Role of epigenetics in neural differentiation: Implications for health and disease

Molecular Mechanisms and Physiology of Disease: Implications for Epigenetics and Health

Volumn , Issue , 2014, Pages 63-79

  Toranõ, Estela G ^a   Fernandez, Agustin F ^a   Urdinguio, Rocio G ^a   Fraga, Mario F ^a,b  

^a DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

DNA methylation; Epigenetics; Histone modifications; Neural differentiation; Neural diseases

Indexed keywords

EID: 84929870624     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4939-0706-9_2     Document Type: Chapter

References (116)

1. Abel T, Zukin RS (2008) Epigenetic targets of HDAC inhibition in neurodegenerative and psychiatric disorders. Curr Opin Pharmacol 8:57-64
2. Ajamian F, Suuronen T, Salminen A, Reeben M (2003) Upregulation of class II histone deacetylases mRNA during neural differentiation of cultured rat hippocampal progenitor cells. Neurosci Lett 346:57-60
3. Bai S, Ghoshal K, Datta J, Majumder S, Yoon SO, Jacob ST (2005) DNA methyltransferase 3b regulates nerve growth factor-induced differentiation of PC12 cells by recruiting histone deacetylase 2. Mol Cell Biol 25:751-766
4. Barber BA, Rastegar M (2010) Epigenetic control of Hox genes during neurogenesis, development, and disease. Ann Anat 192:261-274
5. Ben-Shachar S, Chahrour M, Thaller C, Shaw CA, Zoghbi HY (2009) Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus. Hum Mol Genet 18:2431-2442
6. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315-326
7. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669-681
8. Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321:209-213
9. Bird A (2008) The methyl-CpG-binding protein MeCP2 and neurological disease. Biochem Soc Trans 36:575-583
10. Blaheta RA, Cinatl J Jr (2002) Anti-tumor mechanisms of valproate: a novel role for an old drug. Med Res Rev 22:492-511
11. Bohacek J, Gapp K, Saab BJ, Mansuy IM (2013) Transgenerational epigenetic effects on brain functions. Biol Psychiatry 73:313-320
12. Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, Rosas HD, Hersch SM, Hogarth P, Bouzou B, Jensen RV, Krainc D (2005) Genome-wide expression profi ling of human blood reveals biomarkers for Huntington's disease. Proc Natl Acad Sci USA 102:11023-11028
13. Brooks WH, Le Dantec C, Pers JO, Youinou P, Renaudineau Y (2010) Epigenetics and autoimmunity. J Autoimmun 34:J207-J219
14. Burgold T, Spreafico F, De Santa F, Totaro MG, Prosperini E, Natoli G, Testa G (2008) The histone H3 lysine 27-specific demethylase Jmjd3 is required for neural commitment. PLoS One 3:e3034
15. Calvanese V, Fraga MF (2011) SirT1 brings stemness closer to cancer and aging. Aging (Albany NY) 3:162-167
16. Calvanese V, Lara E, Suarez-Alvarez B, Abu Dawud R, Vazquez-Chantada M, Martinez-Chantar ML, Embade N, Lopez-Nieva P, Horrillo A, Hmadcha A, Soria B, Piazzolla D, Herranz D, Serrano M, Mato JM, Andrews PW, Lopez-Larrea C, Esteller M, Fraga MF (2010) Sirtuin 1 regulation of developmental genes during differentiation of stem cells. Proc Natl Acad Sci USA 107:13736-13741
17. Chahrour M, Jung SY, Shaw C, Zhou X, Wong ST, Qin J, Zoghbi HY (2008) MeCP2, a key contributor to neurological disease, activates and represses transcription. Science 320:1224-1229
18. Chen RZ, Akbarian S, Tudor M, Jaenisch R (2001) Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice. Nat Genet 27:327-331
19. Cheng LC, Pastrana E, Tavazoie M, Doetsch F (2009) miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat Neurosci 12:399-408
20. Chopra V, Quinti L, Kim J, Vollor L, Narayanan KL, Edgerly C, Cipicchio PM, Lauver MA, Choi SH, Silverman RB, Ferrante RJ, Hersch S, Kazantsev AG (2012) The sirtuin 2 inhibitor AK-7 is neuroprotective in Huntington's disease mouse models. Cell Rep 2:1492-1497
