Gene expression profiling of choline-deprived neural precursor cells isolated from mouse brain

Molecular Brain Research

Volumn 134, Issue 2, 2005, Pages 309-322

  Niculescu, Mihai D ^a   Craciunescu, Corneliu N ^a   Zeisel, Steven H ^a  

^a IL   (United States)

Author keywords

Cell proliferation; Choline deficiency; Gene array; Gene expression; Neural precursor cells; Neuronal development

Indexed keywords

CALCIUM BINDING PROTEIN; CHOLINE; METHYL GROUP;

ANIMAL CELL; APOPTOSIS; ARTICLE; BRAIN CELL; CELL DIFFERENTIATION; CELL PROLIFERATION; CONTROLLED STUDY; DNA METHYLATION; DNA MICROARRAY; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENETIC ANALYSIS; METABOLISM; MOUSE; NEURAL STEM CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; ONTOGENY; PRIORITY JOURNAL; PROMOTER REGION;

RODENTIA;

EID: 17044394694     PISSN: 0169328X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molbrainres.2004.11.001     Document Type: Article

References (87)

1. C.D. Albright, A.Y. Tsai, M.-H. Mar, and S.H. Zeisel Choline availability modulates the expression of TGFβ1 and cytoskeletal proteins in the hippocampus of developing rat brain Neurochem. Res. 23 1998 751 758
2. C.D. Albright, C.B. Friedrich, E.C. Brown, M.H. Mar, and S.H. Zeisel Maternal dietary choline availability alters mitosis, apoptosis and the localization of toad-64 protein in the developing fetal rat septum Brain Res. Dev. Brain Res. 115 1999 123 129
3. C.D. Albright, A.Y. Tsai, C.B. Friedrich, M.H. Mar, and S.H. Zeisel Choline availability alters embryonic development of the hippocampus and septum in the rat Brain Res. Dev. Brain Res. 113 1999 13 20
4. C.D. Albright, M.H. Mar, C.B. Friedrich, E.C. Brown, and S.H. Zeisel Maternal choline availability alters the localization of p15ink4b and p27Kip1 cyclin-dependent kinase inhibitors in the developing fetal rat brain hippocampus Dev. Neurosci. 23 2001 100 106
5. C.D. Albright, D.F. Siwek, C.N. Craciunescu, M.H. Mar, N.W. Kowall, C.L. Williams, and S.H. Zeisel Choline availability during embryonic development alters the localization of calretinin in developing and aging mouse hippocampus Nutr. Neurosci. 6 2003 129 134
6. N. Bertrand, D.S. Castro, and F. Guillemot Proneural genes and the specification of neural cell types Nat. Rev., Neurosci. 3 2002 517 530
7. E.A. Braga, V.I. Kashuba, A.V. Maliukova, V.I. Loginov, V.N. Senchenko, I.V. Bazov, L.L. Kiselev, and E.R. Zabarovskii New tumor suppressor genes in hot spots of human chromosome 3: new methods of identification Mol. Biol. (Mosk.) 37 2003 194 211
8. C. Brandner Perinatal choline treatment modifies the effects of a visuo-spatial attractive cue upon spatial memory in naive adult rats Brain Res. 928 2002 85 95
9. M.D. Brandt, S. Jessberger, B. Steiner, G. Kronenberg, K. Reuter, A. Bick-Sander, W.V.D. Behrens, and G. Kempermann Transient calretinin expression defines early postmitotic step of neuronal differentiation in adult hippocampal neurogenesis of mice Mol. Cell. Neurosci. 24 2003 603 613
10. V.L. Buchman, N.N. Ninkina, Y.D. Bogdanov, A.L. Bortvin, H.N. Akopian, S.L. Kiselev, O.Y. Krylova, K.V. Anokhin, and G.P. Georgiev Differential splicing creates a diversity of transcripts from a neurospecific developmentally regulated gene encoding a protein with new zinc-finger motifs Nucleic Acids Res. 20 1992 5579 5585
11. P.-F. Cartron, L. Oliver, S. Martin, C. Moreau, M.-T. LeCabellec, P. Jezequel, K. Meflah, and F.M. Vallette The expression of a new variant of the pro-apoptotic molecule bax, bax{psi}, is correlated with an increased survival of glioblastoma multiforme patients Hum. Mol. Genet. 11 2002 675 687
