2001; 7:1509-21.
15. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409:363-6.
16. Zamore P, Tuschl T, Sharp P, Bartel D. RNAi: double-stranded RNA directs the ATP-dependent dleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000; 101:25-33.
17. Gu S, Rossi JJ. Uncoupling of RNAi from active translation in mammalian cells. RNA 2005; 11:38-44.
18. Sen GL, Blau HM. Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat Cell Biol 2005; 7:633.
19. Thatcher E, Flynt A, Li N, Patton J. MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways. Dev Dyn 2007; 236:2172-80.
20. Wienholds E, Kloosterman WP, Miska E, Alvarez- Saavedra E, Berezikov E, de Bruijn E, et al. MicroRNA Expression in Zebrafish Embryonic Development. Science 2005; 309:310-1.
21. Lena AM, Shalom-Feuerstein R, Rivetti di Val Cervo P, Aberdam D, Knight RA, Melino G, et al. miR-203 represses 'stemness' by repressing DeltaNp63. Cell Death Differ 2008; 15:1187-95.
22. Melton C, Judson RL, Blelloch R. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature 2010; 1-8.
23. Thatcher E, Paydar I, Anderson KK, Patton J. Regulation of zebrafish fin regeneration by microRNAs. Proc Natl Acad Sci USA 2008; 105:18384-9.
24. 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; 39:380-5.
25. Yi R, Poy MN, Stoffel M, Fuchs E. A skin microRNA promotes differentiation by repressing 'stemness'. Nature 2008; 452:225-9.
26. Houbaviy HB, Murray MF, Sharp PA. Embryonic stem cell-specific MicroRNAs. Dev Cell 2003; 5:351-8.
27. Tang F, Hajkova P, Barton SC, Lao K, Surani MA. MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res 2006; 34:9.
28. Forstemann K, Tomari Y, Du T, Vagin VV, Denli AM, Bratu DP, et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol 2005; 3:236.
29. Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, Li MZ, et al. Dicer is essential for mouse development. Nat Genet 2003; 35:215-7.
30. Yang WJ, Yang DD, Na S, Sandusky GE, Zhang Q, Zhao G. Dicer is required for embryonic angiogenesis during mouse development. J Biol Chem 2005; 280:9330-5.
31. Murchison EP, Partridge JF, Tam OH, Cheloufi S, Hannon GJ. Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci USA 2005; 102:12135-40.
32. Wang Y, Baskerville S, Shenoy A, Babiarz JE, Baehner L, Blelloch R. Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet 2008; 40:1478-83.
33. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, et al. MicroRNAs Regulate Brain Morphogenesis in Zebrafish. Science 2005; 308:833-8.
34. Wienholds E, Plasterk RH. MicroRNA function in animal development. FEBS Lett 2005; 579:5911-22.
35. Heo I, Joo C, Cho J, Ha M, Han J, Kim VN. Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 2008; 32:276-84.
36. Lehrbach NJ, Armisen J, Lightfoot HL, Murfitt KJ, Bugaut A, Balasubramanian S, et al. LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nat Struct Mol Biol 2009; 16:1016-20.
37. Newman MA, Thomson JM, Hammond SM. Lin- 28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 2008; 14:1539-49.
38. Rybak A, Fuchs H, Smirnova L, Brandt C, Pohl EE, Nitsch R, et al. A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat Cell Biol 2008; 10:987-93.
39. Viswanathan SR, Daley GQ, Gregory RI. Selective blockade of microRNA processing by Lin28. Science 2008; 320:97-100.
40. Thomson JM, Parker JS, Hammond SM. Microarray Analysis of miRNA Gene Expression. Methods Enzymol 2007; 427:107-22.
41. Sehm T, Sachse C, Frenzel C, Echeverri K. miR-196 is an essential early-stage regulator of tail regeneration, upstream of key spinal cord patterning events. Dev Biol 2009; 334:468-80.
42. Palakodeti D, Smielewska M, Lu YC, Yeo GW, Graveley BR. The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA 2008; 14:1174-86.
43. Reddien PW, Oviedo NJ, Jennings JR, Jenkin JC, Sanchez Alvarado A. SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science 2005; 310:1327-30.
44. Guo T, Peters AH, Newmark PA. A Bruno-like gene is required for stem cell maintenance in planarians. Dev Cell 2006; 11:159-69.
45. Friedlander MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, et al. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci USA 2009; 106:11546-51.
46. Gonzalez-Estevez C, Arseni V, Thambyrajah RS, Felix DA, Aboobaker AA. Diverse miRNA spatial expression patterns suggest important roles in homeostasis and regeneration in planarians. Int J Dev Biol 2009; 53:493-505.
47. Stoick-Cooper CL, Moon RT, Weidinger G. Advances in signaling in vertebrate regeneration as a prelude to regenerative medicine. Genes Dev 2007; 21:1292-315.
48. Yin VP, Thomson JM, Thummel R, Hyde DR, Hammond SM, Poss KD. Fgf-dependent depletion of microRNA-133 promotes appendage regeneration in zebrafish. Genes Dev 2008; 22:728-33.
49. Schebesta M, Lien CL, Engel FB, Keating MT. Transcriptional profiling of caudal fin regeneration in zebrafish. ScientificWorldJournal 2006; 6:38-54.
50. Niethammer P, Grabher C, Look AT, Mitchison TJ. A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish. Nature 2009; 459:996-9.