21. Chuang DM, Leng Y, Marinova Z, Kim HJ, Chiu CT (2009) Multiple roles of HDAC inhibition in neurodegenerative conditions. Trends Neurosci 32:591-601
22. Cloos PA, Christensen J, Agger K, Helin K (2008) Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev 22:1115-1140
23. Coppede F (2012) Genetics and epigenetics of Parkinson's disease. Scientific World Journal 2012:489830
24. Croce CM (2009) Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet 10:704-714
25. Defossez PA, Stancheva I (2011) Biological functions of methyl-CpG-binding proteins. Prog Mol Biol Transl Sci 101:377-398
26. Delcuve GP, Rastegar M, Davie JR (2009) Epigenetic control. J Cell Physiol 219:243-250
27. Dietrich J, Han R, Yang Y, Mayer-Proschel M, Noble M (2006) CNS progenitor cells and oligodendrocytes are targets of chemotherapeutic agents in vitro and in vivo. J Biol 5:22
28. Dokmanovic M, Clarke C, Marks PA (2007) Histone deacetylase inhibitors: overview and perspectives. Mol Cancer Res 5:981-989
29. Ellis L, Atadja PW, Johnstone RW (2009) Epigenetics in cancer: targeting chromatin modifications. Mol Cancer Ther 8:1409-1420
30. Fan G, Hutnick L (2005) Methyl-CpG binding proteins in the nervous system. Cell Res 15: 255-261
31. Feng J, Chang H, Li E, Fan G (2005) Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system. J Neurosci Res 79:734-746
32. Feng J, Fouse S, Fan G (2007) Epigenetic regulation of neural gene expression and neuronal function. Pediatr Res 61:58R-63R
33. Flici H, Erkosar B, Komonyi O, Karatas OF, Laneve P, Giangrande A (2011) Gcm/Glide-dependent conversion into glia depends on neural stem cell age, but not on division, triggering a chromatin signature that is conserved in vertebrate glia. Development 138:4167-4178
34. Gillardon F, Mack M, Rist W, Schnack C, Lenter M, Hildebrandt T, Hengerer B (2008) MicroRNA and proteome expression profi ling in early-symptomatic alpha-synuclein(A30P)-transgenic mice. Proteomics Clin Appl 2:697-705
35. Gray SG (2010) Targeting histone deacetylases for the treatment of Huntington's disease. CNS Neurosci Ther 16:348-361
36. Gray SG (2011) Targeting Huntington's disease through histone deacetylases. Clin Epigenetics 2:257-277
37. Guan JS, Haggarty SJ, Giacometti E, Dannenberg JH, Joseph N, Gao J, Nieland TJ, Zhou Y, Wang X, Mazitschek R, Bradner JE, Depinho RA, Jaenisch R, Tsai LH (2009) HDAC2 negatively regulates memory formation and synaptic plasticity. Nature 459:55-60
38. Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-840
39. Guy J, Hendrich B, Holmes M, Martin JE, Bird A (2001) A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. Nat Genet 27:322-326
40. Guy J, Gan J, Selfridge J, Cobb S, Bird A (2007) Reversal of neurological defects in a mouse model of Rett syndrome. Science 315:1143-1147
41. Haberland M, Mokalled MH, Montgomery RL, Olson EN (2009a) Epigenetic control of skull morphogenesis by histone deacetylase 8. Genes Dev 23:1625-1630
42. Haberland M, Montgomery RL, Olson EN (2009b) The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet 10:32-42
43. Hardy J (2010) Genetic analysis of pathways to Parkinson disease. Neuron 68:201-206
44. Herman JG, Baylin SB (2003) Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 349:2042-2054
45. Hirabayashi Y, Gotoh Y (2010) Epigenetic control of neural precursor cell fate during development. Nat Rev Neurosci 11:377-388
46. Hsieh J, Eisch AJ (2010) Epigenetics, hippocampal neurogenesis, and neuropsychiatric disorders: unraveling the genome to understand the mind. Neurobiol Dis 39:73-84
