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DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation
Keri Martinowich,1,2Daisuke Hattori,3*Hao Wu,2*Shaun Fouse,4*Fei He,2Yan Hu,4Guoping Fan,1,4Yi E. Sun1,2
In conjunction with histone modifications, DNA methylation playscritical roles in gene silencing through chromatin remodeling.Changes in DNA methylation perturb neuronal function, and mutationsin a methyl-CpGbinding protein, MeCP2, are associatedwith Rett syndrome. We report that increased synthesis of brain-derivedneurotrophic factor (BDNF) in neurons after depolarization correlateswith a decrease in CpG methylation within the regulatory regionof the Bdnf gene. Moreover, increased Bdnf transcription involvesdissociation of the MeCP2histone deacetylasemSin3Arepression complex from its promoter. Our findings suggest thatDNA methylationrelated chromatin remodeling is importantfor activity-dependent gene regulation that may be criticalfor neural plasticity.
1 Neuroscience Interdepartmental Program, UCLA School of Medicine, 760 Westwood Plaza, Los Angeles, CA 90095, USA. 2 Departments of Molecular and Medical Pharmacology and Psychiatry and Behavioral Sciences, UCLA School of Medicine, 760 Westwood Plaza, Los Angeles, CA 90095, USA. 3 University of California, Los Angeles (UCLA) ACCESS program, UCLA School of Medicine, 760 Westwood Plaza, Los Angeles, CA 90095, USA. 4 Department of Human Genetics, UCLA School of Medicine, 760 Westwood Plaza, Los Angeles, CA 90095, USA.
* These authors contributed equally to the work.
To whom correspondence should be addressed. E-mail: ysun{at}mednet.ucla.edu (Y.E.S.); gfan{at}mednet.ucla.edu (G.F.)
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320, 1224-1229
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M. Kawaguchi, T. Toyama, R. Kaneko, T. Hirayama, Y. Kawamura, and T. Yagi (2008)
J. Biol. Chem.
283, 12064-12075
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MeCP2-dependent repression of an imprinted miR-184 released by depolarization.
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Hum. Mol. Genet.
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|Abstract »|Full Text »|PDF »
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|Abstract »|Full Text »|PDF »
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J. Cell Sci.
121, 1128-1137
|Abstract »|Full Text »|PDF »
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A D. Smith, Y.-I. Kim, and H. Refsum (2008)
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X. Jiang, F. Tian, Y. Du, N. G. Copeland, N. A. Jenkins, L. Tessarollo, X. Wu, H. Pan, X.-Z. Hu, K. Xu, et al. (2008)
J. Neurosci.
28, 1118-1130
|Abstract »|Full Text »|PDF »
Activity-Dependent Suppression of Miniature Neurotransmission through the Regulation of DNA Methylation.
E. D. Nelson, E. T. Kavalali, and L. M. Monteggia (2008)
J. Neurosci.
28, 395-406
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104, 19416-19421
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J. Neurosci.
27, 10912-10917
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21, 2085-2098
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27, 6163-6173
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Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear.
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|Abstract »|Full Text »|PDF »
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|Abstract »|Full Text »|PDF »
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26, 319-327
|Abstract »|Full Text »|PDF »
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G. J. P. Filion, S. Zhenilo, S. Salozhin, D. Yamada, E. Prokhortchouk, and P.-A. Defossez (2006)
Mol. Cell. Biol.
26, 169-181
|Abstract »|Full Text »|PDF »
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26, 199-208
|Abstract »|Full Text »|PDF »
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J. I. Young, E. P. Hong, J. C. Castle, J. Crespo-Barreto, A. B. Bowman, M. F. Rose, D. Kang, R. Richman, J. M. Johnson, S. Berget, et al. (2005)
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102, 17551-17558
|Abstract »|Full Text »|PDF »
Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain.
Dissecting MECP2 Function in the Central Nervous System.
N. Kishi and J. D. Macklis (2005)
J Child Neurol
20, 753-759
|Abstract »|PDF »
Rett Syndrome and Neuronal Development.
M. V. Johnston, M. E. Blue, and S. Naidu (2005)
J Child Neurol
20, 759-763
|Abstract »|PDF »
Neuron-specific relaxation of Igf2r imprinting is associated with neuron-specific histone modifications and lack of its antisense transcript Air.
Y. Yamasaki, T. Kayashima, H. Soejima, A. Kinoshita, K.-i. Yoshiura, N. Matsumoto, T. Ohta, T. Urano, H. Masuzaki, T. Ishimaru, et al. (2005)
Hum. Mol. Genet.