12. L.H. Chadwick, S.E. McCandless, G.L. Silverman, S. Schwartz, D. Westaway, and J.H. Nadeau Betaine-homocysteine methyltransferase-2: cDNA cloning, gene sequence, physical mapping, and expression of the human and mouse genes*1,*2 Genomics 70 2000 66 73
13. X. Chen Cycling: a regulator of the p53-mdm2 network Dev. Cell 2 2002 518 519
14. H. Chen, S. Toyooka, A.F. Gazdar, and J.T. Hsieh Epigenetic regulation of a novel tumor suppressor gene (hdab2ip) in prostate cancer cell lines J. Biol. Chem. 278 2003 3121 3130
15. Y.-H. Choi, K.-B. Kim, H.-H. Kim, G.-S. Hong, Y.-K. Kwon, C.-W. Chung, Y.-M. Park, Z.-J. Shen, B.J. Kim, S.-Y. Lee, and Y.-K. Jung Flash coordinates NF-kappa B activity via traf2 J. Biol. Chem. 276 2001 25073 25077
16. C.N. Craciunescu, C.D. Albright, M.-H. Mar, J. Song, and S.H. Zeisel Choline availability during embryonic development alters progenitor cell mitosis in developing mouse hippocampus J. Nutr. 133 2003 3614 3618
17. G. Deng, G.-A. Song, E. Pong, M. Sleisenger, and Y.S. Kim Promoter methylation inhibits apc gene expression by causing changes in chromatin conformation and interfering with the binding of transcription factor CCAAT-binding factor Cancer Res. 64 2004 2692 2698
18. R. Deves, G. Reyes, and R.M. Krupka The carrier reorientation step in erythrocyte choline transport: ph effects and the involvement of a carrier ionizing group J. Membr. Biol. 93 1986 165 175
19. L.A. Dickinson, A.J. Edgar, J. Ehley, and J.M. Gottesfeld Cyclin l is an RS domain protein involved in pre-mRNA splicing J. Biol. Chem. 277 2002 25465 25473
20. K. Dobbin, J.H. Shih, and R. Simon Statistical design of reverse dye microarrays Bioinformatics 19 2003 803 810
21. A.A. Dombkowski, B.J. Thibodeau, S.L. Starcevic, and R.F. Novak Gene-specific dye bias in microarray reference designs FEBS Lett. 560 2004 120 124
22. 2+ Biochim. Biophys. Acta, Biomembr. 1421 1999 353 360
23. 2+ efflux from rat erythrocytes Biochim. Biophys. Acta, Biomembr. 1559 2002 135 144
24. M. Esteller Profiling aberrant DNA methylation in hematologic neoplasms: a view from the tip of the iceberg Clin. Immunol. 109 2003 80 88
25. J.D. Finkelstein Pathways and regulation of homocysteine metabolism in mammals Semin. Thromb. Hemost. 26 2000 219 225
26. W.N. Fu, F. Bertoni, S.M. Kelsey, S.M. McElwaine, F.E. Cotter, A.C. Newland, and L. Jia Role of DNA methylation in the suppression of Apaf-1 protein in human leukaemia Oncogene 22 2003 451 455
27. B. Garbay, and C. Cassagne Expression of the ceramide galactosyltransferase gene during myelination of the mouse nervous system. Comparison with the genes encoding myelin basic proteins, choline kinase and CTP:phosphocholine cytidylyltransferase Brain Res. Dev. Brain Res. 83 1994 119 124
28. R. Giegerich, F. Meyer, and C. Schleiermacher Genefisher-software support for the detection of postulated genes Proc. Int. Conf. Intell. Syst. Mol. Biol. 4 1996 68 77
29. R.M. Gueant-Rodriguez, C. Rendeli, B. Namour, L. Venuti, A. Romano, G. Anello, P. Bosco, R. Debard, P. Gerard, and M. Viola Transcobalamin and methionine synthase reductase mutated polymorphisms aggravate the risk of neural tube defects in humans Neurosci. Lett. 344 2003 189 192
30. G.L. Holmes, Y. Yang, Z. Liu, J.M. Cermak, M.R. Sarkisian, C.E. Stafstrom, J.C. Neill, and J.K. Blusztajn Seizure-induced memory impairment is reduced by choline supplementation before or after status epilepticus Epilepsy Res. 48 2002 3 13
31. 12, Panthothenic Acid, Biotin, and Choline 1998 National Academy Press Washington, DC
