1 |
Walsh CP, Chaillet JR and Bestor TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20, 116
DOI
|
2 |
Hermann A, Gowher H and Jeltsch A (2004) Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 61, 2571-2587
DOI
|
3 |
Okano M, Bell DW, Haber DA and Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247-257
DOI
|
4 |
Gruenbaum Y, Cedar H and Razin A (1982) Substrate and sequence specificity of a eukaryotic DNA methylase. Nature 295, 620
DOI
|
5 |
Guo JU, Su Y, Shin JH et al (2014) Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci 17, 215
DOI
|
6 |
Feng J, Zhou Y, Campbell SL et al (2010) Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13, 423
DOI
|
7 |
Veldic M, Caruncho H, Liu W et al (2004) DNAmethyltransferase 1 mRNA is selectively overexpressed in telencephalic GABAergic interneurons of schizophrenia brains. Proc Natl Acad Sci U S A 101, 348-353
DOI
|
8 |
Kriaucionis S and Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930
DOI
|
9 |
Tahiliani M, Koh KP, Shen Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935
DOI
|
10 |
He YF, Li BZ, Li Z et al (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303-1307
DOI
|
11 |
Ito S, Shen L, Dai Q et al (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303
DOI
|
12 |
Yu M, Hon GC, Szulwach KE et al (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368-1380
DOI
|
13 |
Wyatt G (1951) Recognition and estimation of 5-methylcytosine in nucleic acids. Biochem J 48, 581
DOI
|
14 |
Hotchkiss RD (1948) The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem 175, 315-332
DOI
|
15 |
Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8, 1499-1504
DOI
|
16 |
Illingworth RS, Gruenewald-Schneider U, Webb S et al (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6, e1001134
DOI
|
17 |
Ladd-Acosta C, Pevsner J, Sabunciyan S et al (2007) DNA methylation signatures within the human brain. Am J Hum Genet 81, 1304-1315
DOI
|
18 |
Siegmund KD, Connor CM, Campan M et al (2007) DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PLoS One 2, e895
DOI
|
19 |
Boyes J and Bird A (1992) Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J 11, 327-333
DOI
|
20 |
Hsieh CL (1994) Dependence of transcriptional repression on CpG methylation density. Mol Cell Biol 14, 5487-5494
DOI
|
21 |
Laurent L, Wong E, Li G et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20, 320-331
DOI
|
22 |
Zhang L, Lu X, Lu J et al (2012) Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol 8, 328
DOI
|
23 |
Rai K, Huggins IJ, James SR, Karpf AR, Jones DA and Cairns BR (2008) DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135, 1201-1212
DOI
|
24 |
Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY and Blau HM (2010) Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 463, 1042
DOI
|
25 |
Bhutani N, Burns DM and Blau HM (2011) DNA demethylation dynamics. Cell 146, 866-872
DOI
|
26 |
Santiago M, Antunes C, Guedes M, Sousa N and Marques CJ (2014) TET enzymes and DNA hydroxymethylation in neural development and function-how critical are they? Genomics 104, 334-340
DOI
|
27 |
Ito S, D'alessio AC, Taranova OV, Hong K, Sowers LC and Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129
DOI
|
28 |
Dawlaty MM, Breiling A, Le T et al (2013) Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. Dev Cell 24, 310-323
DOI
|
29 |
Portela A and Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28, 1057
DOI
|
30 |
Heyward FD and Sweatt JD (2015) DNA methylation in memory formation: emerging insights. Neuroscientist 21, 475-489
DOI
|
31 |
Antequera F and Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci U S A 90, 11995-11999
DOI
|
32 |
Yu L, Chibnik LB, Srivastava GP et al (2015) Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease. JAMA Neurol 72, 15-24
DOI
|
33 |
Consortium IHGS (2001) Initial sequencing and analysis of the human genome. Nature 409, 860
DOI
|
34 |
Sanchez-Mut JV, Aso E, Panayotis N et al (2013) DNA methylation map of mouse and human brain identifies target genes in Alzheimer's disease. Brain 136, 3018-3027
DOI
|
35 |
Sanchez-Mut JV, Aso E, Heyn H et al (2014) Promoter hypermethylation of the phosphatase DUSP22 mediates PKA-dependent TAU phosphorylation and CREB activation in Alzheimer's disease. Hippocampus 24, 363-368
DOI
|
36 |
De Jager PL, Srivastava G, Lunnon K et al (2014) Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci 17, 1156
DOI
|
37 |
