期刊论文详细信息
Epigenetics & Chromatin
'Memory and molecular turnover,’ 30 years after inception
Richard B Meagher1 
[1] Genetics Department, University of Georgia, Athens, GA 30602, USA
关键词: Nucleosomes;    Acetylation;    Histones;    Post-translational modification;    Hydroxymethylcytosine;    Methylcytosine;   
Others  :  1115070
DOI  :  10.1186/1756-8935-7-37
 received in 2014-10-29, accepted in 2014-11-28,  发布年份 2014
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【 摘 要 】

In 1984 Sir Francis Crick hypothesized that memory is recorded in the brain as reversible modifications to DNA and protein, but acknowledged that most biomolecules turn over too rapidly to account for long-term memories. To accommodate this possible paradox he modeled an enzymatic mechanism to maintain modifications on hemi-modified multimeric symmetrical molecules. While studies on the turnover of chromatin modifications that may be involved in memory are in their infancy, an exploration of his model in the light of modern epigenetics produced somewhat surprising results. The molecular turnover rates for two classes of chromatin modifications believed to record and store durable memories were approximated from experiments using diverse approaches and were found to be remarkably short. The half-lives of DNA cytosine methylation and post-translationally modified nucleosomal histones are measured in hours and minutes, respectively, for a subset of sites on chromatin controlling gene expression. It appears likely that the turnover of DNA methylation in the brain and in neurons, in particular, is even more rapid than in other cell types and organs, perhaps accommodating neuronal plasticity, learning, and memory. The machinery responsible for the rapid turnover of DNA methylation and nucleosomal histone modifications is highly complex, partially redundant, and appears to act in a sequence specific manner. Molecular symmetry plays an important part in maintaining site-specific turnover, but its particular role in memory maintenance is unknown. Elucidating Crick’s paradox, the contradiction between rapid molecular turnover of modified biomolecules and long-term memory storage, appears fundamental to understanding cognitive function and neurodegenerative disease.

【 授权许可】

   
2014 Meagher; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Crick F: Memory and molecular turnover. Nature 1984, 312:101.
  • [2]Sweatt JD: The emerging field of neuroepigenetics. Neuron 2013, 80:624-632.
  • [3]Zovkic IB, Guzman-Karlsson MC, Sweatt JD: Epigenetic regulation of memory formation and maintenance. Learn Mem 2013, 20:61-74.
  • [4]Rudenko A, Tsai LH: Epigenetic regulation in memory and cognitive disorders. Neuroscience 2014, 264:51-63.
  • [5]Zovkic IB, Paulukaitis BS, Day JJ, Etikala DM, Sweatt JD: Histone H2A.Z subunit exchange controls consolidation of recent and remote memory. Nature 2014, 515:582-586.
  • [6]Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, Le T, Faull KF, Jaenisch R, Tsai LH: Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron 2013, 79:1109-1122.
  • [7]Levenson JM, Sweatt JD: Epigenetic mechanisms in memory formation. Nat Rev Neurosci 2005, 6:108-118.
  • [8]Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE: UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007, 317:1760-1764.
  • [9]Yu N-K, Baek SH, Kaang B-K: DNA methylation-mediated control of learning and memory. Mol Brain 2011, 4:5. BioMed Central Full Text
  • [10]Day JJ, Sweatt JD: DNA methylation and memory formation. Nat Neurosci 2010, 13:1319-1323.
  • [11]Meagher RB, Mussar KJ: The influence of DNA sequence on epigenome-induced pathologies. Epigenetics Chromatin 2012, 5:11-35. BioMed Central Full Text
  • [12]Morris MJ, Adachi M, Na ES, Monteggia LM: Selective role for DNMT3a in learning and memory. Neurobiol Learn Mem 2014, 115:30-37.
  • [13]Miller CA, Sweatt JD: Covalent modification of DNA regulates memory formation. Neuron 2007, 53:857-869.
  • [14]Lai F, Shiekhattar R: Where long noncoding RNAs meet DNA methylation. Cell Res 2014, 24:263-264.
  • [15]Matzke MA, Mosher RA: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 2014, 15:394-408.