14, 2511-2520
|Abstract »|Full Text »|PDF »
Reelin and glutamic acid decarboxylase67 promoter remodeling in an epigenetic methionine-induced mouse model of schizophrenia.
E. Dong, R. C. Agis-Balboa, M. V. Simonini, D. R. Grayson, E. Costa, and A. Guidotti (2005)
PNAS
102, 12578-12583
|Abstract »|Full Text »|PDF »
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N. Kishi and J. D. Macklis (2005)
J Child Neurol
20, 753-759
|Abstract »|PDF »
Rett Syndrome and Neuronal Development.
M. V. Johnston, M. E. Blue, and S. Naidu (2005)
J Child Neurol
20, 759-763
|Abstract »|PDF »
Up-regulation of glucocorticoid-regulated genes in a mouse model of Rett syndrome.
U. A. Nuber, S. Kriaucionis, T. C. Roloff, J. Guy, J. Selfridge, C. Steinhoff, R. Schulz, B. Lipkowitz, H. H. Ropers, M. C. Holmes, et al. (2005)
Hum. Mol. Genet.
14, 2247-2256
|Abstract »|Full Text »|PDF »
DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling.
G. Fan, K. Martinowich, M. H. Chin, F. He, S. D. Fouse, L. Hutnick, D. Hattori, W. Ge, Y. Shen, H. Wu, et al. (2005)
Development
132, 3345-3356
|Abstract »|Full Text »|PDF »
DNA methylation of Sleeping Beauty with transposition into the mouse genome.
C. W. Park, B. T. Kren, D. A. Largaespada, and C. J. Steer (2005)
Genes Cells
10, 763-776
|Abstract »|Full Text »|PDF »
Specific binding of the methyl binding domain protein 2 at the BRCA1-NBR2 locus.
E. Auriol, L.-M. Billard, F. Magdinier, and R. Dante (2005)
Nucleic Acids Res.
33, 4243-4254
|Abstract »|Full Text »|PDF »
CDKL5 belongs to the same molecular pathway of MeCP2 and it is responsible for the early-onset seizure variant of Rett syndrome.
F. Mari, S. Azimonti, I. Bertani, F. Bolognese, E. Colombo, R. Caselli, E. Scala, I. Longo, S. Grosso, C. Pescucci, et al. (2005)
Hum. Mol. Genet.
14, 1935-1946
|Abstract »|Full Text »|PDF »
MeCP2 deficiency in Rett syndrome causes epigenetic aberrations at the PWS/AS imprinting center that affects UBE3A expression.
K. Makedonski, L. Abuhatzira, Y. Kaufman, A. Razin, and R. Shemer (2005)
Hum. Mol. Genet.
14, 1049-1058
|Abstract »|Full Text »|PDF »
MeCP2 in neurons: closing in on the causes of Rett syndrome.
Mild overexpression of MeCP2 causes a progressive neurological disorder in mice.
A. L. Collins, J. M. Levenson, A. P. Vilaythong, R. Richman, D. L. Armstrong, J. L. Noebels, J. David Sweatt, and H. Y. Zoghbi (2004)
Hum. Mol. Genet.
13, 2679-2689
|Abstract »|Full Text »|PDF »
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L.-Y. Wong, G. A. Matchett, and A. C. Wilson (2004)
J. Virol.
78, 10074-10085
|Abstract »|Full Text »|PDF »
Cell-type-specific binding of the transcription factor CREB to the cAMP-response element.
H. Cha-Molstad, D. M. Keller, G. S. Yochum, S. Impey, and R. H. Goodman (2004)
PNAS
101, 13572-13577
|Abstract »|Full Text »|PDF »
X-Chromosome inactivation ratios affect wild-type MeCP2 expression within mosaic Rett syndrome and Mecp2-/+ mouse brain.
D. Braunschweig, T. Simcox, R. C. Samaco, and J. M. LaSalle (2004)
Hum. Mol. Genet.
13, 1275-1286
|Abstract »|Full Text »|PDF »
Mbd1 Is Recruited to both Methylated and Nonmethylated CpGs via Distinct DNA Binding Domains.
H. F. Jorgensen, I. Ben-Porath, and A. P. Bird (2004)
Mol. Cell. Biol.
24, 3387-3395
|Abstract »|Full Text »|PDF »
The major form of MeCP2 has a novel N-terminus generated by alternative splicing.