47. Hsieh J, Nakashima K, Kuwabara T, Mejia E, Gage FH (2004) Histone deacetylase inhibitionmediated neuronal differentiation of multipotent adult neural progenitor cells. Proc Natl Acad Sci USA 101:16659-16664
48. Ittner LM, Gotz J (2011) Amyloid-beta and tau-a toxic pas de deux in Alzheimer's disease. Nat Rev Neurosci 12:65-72
49. Jobe EM, Mcquate AL, Zhao X (2012) Crosstalk among epigenetic pathways regulates neurogenesis. Front Neurosci 6:59
50. Jordan C, Li HH, Kwan HC, Francke U (2007) Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets. BMC Med Genet 8:36
51. Junn E, Mouradian MM (2012) MicroRNAs in neurodegenerative diseases and their therapeutic potential. Pharmacol Ther 133:142-150
52. Kanai Y (2008) Alterations of DNA methylation and clinicopathological diversity of human cancers. Pathol Int 58:544-558
53. Kilgore M, Miller CA, Fass DM, Hennig KM, Haggarty SJ, Sweatt JD, Rumbaugh G (2010) Inhibitors of class 1 histone deacetylases reverse contextual memory defi cits in a mouse model of Alzheimer's disease. Neuropsychopharmacology 35:870-880
54. Kreth FW, Thon N, Tonn JC (2012) Low-grade gliomas. J Neurosurg 116:468-70; author reply 469-70
55. Kretsovali A, Hadjimichael C, Charmpilas N (2012) Histone deacetylase inhibitors in cell pluripotency, differentiation, and reprogramming. Stem Cells Int 2012:184154
56. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn't fi t all. Nat Rev Mol Cell Biol 8:284-295
57. Li X, Zhao X (2008) Epigenetic regulation of mammalian stem cells. Stem Cells Dev 17: 1043-1052
58. Lilja T, Heldring N, Hermanson O (2013) Like a rolling histone: epigenetic regulation of neural stem cells and brain development by factors controlling histone acetylation and methylation. Biochim Biophys Acta 1830:2354-2360
59. Lyst MJ, Ekiert R, Ebert DH, Merusi C, Nowak J, Selfridge J, Guy J, Kastan NR, Robinson ND, De Lima Alves F, Rappsilber J, Greenberg ME, Bird A (2013) Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor. Nat Neurosci 16:898-902
60. Macdonald VE, Howe LJ (2009) Histone acetylation: where to go and how to get there. Epigenetics 4:139-143
61. Macdonald JL, Roskams AJ (2008) Histone deacetylases 1 and 2 are expressed at distinct stages of neuro-glial development. Dev Dyn 237:2256-2267
62. Majdzadeh N, Wang L, Morrison BE, Bassel-Duby R, Olson EN, D'Mello SR (2008) HDAC4 inhibits cell-cycle progression and protects neurons from cell death. Dev Neurobiol 68: 1076-1092
63. Makeyev EV, Zhang J, Carrasco MA, Maniatis T (2007) The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell 27:435-448
64. Martinez R, Martin-Subero JI, Rohde V, Kirsch M, Alaminos M, Fernandez AF, Ropero S, Schackert G, Esteller M (2009) A microarray-based DNA methylation study of glioblastoma multiforme. Epigenetics 4:255-264
65. Matsumoto L, Takuma H, Tamaoka A, Kurisaki H, Date H, Tsuji S, Iwata A (2010) CpG demethylation enhances alpha-synuclein expression and affects the pathogenesis of Parkinson's disease. PLoS One 5:e15522
66. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770
67. Meshorer E, Yellajoshula D, George E, Scambler PJ, Brown DT, Misteli T (2006) Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 10:105-116
68. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560
69. Minucci S, Pelicci PG (2006) Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer 6:38-51
70. Miyake K, Yang C, Minakuchi Y, Ohori K, Soutome M, Hirasawa T, Kazuki Y, Adachi N, Suzuki S, Itoh M, Goto YI, Andoh T, Kurosawa H, Oshimura M, Sasaki M, Toyoda A, Kubota T (2013) Comparison of genomic and epigenomic expression in monozygotic twins discordant for Rett syndrome. PLoS One 8:e66729