51. Iovine MK. Conserved mechanisms regulate outgrowth in zebrafish fins. Nat Chem Biol 2007; 3:613-8.
52. Williams AH, Liu N, van Rooij E, Olson EN. MicroRNA control of muscle development and disease. Curr Opin Cell Biol 2009; 21:461-9.
53. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2006; 38:228-33.
54. Kwon C, Han Z, Olson EN, Srivastava D. MicroRNA1 influences cardiac differentiation in Drosophila and regulates Notch signaling. Proc Natl Acad Sci USA 2005; 102:18986-91.
55. Rao PK, Kumar RM, Farkhondeh M, Baskerville S, Lodish HF. Myogenic factors that regulate expression of muscle-specific microRNAs. Proc Natl Acad Sci USA 2006; 103:8721-6.
56. Sokol NS, Ambros V. Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev 2005; 19:2343-54.
57. Zhao Y, Samal E, Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005; 436:214-20.
58. Zhao Y, Ransom JF, Li A, Vedantham V, von Drehle M, Muth AN, et al. Dysregulation of cardiogenesis, cardiac conduction and cell cycle in mice lacking miRNA-1-2. Cell 2007; 129:303-17.
59. Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A. Muscle-specific microRNA miR-206 promotes muscle differentiation. J Cell Biol 2006; 174:677-87.
60. Rosenberg MI, Georges SA, Asawachaicharn A, Analau E, Tapscott SJ. MyoD inhibits Fstl1 and Utrn expression by inducing transcription of miR-206. J Cell Biol 2006; 175:77-85.
61. Buckingham M, Relaix F. The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions. Annu Rev Cell Dev Biol 2007; 23:645-73.
62. Crist CG, Montarras D, Pallafacchina G, Rocancourt D, Cumano A, Conway SJ, et al. Muscle stem cell behavior is modified by microRNA-27 regulation of Pax3 expression. Proc Natl Acad Sci USA 2009; 106:13383-7.
63. Heremans Y, Van De Casteele M, in't Veld P, Gradwohl G, Serup P, Madsen O, et al. Recapitulation of embryonic neuroendocrine differentiation in adult human pancreatic duct cells expressing neurogenin 3. J Cell Biol 2002; 159:303-12.
64. Baroukh N, Ravier MA, Loder MK, Hill EV, Bounacer A, Scharfmann R, et al. MicroRNA-124a regulates Foxa2 expression and intracellular signaling in pancreatic beta-cell lines. J Biol Chem 2007; 282:19575-88.
65. Fukuda A, Kawaguchi Y, Furuyama K, Kodama S, Horiguchi M, Kuhara T, et al. Ectopic pancreas formation in Hes1-knockout mice reveals plasticity of endodermal progenitors of the gut, bile duct and pancreas. J Clin Invest 2006; 116:1484-93.
66. Lynn FC, Skewes-Cox P, Kosaka Y, McManus MT, Harfe BD, German MS. MicroRNA expression is required for pancreatic islet cell genesis in the mouse. Diabetes 2007; 56:2938-45.
67. Gradwohl G, Dierich A, LeMeur M, Guillemot F. neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas. Proc Natl Acad Sci USA 2000; 97:1607-11.
68. Gu G, Brown JR, Melton DA. Direct lineage tracing reveals the ontogeny of pancreatic cell fates during mouse embryogenesis. Mech Dev 2003; 120:35-43.
69. Hara M, Dizon RF, Glick BS, Lee CS, Kaestner KH, Piston DW, et al. Imaging pancreatic beta-cells in the intact pancreas. Am J Physiol Endocrinol Metab 2006; 290:1041-7.
70. Jenny M, Uhl C, Roche C, Duluc I, Guillermin V, Guillemot F, et al. Neurogenin3 is differentially required for endocrine cell fate specification in the intestinal and gastric epithelium. EMBO J 2002; 21:6338-47.
71. Joglekar MV, Parekh VS, Mehta S, Bhonde RR, Hardikar AA. MicroRNA profiling of developing and regenerating pancreas reveal post-transcriptional regulation of neurogenin3. Dev Biol 2007; 311:603-12.
72. Kimura H, Kawasaki H, Taira K. Mouse microRNA-23b regulates expression of Hes1 gene in P19 cells. Nucleic Acids Symp Ser (Oxf ) 2004; 213-4.
73. Imayoshi I, Sakamoto M, Yamaguchi M, Mori K, Kageyama R. Essential roles of Notch signaling in maintenance of neural stem cells in developing and adult brains. J Neurosci 30:3489-98.
74. Hatakeyama J, Bessho Y, Katoh K, Ookawara S, Fujioka M, Guillemot F, et al. Hes genes regulate size, shape and histogenesis of the nervous system by control of the timing of neural stem cell differentiation. Development 2004; 131:5539-50.
75. Bommer GT, Gerin I, Feng Y, Kaczorowski AJ, Kuick R, Love RE, et al. p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol 2007; 17:1298-307.
76. He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, et al. A microRNA component of the p53 tumour suppressor network. Nature 2007; 447:1130-4.
77. Ji Q, Hao X, Zhang M, Tang W, Yang M, Li L, et al. MicroRNA miR-34 inhibits human pancreatic cancer tumor-initiating cells. PLoS One 2009; 4:6816.