  • [16]Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER: A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 2012, 149:693-707.
  • [17]Schimke RT: Methods for analysis of enzyme synthesis and degradation in animal tissues. Methods Enzymol 1975, 40:241-266.
  • [18]Yamagata Y, Szabo P, Szuts D, Bacquet C, Aranyi T, Paldi A: Rapid turnover of DNA methylation in human cells. Epigenetics 2012, 7:141-145.
  • [19]Ueno M, Katayama K, Yamauchi H, Yasoshima A, Nakayama H, Doi K: Repair process of fetal brain after 5-azacytidine-induced damage. Eur J Neurosci 2006, 24:2758-2768.
  • [20]Metivier R, Gallais R, Tiffoche C, Le Peron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G: Cyclical DNA methylation of a transcriptionally active promoter. Nature 2008, 452:45-50.
  • [21]Wu H, Zhang Y: Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 2014, 156:45-68.
  • [22]Niehrs C, Schafer A: Active DNA demethylation by Gadd45 and DNA repair. Trends Cell Biol 2012, 22:220-227.
  • [23]Barreto G, Schafer A, Marhold J, Stach D, Swaminathan SK, Handa V, Doderlein G, Maltry N, Wu W, Lyko F, Niehrs C: Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 2007, 445:671-675.
  • [24]Jin SG, Guo C, Pfeifer GP: GADD45A does not promote DNA demethylation. PLoS Genet 2008, 4:e1000013.
  • [25]Engel N, Tront JS, Erinle T, Nguyen N, Latham KE, Sapienza C, Hoffman B, Liebermann DA: Conserved DNA methylation in Gadd45a(-/-) mice. Epigenetics 2009, 4:98-99.
  • [26]Sabag O, Zamir A, Keshet I, Hecht M, Ludwig G, Tabib A, Moss J, Cedar H: Establishment of methylation patterns in ES cells. Nat Struct Mol Biol 2014, 21:110-112.
  • [27]Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR: Global epigenomic reconfiguration during mammalian brain development. Science 2013, 341:1237905.
  • [28]Ma DK, Jang MH, Guo JU, Kitabatake Y, Chang ML, Pow-Anpongkul N, Flavell RA, Lu B, Ming GL, Song H: Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 2009, 323:1074-1077.
  • [29]Powell C, Grant AR, Cornblath E, Goldman D: Analysis of DNA methylation reveals a partial reprogramming of the Muller glia genome during retina regeneration. Proc Natl Acad Sci U S A 2013, 110:19814-19819.
  • [30]Yu P, McKinney EC, Kandasamy MM, Albert AL, Meagher RB: Characterization of brain cell nuclei with decondensed chromatin. Dev Neurobiol 2014. doi:10.1002/dneu.22245
  • [31]Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C: Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012, 149:1368-1380.
  • [32]Navarro A, Yin P, Ono M, Monsivais D, Moravek MB, Coon JS 5th, Dyson MT, Wei JJ, Bulun SE: 5-hydroxymethylcytosine promotes proliferation of human uterine leiomyoma: a biological link to a new epigenetic modification in benign tumors. J Clin Endocrinol Metab 2014, 99:E2437-E2445.
  • [33]Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K: TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473:343-348.
  • [34]Jin C, Lu Y, Jelinek J, Liang S, Estecio MR, Barton MC, Issa JP: TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells. Nucleic Acids Res 2014, 42:6956-6971.
  • [35]Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S, Bruckl T, Biel M, Carell T: Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010, 5:e15367.
  • [36]Kriaucionis S, Heintz N: The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930.
  • [37]Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, Vasanthakumar A, Godley LA, Chang Q, Cheng X, He C, Jin P: 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci 2011, 14:1607-1616.
  • [38]Yoshida M, Kijima M, Akita M, Beppu T: Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A. J Biol Chem 1990, 265:17174-17179.
  • [39]Waterborg JH: Dynamics of histone acetylation in vivo. A function for acetylation turnover? Biochem Cell Biol 2002, 80:363-378.
  • [40]Jamai A, Imoberdorf RM, Strubin M: Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell 2007, 25:345-355.