71. Mizutani K, Yoon K, Dang L, Tokunaga A, Gaiano N (2007) Differential Notch signalling distinguishes neural stem cells from intermediate progenitors. Nature 449:351-355
72. Mohamed Ariff I, Mitra A, Basu A (2012) Epigenetic regulation of self-renewal and fate determination in neural stem cells. J Neurosci Res 90:529-539
73. Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schubeler D (2008) Lineage-specific polycomb targets and de novo DNA methylation defi ne restriction and potential of neuronal progenitors. Mol Cell 30:755-766
74. Montgomery RL, Hsieh J, Barbosa AC, Richardson JA, Olson EN (2009) Histone deacetylases 1 and 2 control the progression of neural precursors to neurons during brain development. Proc Natl Acad Sci USA 106:7876-7881
75. Monti B, Gatta V, Piretti F, Raffaelli SS, Virgili M, Contestabile A (2010) Valproic acid is neuroprotective in the rotenone rat model of Parkinson's disease: involvement of alpha-synuclein. Neurotox Res 17:130-141
76. Mosammaparast N, Shi Y (2010) Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem 79:155-179
77. Nagarajan RP, Costello JF (2009) Epigenetic mechanisms in glioblastoma multiforme. Semin Cancer Biol 19:188-197
78. Namihira M, Kohyama J, Abematsu M, Nakashima K (2008) Epigenetic mechanisms regulating fate specification of neural stem cells. Philos Trans R Soc Lond B Biol Sci 363:2099-2109
79. Neul JL, Fang P, Barrish J, Lane J, Caeg EB, Smith EO, Zoghbi H, Percy A, Glaze DG (2008) specific mutations in methyl-CpG-binding protein 2 confer different severity in Rett syndrome. Neurology 70:1313-1321
80. Ng RK, Gurdon JB (2008) Epigenetic inheritance of cell differentiation status. Cell Cycle 7:1173-1177
81. Nuytemans K, Theuns J, Cruts M, Van Broeckhoven C (2010) Genetic etiology of Parkinson disease associated with mutations in the SNCA, PARK2, PINK1, PARK7, and LRRK2 genes: a mutation update. Hum Mutat 31:763-780
82. Olynik BM, Rastegar M (2012) The genetic and epigenetic journey of embryonic stem cells into mature neural cells. Front Genet 3:81
83. Oury F, Rijli FM (2007) [Hoxa2: a key gene for the facial somatosensory map]. Med Sci (Paris) 23:247-9
84. Pasini D, Hansen KH, Christensen J, Agger K, Cloos PA, Helin K (2008) Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2. Genes Dev 22:1345-1355
85. Poulsen P, Esteller M, Vaag A, Fraga MF (2007) The epigenetic basis of twin discordance in agerelated diseases. Pediatr Res 61:38R-42R
86. Ramirez A, Heimbach A, Grundemann J, Stiller B, Hampshire D, Cid LP, Goebel I, Mubaidin AF, Wriekat AL, Roeper J, Al-Din A, Hillmer AM, Karsak M, Liss B, Woods CG, Behrens MI, Kubisch C (2006) Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase. Nat Genet 38:1184-1191
87. Rett A (1986) Rett syndrome. History and general overview. Am J Med Genet Suppl 1:21-25
88. Ringrose L, Paro R (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134:223-232
89. Robertson KD (2001) DNA methylation, methyltransferases, and cancer. Oncogene 20: 3139-3155
90. Roth TL, Lubin FD, Sodhi M, Kleinman JE (2009) Epigenetic mechanisms in schizophrenia. Biochim Biophys Acta 1790:869-877
91. Rubinsztein DC (2006) The roles of intracellular protein-degradation pathways in neurodegeneration. Nature 443:780-786
92. Samaco RC, Neul JL (2011) Complexities of Rett syndrome and MeCP2. J Neurosci 31: 7951-7959
93. Sawa A, Snyder SH (2002) Schizophrenia: diverse approaches to a complex disease. Science 296:692-695
94. Schneider JW, Gao Z, Li S, Farooqi M, Tang TS, Bezprozvanny I, Frantz DE, Hsieh J (2008) Small-molecule activation of neuronal cell fate. Nat Chem Biol 4:408-410
95. Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007) Genome regulation by polycomb and trithorax proteins. Cell 128:735-745