32. C.J. Jolly, and M.S. Neuberger Somatic hypermutation of immunoglobulin kappa transgenes: association of mutability with demethylation Immunol. Cell Biol. 79 2001 18 22
33. C. Kintner Neurogenesis in embryos and in adult neural stem cells J. Neurosci. 22 2002 639 643
34. S. Ledoux, J. Nalbantoglu, and N.R. Cashman Amyloid precursor protein gene expression in neural cell lines: influence of DNA cytosine methylation Brain Res. Mol. Brain Res. 24 1994 140 144
35. U. Lendahl, L.B. Zimmerman, and R.D. McKay CNS stem cells express a new class of intermediate filament protein Cell 60 1990 585 595
36. Y. Li, H. Nagai, T. Ohno, M. Yuge, S. Hatano, E. Ito, N. Mori, H. Saito, and T. Kinoshita Aberrant DNA methylation of p57kip2 gene in the promoter region in lymphoid malignancies of B-cell phenotype Blood 100 2002 2572 2577
37. K.W. Lo, Y.S. Tsang, J. Kwong, K.F. To, P.M. Teo, and D.P. Huang Promoter hypermethylation of the ednrb gene in nasopharyngeal carcinoma Int. J. Cancer 98 2002 651 655
38. M. Lubbert, C.W. Miller, and H.P. Koeffler Changes of DNA methylation and chromatin structure in the human myeloperoxidase gene during myeloid differentiation Blood 78 1991 345 356
39. K. Matsuo, S.H. Tang, K. Zeki, R.A. Gutman, and J.A. Fagin Aberrant deoxyribonucleic acid methylation in human thyroid tumors J. Clin. Endocrinol. Metab. 77 1993 991 995
40. W. Meck, and C. Williams Characterization of the facilitative effects of perinatal choline supplementation on timing and temporal memory NeuroReport 8 1997 2831 2835
41. W.H. Meck, and C.L. Williams Metabolic imprinting of choline by its availability during gestation: implications for memory and attentional processing across the lifespan Neurosci. Biobehav. Rev. 27 2003 385 399
42. W.H. Meck, R.A. Smith, and C.L. Williams Pre- and postnatal choline supplementation produces long-term facilitation of spatial memory Dev. Psychobiol. 21 1988 339 353
43. J.P. Medema Apoptosis: life and death in a flash Nature 398 1999 756 757
44. J. Milosevic, A. Storch, and J. Schwarz Spontaneous apoptosis in murine free-floating neurospheres Exp. Cell Res. 294 2004 9 17
45. E.J. Morris, and N.J. Dyson Retinoblastoma protein partners Adv. Cancer Res. 82 2001 1 54
46. M.D. Niculescu, Y. Yamamuro, and S.H. Zeisel Choline availability modulates human neuroblastoma cell proliferation and alters the methylation of the promoter region of the cyclin-dependent kinase inhibitor 3 gene J. Neurochem. 89 2004 1252 1259
47. M.D. Niculescu, Y. Yamamuro, and S.H. Zeisel Choline availability modulates human neuroblastoma cell proliferation and alters the methylation of the promoter region of the cyclin-dependent kinase inhibitor 3 gene J. Neurochem. 89 2004 1252 1259
48. V. Novitskaya, M. Grigorian, M. Kriajevska, S. Tarabykina, I. Bronstein, V. Berezin, E. Bock, and E. Lukanidin Oligomeric forms of the metastasis-related mts1 (s100a4) protein stimulate neuronal differentiation in cultures of rat hippocampal neurons J. Biol. Chem. 275 2000 41278 41286
49. K. Okamoto, and C. Prives A role of cyclin G in the process of apoptosis Oncogene 18 1999 4606 4615
50. W. Pan A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments Bioinformatics 18 2002 546 554
51. W. Pan On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression Bioinformatics 19 2003 1333 1340
52. C. Rosty, T. Ueki, P. Argani, M. Jansen, C.J. Yeo, J.L. Cameron, R.H. Hruban, and M. Goggins Overexpression of s100a4 in pancreatic ductal adenocarcinomas is associated with poor differentiation and DNA hypomethylation Am. J. Pathol. 160 2002 45 50