Lunnon K, Smith R, Hannon E et al (2014) Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease. Nat Neurosci 17, 1164
DOI
|
38 |
Bae JR and Kim SH (2017) Synapses in neurodegenerative diseases. BMB Rep 50, 237-246
DOI
|
39 |
Delgado-Morales R and Esteller M (2017) Opening up the DNA methylome of dementia. Mol Psychiatry 22, 485
DOI
|
40 |
Giri M, Zhang M and Lu Y (2016) Genes associated with Alzheimer's disease: an overview and current status. Clin Interv Aging 11, 665
DOI
|
41 |
Cho S, Ahn E, An H et al (2017) Association of miR-938G> A polymorphisms with primary ovarian insufficiency (POI)-related gene expression. Int J Mol Sci 18, 1255
DOI
|
42 |
Gibbs JR, van der Brug MP, Hernandez DG et al (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6, e1000952
DOI
|
43 |
Lord J and Cruchaga C (2014) The epigenetic landscape of Alzheimer's disease. Nat Neurosci 17, 1138
DOI
|
44 |
Sanchez-Mut JV, Heyn H, Vidal E et al (2016) Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Transl Psychiatry 6, e718
DOI
|
45 |
Galpern WR and Lang AE (2006) Interface between tauopathies and synucleinopathies: a tale of two proteins. Ann Neurol 59, 449-458
DOI
|
46 |
Lippa CF, Schmidt ML, Lee VMY and Trojanowski JQ (1999) Antibodies to -synuclein detect Lewy bodies in many Down's syndrome brains with Alzheimer's disease. Ann Neurol 45, 353-357
DOI
|
47 |
van Eijk KR, de Jong S, Boks MP et al (2012) Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC Genomics 13, 636
DOI
|
48 |
Chibnik LB, Yu L, Eaton ML et al (2015) Alzheimer's loci: epigenetic associations and interaction with genetic factors. Ann Clin Transl Neurol 2, 636-647
DOI
|
49 |
Kalia LV and Lang AE (2015) Parkinson's disease. The Lancet 386, 896-912
DOI
|
50 |
Trinh J and Farrer M (2013) Advances in the genetics of Parkinson disease. Nat Rev Neurol 9, 445
DOI
|
51 |
Consortium IPsDG and 2 WTCCC (2011) A two-stage meta-analysis identifies several new loci for Parkinson's disease. PLoS Genet 7, e1002142
DOI
|
52 |
Russ J, Liu EY, Wu K et al (2015) Hypermethylation of repeat expanded C9orf72 is a clinical and molecular disease modifier. Acta Neuropathol 129, 39-52
DOI
|
53 |
Masliah E, Dumaop W, Galasko D and Desplats P (2013) Distinctive patterns of DNA methylation associated with Parkinson disease: identification of concordant epigenetic changes in brain and peripheral blood leukocytes. Epigenetics 8, 1030-1038
DOI
|
54 |
Nalls MA, Pankratz N, Lill CM et al (2014) Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease. Nat Genet 46, 989
DOI
|
55 |
Belzil VV, Katzman RB and Petrucelli L (2016) ALS and FTD: an epigenetic perspective. Acta Neuropathol 132, 487-502
DOI
|
56 |
Ling SC, Polymenidou M and Cleveland DW (2013) Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis. Neuron 79, 416-438
DOI
|
57 |
Liu EY, Russ J, Wu K et al (2014) C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD. Acta Neuropathol 128, 525-541
DOI
|
58 |
Xi Z, Rainero I, Rubino E et al (2014) Hypermethylation of the CpG-island near the C9orf72 G4C2-repeat expansion in FTLD patients. Hum Mol Genet 23, 5630-5637
DOI
|
59 |
McColgan P and Tabrizi SJ (2018) Huntington's disease: a clinical review. Eur J Neurol 25, 24-34
DOI
|
60 |
Bates GP, Dorsey R, Gusella JF et al (2015) Huntington disease. Nat Rev Dis Primers 1, 15005
DOI
|
61 |
Lindberg RL, De Groot CJ, Certa U et al (2004) Multiple sclerosis as a generalized CNS disease-comparative microarray analysis of normal appearing white matter and lesions in secondary progressive MS. J Neuroimmunol 152, 154-167
DOI
|
62 |
De Souza RA, Islam SA, McEwen LM et al (2016) DNA methylation profiling in human Huntington's disease brain. Hum Mol Genet 25, 2013-2030
DOI
|
63 |
Villar-Menendez I, Blanch M, Tyebji S et al (2013) Increased 5-methylcytosine and decreased 5-hydroxymethylcytosine levels are associated with reduced striatal A 2A R levels in Huntington's disease. Neuromolecular Med 15, 295-309
DOI
|
64 |
Faguy K (2016) Multiple sclerosis: An update. Radiol Technol 87, 529-550
|
65 |
Pedre X, Mastronardi F, Bruck W, Lopez-Rodas G, Kuhlmann T and Casaccia P (2011) Changed histone acetylation patterns in normal-appearing white matter and early multiple sclerosis lesions. J Neurosci 31, 3435-3445
DOI
|
66 |
Illingworth R, Kerr A, DeSousa D et al (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6, e22
DOI
|
67 |