96. Scott CE, Wynn SL, Sesay A, Cruz C, Cheung M, Gomez Gaviro MV, Booth S, Gao B, Cheah KS, Lovell-Badge R, Briscoe J (2010) SOX9 induces and maintains neural stem cells. Nat Neurosci 13:1181-1189
97. Sikorska M, Sandhu JK, Deb-Rinker P, Jezierski A, Leblanc J, Charlebois C, Ribecco-Lutkiewicz M, Bani-Yaghoub M, Walker PR (2008) Epigenetic modifications of SOX2 enhancers, SRR1 and SRR2, correlate with in vitro neural differentiation. J Neurosci Res 86:1680-1693
98. Silva PN, Gigek CO, Leal MF, Bertolucci PH, de Labio RW, Payaõ SL, Smith Mde A (2008) Promoter methylation analysis of SIRT3, SMARCA5, HTERT and CDH1 genes in aging and Alzheimer's disease. J Alzheimers Dis 13:173-176
99. Soshnikova N, Duboule D (2008) Epigenetic regulation of Hox gene activation: the waltz of methyls. Bioessays 30:199-202
100. Steffan JS, Kazantsev A, Spasic-Boskovic O, Greenwald M, Zhu YZ, Gohler H, Wanker EE, Bates GP, Housman DE, Thompson LM (2000) The Huntington's disease protein interacts with p53 and CREB-binding protein and represses transcription. Proc Natl Acad Sci USA 97: 6763-6768
101. Sun G, Yu RT, Evans RM, Shi Y (2007) Orphan nuclear receptor TLX recruits histone deacetylases to repress transcription and regulate neural stem cell proliferation. Proc Natl Acad Sci USA 104:15282-15287
102. Thomas B, Beal MF (2011) Molecular insights into Parkinson's disease. F1000 Med Rep 3:7
103. Tudor M, Akbarian S, Chen RZ, Jaenisch R (2002) Transcriptional profi ling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci USA 99:15536-15541
104. Urdinguio RG, Sanchez-Mut JV, Esteller M (2009) Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol 8:1056-1072
105. Van Esch H, Bauters M, Ignatius J, Jansen M, Raynaud M, Hollanders K, Lugtenberg D, Bienvenu T, Jensen LR, Gecz J, Moraine C, Marynen P, Fryns JP, Froyen G (2005) Duplication of the MECP2 region is a frequent cause of severe mental retardation and progressive neurological symptoms in males. Am J Hum Genet 77:442-453
106. Verdin E, Hirschey MD, Finley LW, HAIGIS MC (2010) Sirtuin regulation of mitochondria: energy production, apoptosis, and signaling. Trends Biochem Sci 35:669-675
107. Walker FO (2007) Huntington's disease. Lancet 369:218-228
108. Watanabe D, Uchiyama K, Hanaoka K (2006) Transition of mouse de novo methyltransferases expression from Dnmt3b to Dnmt3a during neural progenitor cell development. Neuroscience 142:727-737
109. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457-466
110. Wu Z, Huang K, Yu J, Le T, Namihira M, Liu Y, Zhang J, Xue Z, Cheng L, Fan G (2012) Dnmt3a regulates both proliferation and differentiation of mouse neural stem cells. J Neurosci Res 90:1883-1891
111. Xu WS, Parmigiani RB, Marks PA (2007) Histone deacetylase inhibitors: molecular mechanisms of action. Oncogene 26:5541-5552
112. Yang XJ, Seto E (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9:206-218
113. Yazdani M, Deogracias R, Guy J, Poot RA, Bird A, Barde YA (2012) Disease modeling using embryonic stem cells: MeCP2 regulates nuclear size and RNA synthesis in neurons. Stem Cells 30:2128-2139
114. Zachariah RM, Rastegar M (2012) Linking epigenetics to human disease and Rett syndrome: the emerging novel and challenging concepts in MeCP2 research. Neural Plast 2012:415825
115. Zhao C, Sun G, Li S, Shi Y (2009) A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination. Nat Struct Mol Biol 16:365-371
116. Zhao C, Sun G, Li S, Lang MF, Yang S, Li W, Shi Y (2010) MicroRNA let-7b regulates neural stem cell proliferation and differentiation by targeting nuclear receptor TLX signaling. Proc Natl Acad Sci USA 107:1876-1881