-
1
-
-
66149123748
-
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain
-
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930 (2009).
-
(2009)
Science
, vol.324
, pp. 929-930
-
-
Kriaucionis, S.1
Heintz, N.2
-
2
-
-
0015298215
-
The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid
-
Penn, N.W., Suwalski, R., O'Riley, C., Bojanowski, K. & Yura, R. The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem. J. 126, 781-790 (1972).
-
(1972)
Biochem. J.
, vol.126
, pp. 781-790
-
-
Penn, N.W.1
Suwalski, R.2
O'Riley, C.3
Bojanowski, K.4
Yura, R.5
-
3
-
-
66149146320
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
-
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935 (2009).
-
(2009)
Science
, vol.324
, pp. 930-935
-
-
Tahiliani, M.1
-
4
-
-
77749277177
-
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing
-
Huang, Y. et al. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS ONE 5, e8888 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Huang, Y.1
-
5
-
-
78650826181
-
Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates
-
Globisch, D. et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 5, e15367 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Globisch, D.1
-
6
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton, A.M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev. 25, 1010-1022 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 1010-1022
-
-
Deaton, A.M.1
Bird, A.2
-
7
-
-
79960249232
-
Genomic mapping of 5-hydroxymethylcytosine in the human brain
-
Jin, S.-G., Wu, X., Li, A.X. & Pfeifer, G.P. Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res. 39, 5015-5024 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 5015-5024
-
-
Jin, S.-G.1
Wu, X.2
Li, A.X.3
Pfeifer, G.P.4
-
8
-
-
78651280460
-
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
-
Song, C.-X. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 29, 68-72 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 68-72
-
-
Song, C.-X.1
-
9
-
-
79955538247
-
Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain
-
Guo, J.U., Su, Y., Zhong, C., Ming, G.L. & Song, H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423-434 (2011).
-
(2011)
Cell
, vol.145
, pp. 423-434
-
-
Guo, J.U.1
Su, Y.2
Zhong, C.3
Ming, G.L.4
Song, H.5
-
10
-
-
80052495940
-
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
-
He, Y.F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303-1307 (2011).
-
(2011)
Science
, vol.333
, pp. 1303-1307
-
-
He, Y.F.1
-
11
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303 (2011).
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
-
12
-
-
84862776719
-
Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine- modified DNA
-
Zhang, L. et al. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat. Chem. Biol. 8, 328-330 (2012).
-
(2012)
Nat. Chem. Biol.
, vol.8
, pp. 328-330
-
-
Zhang, L.1
-
13
-
-
0020480208
-
Digestion of highly modified bacteriophage DNA by restriction endonucleases
-
Huang, L.H., Farnet, C.M., Ehrlich, K.C. & Ehrlich, M. Digestion of highly modified bacteriophage DNA by restriction endonucleases. Nucleic Acids Res. 10, 1579-1591 (1982).
-
(1982)
Nucleic Acids Res.
, vol.10
, pp. 1579-1591
-
-
Huang, L.H.1
Farnet, C.M.2
Ehrlich, K.C.3
Ehrlich, M.4
-
14
-
-
0001587321
-
Glucosylation of deoxyribonucleic acid. III. α-and β-glucosyl transferases from T4-infected Escherichia coli
-
Josse, J. & Kornberg, A. Glucosylation of deoxyribonucleic acid. III. α-and β-glucosyl transferases from T4-infected Escherichia coli. J. Biol. Chem. 237, 1968-1976 (1962).
-
(1962)
J. Biol. Chem.
, vol.237
, pp. 1968-1976
-
-
Josse, J.1
Kornberg, A.2
-
15
-
-
35748982895
-
Getting started in tiling microarray analysis
-
Liu, X.S. Getting started in tiling microarray analysis. PLOS Comput. Biol. 3, 1842-1844 (2007).
-
(2007)
PLOS Comput. Biol.
, vol.3
, pp. 1842-1844
-
-
Liu, X.S.1
-
16
-
-
56449116884
-
Probe signal correction for differential methylation hybridization experiments
-
Potter, D.P., Yan, P., Huang, T.H.M. & Lin, S. Probe signal correction for differential methylation hybridization experiments. BMC Bioinformatics 9, 453 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 453
-
-
Potter, D.P.1
Yan, P.2
Huang, T.H.M.3
Lin, S.4
-
17
-
-
44249093277
-
Expression analysis of G protein-coupled receptors in mouse macrophages
-
Lattin, J.E. et al. Expression analysis of G protein-coupled receptors in mouse macrophages. Immunome Res. 4, 5 (2008).
-
(2008)
Immunome Res.
, vol.4
, pp. 5
-
-
Lattin, J.E.1
-
18
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
19
-
-
38149129457
-
A transcriptome database for astrocytes, neurons, and oligodendrocytes: A new resource for understanding brain development and function
-
Cahoy, J.D. et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci. 28, 264-278 (2008).
-
(2008)
J. Neurosci.
, vol.28
, pp. 264-278
-
-
Cahoy, J.D.1
-
20
-
-
79961185589
-
AMIGO, a toolbox for advanced model identification in systems biology using global optimization
-
Balsa-Canto, E. & Banga, J.R. AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinformatics 27, 2311-2313 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2311-2313
-
-
Balsa-Canto, E.1
Banga, J.R.2
-
21
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu, R.K. et al. Relationship between nucleosome positioning and DNA methylation. Nature 466, 388-392 (2010).
