Abstract
Epigenetic modification of DNA by methylation of the cytosine present in CG dinucleotides constitutes a key regulatory mechanism in the control of gene expression in neurological diseases. In this chapter, we describe an in-depth methodology of methylated DNA immunoprecipitation used in combination with tiling microarrays (MeDIP-chip) in order to analyze genome-wide gene promoter methylation in the hippocampus of mice following status epilepticus (prolonged seizure). While a specific mouse model and array format are described, the method can be applied to DNA from many tissues to analyze the methylation status of promoter regions across whole genomes, using a wide range of available array formats (both custom designed and commercially catalogued). We conclude the chapter with the description of bisulfite sequencing validation of MeDIP-chip results.
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References
Feng J, Fan G (2009) The role of DNA methylation in the central nervous system and neuropsychiatric disorders. Int Rev Neurobiol 89:67–84
Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6:597–610
Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33(Suppl):245–254
Iraola-Guzman S, Estivill X, Rabionet R (2011) DNA methylation in neurodegenerative disorders: a missing link between genome and environment? Clin Genet 80:1–14
Miller CA, Sweatt JD (2007) Covalent modification of DNA regulates memory formation. Neuron 53:857–869
Miller-Delaney SF, Das S, Sano T, Jimenez-Mateos EM, Bryan K, Buckley PG et al (2012) Differential DNA methylation patterns define status epilepticus and epileptic tolerance. J Neurosci 32:1577–1588
Urdinguio RG, Sanchez-Mut JV, Esteller M (2009) Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol 8:1056–1072
Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA et al (2011) Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14:1345–1351
Levenson JM, Roth TL, Lubin FD, Miller CA, Huang IC, Desai P et al (2006) Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J Biol Chem 281:15763–15773
Zhu Q, Wang L, Zhang Y, Zhao FH, Luo J, Xiao Z et al (2012) Increased expression of DNA methyltransferase 1 and 3a in human temporal lobe epilepsy. J Mol Neurosci 46:420–426
Kobow K, Jeske I, Hildebrandt M, Hauke J, Hahnen E, Buslei R et al (2009) Increased reelin promoter methylation is associated with granule cell dispersion in human temporal lobe epilepsy. J Neuropathol Exp Neurol 68:356–364
Aminoff MJ, Simon RP (1980) Status epilepticus. Causes, clinical features and consequences in 98 patients. Am J Med 69:657–666
Fujikawa DG, Itabashi HH, Wu A, Shinmei SS (2000) Status epilepticus-induced neuronal loss in humans without systemic complications or epilepsy. Epilepsia 41:981–991
Hatazaki S, Bellver-Estelles C, Jimenez-Mateos EM, Meller R, Bonner C, Murphy N et al (2007) Microarray profile of seizure damage-refractory hippocampal CA3 in a mouse model of epileptic preconditioning. Neuroscience 150:467–477
Jimenez-Mateos EM, Hatazaki S, Johnson MB, Bellver-Estelles C, Mouri G, Bonner C et al (2008) Hippocampal transcriptome after status epilepticus in mice rendered seizure damage-tolerant by epileptic preconditioning features suppressed calcium and neuronal excitability pathways. Neurobiol Dis 32:442–453
Jimenez-Mateos EM, Henshall DC (2009) Seizure preconditioning and epileptic tolerance: models and mechanisms. Int J Physiol Pathophysiol Pharmacol 1:180–191
Jimenez-Mateos EM, Mouri G, Conroy RM, Henshall DC (2010) Epileptic tolerance is associated with enduring neuroprotection and uncoupling of the relationship between CA3 damage, neuropeptide Y rearrangement and spontaneous seizures following intra-amygdala kainic acid-induced status epilepticus in mice. Neuroscience 171:556–565
Jimenez-Mateos EM, Engel T, Merino-Serrais P, McKiernan RC, Tanaka K, Mouri G et al (2012) Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nat Med 18:1087–1094
Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862
Buckley PG, Das S, Bryan K, Watters KM, Alcock L, Koster J et al (2011) Genome-wide DNA methylation analysis of neuroblastic tumors reveals clinically relevant epigenetic events and large-scale epigenomic alterations localized to telomeric regions. Int J Cancer 128:2296–2305
Das S, Bryan K, Buckley PG, Piskareva O, Bray IM, Foley N et al (2012) Modulation of neuroblastoma disease pathogenesis by an extensive network of epigenetically regulated microRNAs. Oncogene Epub ahead of print
Das S, Foley N, Bryan K, Watters KM, Bray I, Murphy DM et al (2010) MicroRNA mediates DNA demethylation events triggered by retinoic acid during neuroblastoma cell differentiation. Cancer Res 70:7874–7881
Paxinos G, Franklin KBJ (1997) The mouse brain in stereotaxic coordinates. Academic, San Diego, CA
Lein ES, Zhao X, Gage FH (2004) Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. J Neurosci 24:3879–3889
Acknowledgments
This work was supported by the Science Foundation of Ireland (Award 08/IN.1./B1875) and by the Medical Research Charities Group/Health Research Board Joint Funding Scheme through Brainwave, the Irish Epilepsy Association.
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Miller-Delaney, S.F.C., Das, S., Stallings, R.L., Henshall, D.C. (2013). Investigating Gene Promoter Methylation in a Mouse Model of Status Epilepticus . In: Lee, TL., Shui Luk, A. (eds) Tiling Arrays. Methods in Molecular Biology, vol 1067. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-607-8_7
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DOI: https://doi.org/10.1007/978-1-62703-607-8_7
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