Mastronardi FG, Wood DD, Mei J et al (2006) Increased citrullination of histone H3 in multiple sclerosis brain and animal models of demyelination: a role for tumor necrosis factor-induced peptidylarginine deiminase 4 translocation. J Neurosci 26, 11387-11396
DOI
|
68 |
Huynh JL, Garg P, Thin TH et al (2014) Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains. Nat Neurosci 17, 121
DOI
|
69 |
Ioshikhes IP and Zhang MQ (2000) Large-scale human promoter mapping using CpG islands. Nat Genet 26, 61
DOI
|
70 |
Saxonov S, Berg P and Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103, 1412-1417
DOI
|
71 |
Numata S, Ye T, Hyde TM et al (2012) DNA methylation signatures in development and aging of the human prefrontal cortex. Am J Hum Genet 90, 260-272
DOI
|
72 |
Hernandez DG, Nalls MA, Gibbs JR et al (2011) Distinct DNA methylation changes highly correlated with chronological age in the human brain. Hum Mol Genet 20, 1164-1172
DOI
|
73 |
Horvath S, Zhang Y, Langfelder P et al (2012) Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol 13, R97
DOI
|
74 |
Jung SE, Shin KJ and Lee HY (2017) DNA methylationbased age prediction from various tissues and body fluids. BMB Rep 50, 546-553
DOI
|
75 |
Heyn H, Li N, Ferreira HJ et al (2012) Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A 109, 10522-10527
DOI
|
76 |
Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biol 14, 3156
DOI
|
77 |
Hannum G, Guinney J, Zhao L et al (2013) Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell 49, 359-367
DOI
|
78 |
Day K, Waite LL, Thalacker-Mercer A et al (2013) Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol 14, R102
DOI
|
79 |
Horvath S, Mah V, Lu AT et al (2015) The cerebellum ages slowly according to the epigenetic clock. Aging (Albany NY) 7, 294
DOI
|
80 |
Horvath S and Raj K (2018) DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet 19, 371
DOI
|
81 |
Levine ME, Lu AT, Bennett DA and Horvath S (2015) Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer's disease related cognitive functioning. Aging (Albany NY) 7, 1198
DOI
|
82 |
Davies MN, Volta M, Pidsley R et al (2012) Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol 13, R43
DOI
|
83 |
Rao J, Keleshian V, Klein S and Rapoport S (2012) Epigenetic modifications in frontal cortex from Alzheimer's disease and bipolar disorder patients. Transl Psychiatry 2, e132
DOI
|
84 |
Spiers H, Hannon E, Schalkwyk LC et al (2015) Methylomic trajectories across human fetal brain development. Genome Res 25, 338-352
DOI
|
85 |
Lister R, Mukamel EA, Nery JR et al (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905
DOI
|
86 |
Bakulski KM, Dolinoy DC, Sartor MA et al (2012) Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex. J Alzheimers Dis 29, 571-588
DOI
|
87 |
Kaut O, Schmitt I and Wullner U (2012) Genome-scale methylation analysis of Parkinson's disease patients' brains reveals DNA hypomethylation and increased mRNA expression of cytochrome P450 2E1. Neurogenetics 13, 87-91
DOI
|
88 |
Levine ME, Lu AT, Quach A et al (2018) An epigenetic biomarker of aging for lifespan and healthspan. Aging (Albany NY) 10, 573
DOI
|
89 |
Nan X, Ng HH, Johnson CA et al (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386
DOI
|
90 |
Rauch TA, Wu X, Zhong X, Riggs AD and Pfeifer GP (2009) A human B cell methylome at 100- base pair resolution. Proc Natl Acad Sci U S A 106, 671-678
DOI
|
91 |
Domcke S, Bardet AF, Ginno PA, Hartl D, Burger L and Schubeler D (2015) Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575
DOI
|
92 |
Gartler SM and Riggs AD (1983) Mammalian X-chromosome inactivation. Annu Rev Genet 17, 155-190
DOI
|
93 |
Reik W, Collick A, Norris ML, Barton SC and Surani MA (1987) Genomic imprinting determines methylation of parental alleles in transgenic mice. Nature 328, 248
DOI
|
94 |
Swain JL, Stewart TA and Leder P (1987) Parental legacy determines methylation and expression of an autosomal transgene: a molecular mechanism for parental imprinting. Cell 50, 719-727
DOI
|
95 |
Lister R, Pelizzola M, Dowen RH et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315
DOI
|
96 |
Day JJ and Sweatt JD (2010) DNA methylation and memory formation. Nat Neurosci 13, 1319
DOI
|
97 |
Counts JL and Goodman JI (1995) Alterations in DNA methylation may play a variety of roles in carcinogenesis. Cell 83, 13-15
DOI
|
98 |
Jahner D, Stuhlmann H, Stewart CL et al (1982) De novo methylation and expression of retroviral genomes during mouse embryogenesis. Nature 298, 623
DOI
|