53. + distributions in the headgroup region of binary membranes of phosphatidylcholine and phosphatidylserine as seen by deuterium NMR Biochemistry 29 1990 7077 7089
54. A. Sanchez-Aguilera, J. Delgado, F.I. Camacho, M. Sanchez-Beato, L. Sanchez, C. Montalban, M.F. Fresno, C. Martin, M.A. Piris, and J.F. Garcia Silencing of the p18ink4c gene by promoter hypermethylation in Reed-Sternberg cells in Hodgkin lymphomas Blood 103 2004 2351 2357
55. N.J. Sandstrom, R. Loy, and C.L. Williams Prenatal choline supplementation increases NGF levels in the hippocampus and frontal cortex of young and adult rats Brain Res. 947 2002 9 16
56. N. Sato, N. Fukushima, N. Maehara, H. Matsubayashi, J. Koopmann, G.H. Su, R.H. Hruban, and M. Goggins Sparc/osteonectin is a frequent target for aberrant methylation in pancreatic adenocarcinoma and a mediator of tumor-stromal interactions Oncogene 22 2003 5021 5030
57. C.J. Sherr Cancer cell cycles Science 274 1996 1672 1677
58. J.C. Soria, H.Y. Lee, J.I. Lee, L. Wang, J.P. Issa, B.L. Kemp, D.D. Liu, J.M. Kurie, L. Mao, and F.R. Khuri Lack of PTEN expression in non-small cell lung cancer could be related to promoter methylation Clin. Cancer Res. 8 2002 1178 1184
59. C.N. Svendsen, M.G. ter Borg, R.J.E. Armstrong, A.E. Rosser, S. Chandran, T. Ostenfeld, and M.A. Caldwell A new method for the rapid and long term growth of human neural precursor cells J. Neurosci. Methods 85 1998 141 152
60. Y. Takahashi, C. Suzuki, and T. Kamataki Silencing of cyp1a1 expression in rabbits by DNA methylation Biochem. Biophys. Res. Commun. 247 1998 383 386
61. B. Teubner, and W.A. Schulz Exemption of satellite DNA from demethylation in immortalized differentiated derivatives of f9 mouse embryonal carcinoma cells Exp. Cell Res. 210 1994 192 200
62. S.M. Tokuoka, S. Ishii, N. Kawamura, M. Satoh, A. Shimada, S. Sasaki, S. Hirotsune, A. Wynshaw-Boris, and T. Shimizu Involvement of platelet-activating factor and lis1 in neuronal migration Eur. J. Neurosci. 18 2003 563 570
63. J. Trojan, A. Brieger, J. Raedle, M. Esteller, and S. Zeuzem 5′-CPG island methylation of the lkb1/stk11 promoter and allelic loss at chromosome 19p13.3 in sporadic colorectal cancer Gut 47 2000 272 276
64. V.G. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. 98 2001 5116 5121
65. E. Ulleras, S.J. Miller, G.I.R. Adam, C. Kanduri, A.C. Wilcock, and G.C. Franklin Inhibition of histone deacetylase activity causes cell type-specific induction of the PDGF-B promoter only in the absence of activation by its enhancer Exp. Cell Res. 270 2001 188 198
66. M. Unoki, and Y. Nakamura Methylation at CPG islands in intron 1 of EGR2 confers enhancer-like activity FEBS Lett. 554 2003 67 72
67. F.P. Wachs, S. Couillard-Despres, M. Engelhardt, D. Wilhelm, S. Ploetz, M. Vroemen, J. Kaesbauer, G. Uyanik, J. Klucken, C. Karl, J. Tebbing, C. Svendsen, N. Weidner, H.G. Kuhn, J. Winkler, and L. Aigner High efficacy of clonal growth and expansion of adult neural stem cells Lab. Invest. 83 2003 949 962
68. Y. Wang, and J. Qin Msh2 and atr form a signaling module and regulate two branches of the damage response to DNA methylation Proc. Natl. Acad. Sci. 100 2003 15387 15392
69. E. Wang, L.D. Miller, G.A. Ohnmacht, E.T. Liu, and F.M. Marincola High-fidelity mRNA amplification for gene profiling Nat. Biotechnol. 18 2000 457 459
70. Y.-C. Wang, Y.-P. Lu, R.-C. Tseng, R.-K. Lin, J.-W. Chang, J.-T. Chen, C.-M. Shih, and C.-Y. Chen Inactivation of hmlh1 and hmsh2 by promoter methylation in primary non-small cell lung tumors and matched sputum samples J. Clin. Invest. 111 2003 887 895