  • [41]Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ: Dynamics of replication-independent histone turnover in budding yeast. Science 2007, 315:1405-1408.
  • [42]Deal RB, Henikoff JG, Henikoff S: Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 2010, 328:1161-1164.
  • [43]Chen X, Xiong J, Xu M, Chen S, Zhu B: Symmetrical modification within a nucleosome is not required globally for histone lysine methylation. EMBO Rep 2011, 12:244-251.
  • [44]Margueron R, Reinberg D: Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 2010, 11:285-296.
  • [45]Jones PA, Liang G: Rethinking how DNA methylation patterns are maintained. Nat Rev Genet 2009, 10:805-811.
  • [46]Day JJ, Sweatt JD: Cognitive neuroepigenetics: a role for epigenetic mechanisms in learning and memory. Neurobiol Learn Mem 2011, 96:2-12.
  • [47]Buchanan L, Durand-Dubief M, Roguev A, Sakalar C, Wilhelm B, Stralfors A, Shevchenko A, Aasland R, Shevchenko A, Ekwall K, Francis Stewart A: The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains. PLoS Genet 2009, 5:e1000726.
  • [48]Flores O, Deniz O, Soler-Lopez M, Orozco M: Fuzziness and noise in nucleosomal architecture. Nucleic Acids Res 2014, 42:4934-4946.
  • [49]Trifonov EN: Cracking the chromatin code: precise rule of nucleosome positioning. Phys Life Rev 2011, 8:39-50.
  • [50]Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 2007, 446:572-576.
  • [51]Gent JI, Schneider KL, Topp CN, Rodriguez C, Presting GG, Dawe RK: Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. Epigenetics Chromatin 2011, 4:3. BioMed Central Full Text
  • [52]Wierzynski CM, Lubenov EV, Gu M, Siapas AG: State-dependent spike-timing relationships between hippocampal and prefrontal circuits during sleep. Neuron 2009, 61:587-596.
  • [53]Sweegers CC, Takashima A, Fernandez G, Talamini LM: Neural mechanisms supporting the extraction of general knowledge across episodic memories. Neuroimage 2014, 87:138-146.
  • [54]Dammer EB, Duong DM, Diner I, Gearing M, Feng Y, Lah JJ, Levey AI, Seyfried NT: Neuron enriched nuclear proteome isolated from human brain. J Proteome Res 2013, 12:3193-3206.
  • [55]Lu Y, Qu W, Min B, Liu Z, Chen C, Zhang C: Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes. IET Syst Biol 2014, 8:104-115.
  • [56]da Costa NM, Martin KA: Sparse reconstruction of brain circuits: or, how to survive without a microscopic connectome. Neuroimage 2013, 80:27-36.
  • [57]Ho VM, Dallalzadeh LO, Karathanasis N, Keles MF, Vangala S, Grogan T, Poirazi P, Martin KC: GluA2 mRNA distribution and regulation by miR-124 in hippocampal neurons. Mol Cell Neurosci 2014, 61:1-12.
  • [58]Feltrin D, Fusco L, Witte H, Moretti F, Martin K, Letzelter M, Fluri E, Scheiffele P, Pertz O: Growth cone MKK7 mRNA targeting regulates MAP1b-dependent microtubule bundling to control neurite elongation. PLoS Biol 2012, 10:e1001439.
  • [59]Ho VM, Lee JA, Martin KC: The cell biology of synaptic plasticity. Science 2011, 334:623-628.
  • [60]Ch’ng TH, Uzgil B, Lin P, Avliyakulov NK, O’Dell TJ, Martin KC: Activity-dependent transport of the transcriptional coactivator CRTC1 from synapse to nucleus. Cell 2012, 150:207-221.
  • [61]Ch’ng TH, Martin KC: Synapse-to-nucleus signaling. Curr Opin Neurobiol 2011, 21:345-352.
  • [62]Rudenko A, Tsai LH: Epigenetic modifications in the nervous system and their impact upon cognitive impairments. Neuropharmacology 2014, 80:70-82.
  • [63]Deal RB, Henikoff S: The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc 2011, 6:56-68.
  • [64]Deal RB, Henikoff S: A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 2010, 18:1030-1040.
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