71. K.J. Way, K. Isshiki, K. Suzuma, T. Yokota, D. Zvagelsky, F.J. Schoen, G.E. Sandusky, P.A. Pechous, C.J. Vlahos, H. Wakasaki, and G.L. King Expression of connective tissue growth factor is increased in injured myocardium associated with protein kinase C {beta}2 activation and diabetes Diabetes 51 2002 2709 2718
72. L. Wolff, M.T. Garin, R. Koller, J. Bies, W. Liao, M. Malumbres, L. Tessarollo, D. Powell, and C. Perella Hypermethylation of the ink4b locus in murine myeloid leukemia and increased susceptibility to leukemia in p15(ink4b)-deficient mice Oncogene 22 2003 9265 9274
73. L. Yang, N. Li, C. Wang, Y. Yu, L. Yuan, M. Zhang, and X. Cao Cyclin l2, a novel RNA polymerase II-associated cyclin, is involved in pre-mRNA splicing and induces apoptosis of human hepatocellular carcinoma cells J. Biol. Chem. 279 2004 11639 11648
74. P.A. Yates, R. Burman, J. Simpson, O.N. Ponomoreva, M.J. Thayer, and M.S. Turker Silencing of mouse aprt is a gradual process in differentiated cells Mol. Cell. Biol. 23 2003 4461 4470
75. C.L. Yen, M.H. Mar, and S.H. Zeisel Choline deficiency-induced apoptosis in pc12 cells is associated with diminished membrane phosphatidylcholine and sphingomyelin, accumulation of ceramide and diacylglycerol, and activation of a caspase FASEB J. 13 1999 135 142
76. C.L. Yen, M.H. Mar, R.B. Meeker, A. Fernandes, and S.H. Zeisel Choline deficiency induces apoptosis in primary cultures of fetal neurons FASEB J. 15 2001 1704 1710
77. C.L. Yen, M.H. Mar, C.N. Craciunescu, L.J. Edwards, and S.H. Zeisel Deficiency in methionine, tryptophan, isoleucine, or choline induces apoptosis in cultured cells J. Nutr. 132 2002 1840 1847
78. J. Yu, W.K. Leung, M.P. Ebert, R.W. Leong, P.C. Tse, M.W. Chan, A.H. Bai, K.F. To, P. Malfertheiner, and J.J. Sung Absence of cyclin d2 expression is associated with promoter hypermethylation in gastric cancer Br. J. Cancer 88 2003 1560 1565
79. M.R. Yuille, A. Condie, E.M. Stone, J. Wilsher, P.S. Bradshaw, L. Brooks, and D. Catovsky Tcl1 is activated by chromosomal rearrangement or by hypomethylation Genes Chromosomes Cancer 30 2001 336 341
80. J. Yun, C.W. Park, Y.J. Lee, and J.H. Chung Allele-specific methylation at the promoter-associated CPG island of mouse copg2 Mamm. Genome 14 2003 376 382
81. B. Zeeberg, W. Feng, G. Wang, M. Wang, A. Fojo, M. Sunshine, S. Narasimhan, D. Kane, W. Reinhold, S. Lababidi, K. Bussey, J. Riss, J. Barrett, and J. Weinstein Gominer: a resource for biological interpretation of genomic and proteomic data Genome Biol. 4 2003 R28
82. S.H. Zeisel Choline and phosphatidylcholine A.C. Ross Modern Nutrition in Health and Disease 1999 Williams and Wilkins Baltimore 513 523
83. S.H. Zeisel, and J.K. Blusztajn Choline and human nutrition Annu. Rev. Nutr. 14 1994 269 296
84. S.H. Zeisel, M.H. Mar, J.C. Howe, and J.M. Holden Concentrations of choline-containing compounds and betaine in common foods J. Nutr. 133 2003 1302 1307
85. Q. Zhou, and D.J. Anderson The bhlh transcription factors olig2 and olig1 couple neuronal and glial subtype specification Cell 109 2002 61 73
86. W.-G. Zhu, K. Srinivasan, Z. Dai, W. Duan, L.J. Druhan, H. Ding, L. Yee, M.A. Villalona-Calero, C. Plass, and G.A. Otterson Methylation of adjacent CPG sites affects sp1/sp3 binding and activity in the p21cip1 promoter Mol. Cell. Biol. 23 2003 4056 4065
87. X. Zhu, M.-H. Mar, J. Song, and S.H. Zeisel Deletion of the pemt gene increases progenitor cell mitosis, DNA and protein methylation and decreases calretinin expression in embryonic day 17 mouse hippocampus Dev. Brain Res. 149 2004 121 129