-
(2010)
Nature
, vol.466
, pp. 388-392
-
-
Chodavarapu, R.K.1
-
22
-
-
77649267695
-
Dynamic changes in the human methylome during differentiation
-
Laurent, L. et al. Dynamic changes in the human methylome during differentiation. Genome Res. 20, 320-331 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 320-331
-
-
Laurent, L.1
-
23
-
-
0034601620
-
The Stanley Foundation brain collection and neuropathology consortium
-
Torrey, E.F., Webster, M., Knable, M., Johnston, N. & Yolken, R.H. The Stanley Foundation brain collection and neuropathology consortium. Schizophr. Res. 44, 151-155 (2000).
-
(2000)
Schizophr. Res.
, vol.44
, pp. 151-155
-
-
Torrey, E.F.1
Webster, M.2
Knable, M.3
Johnston, N.4
Yolken, R.H.5
-
24
-
-
77957092153
-
Single-molecule sequencing: Sequence methods to enable accurate quantitation
-
Hart, C. et al. Single-molecule sequencing: sequence methods to enable accurate quantitation. Methods Enzymol. 472, 407-430 (2010).
-
(2010)
Methods Enzymol.
, vol.472
, pp. 407-430
-
-
Hart, C.1
-
25
-
-
33947368681
-
Histone deacetylase inhibitor trichostatin A induces global and gene-specific DNA demethylation in human cancer cell lines
-
Ou, J.N. et al. Histone deacetylase inhibitor trichostatin A induces global and gene-specific DNA demethylation in human cancer cell lines. Biochem. Pharmacol. 73, 1297-1307 (2007).
-
(2007)
Biochem. Pharmacol.
, vol.73
, pp. 1297-1307
-
-
Ou, J.N.1
-
26
-
-
79551650971
-
Histone deacetylase activity modulates alternative splicing
-
Hnilicová, J. et al. Histone deacetylase activity modulates alternative splicing. PLoS ONE 6, e16727 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Hnilicová, J.1
-
27
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343-348 (2011).
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
-
28
-
-
80355145916
-
High sensitivity 5-hydroxymethylcytosine detection in Balb/C brain tissue
-
Davis, T. & Vaisvila, R. High sensitivity 5-hydroxymethylcytosine detection in Balb/C brain tissue. J. Vis. Exp. 48, e2661 (2011).
-
(2011)
J. Vis. Exp.
, vol.48
-
-
Davis, T.1
Vaisvila, R.2
-
29
-
-
77954362183
-
Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine
-
Jin, S.-G., Kadam, S. & Pfeifer, G.P. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 38, e125 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Jin, S.-G.1
Kadam, S.2
Pfeifer, G.P.3
-
30
-
-
18944404300
-
The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes
-
Kondo, E., Gu, Z., Horii, A. & Fukushige, S. The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes. Mol. Cell Biol. 25, 4388-4396 (2005).
-
(2005)
Mol. Cell Biol.
, vol.25
, pp. 4388-4396
-
-
Kondo, E.1
Gu, Z.2
Horii, A.3
Fukushige, S.4
-
31
-
-
4043112183
-
Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)
-
Valinluck, V. et al. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 32, 4100-4108 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 4100-4108
-
-
Valinluck, V.1
-
32
-
-
77950187447
-
Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons
-
Feng, J. et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat. Neurosci. 13, 423-430 (2010).
-
(2010)
Nat. Neurosci.
, vol.13
, pp. 423-430
-
-
Feng, J.1
-
33
-
-
33847614418
-
Covalent modification of DNA regulates memory formation
-
Miller, C.A. & Sweatt, J.D. Covalent modification of DNA regulates memory formation. Neuron 53, 857-869 (2007).
-
(2007)
Neuron
, vol.53
, pp. 857-869
-
-
Miller, C.A.1
Sweatt, J.D.2
-
34
-
-
82255192294
-
5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging
-
Szulwach, K.E. et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 14, 1607-1616 (2011).
-
(2011)
Nat. Neurosci.
, vol.14
, pp. 1607-1616
-
-
Szulwach, K.E.1
-
35
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu, R.K. et al. Relationship between nucleosome positioning and DNA methylation. Nature 466, 388-392 (2010).
-
(2010)
Nature
, vol.466
, pp. 388-392
-
-
Chodavarapu, R.K.1
-
36
-
-
69749092741
-
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
-
Hodges, E. et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 19, 1593-1605 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1593-1605
-
-
Hodges, E.1
-
37
-
-
21244464349
-
Phase i study of an oral histone deacetylase inhibitor, suberoylanilide hydroxamic acid, in patients with advanced cancer
-
Kelly, W.K. et al. Phase I study of an oral histone deacetylase inhibitor, suberoylanilide hydroxamic acid, in patients with advanced cancer. J. Clin. Oncol. 23, 3923-3931 (2005).
-
(2005)
J. Clin. Oncol.
, vol.23
, pp. 3923-3931
-
-
Kelly, W.K.1
-
38
-
-
61349098460
-
Differential chromatin marking of introns and expressed exons by H3K36me3
-
Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376-381 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
-
39
-
-
69949132191
-
Chromatin organization marks exon-intron structure
-
Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16, 990-995 (2009).
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 990-995
-
-
Schwartz, S.1
Meshorer, E.2
Ast, G.3
-
40
-
-
69949124307
-
Nucleosome positioning as a determinant of exon recognition
-
Tilgner, H. et al. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 16, 996-1001 (2009).
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 996-1001
-
-
Tilgner, H.1
-
41
-
-
77149175671
-
Regulation of alternative splicing by histone modifications
-
Luco, R.F. et al. Regulation of alternative splicing by histone modifications. Science 327, 996-1000 (2010).
-
(2010)
Science
, vol.327
, pp. 996-1000
-
-
Luco, R.F.1
-
42
-
-
70349333201
-
Nucleosomes are well positioned in exons and carry characteristic histone modifications
-
Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C. & Komorowski, J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 19, 1732-1741 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1732-1741
-
-
Andersson, R.1
Enroth, S.2
Rada-Iglesias, A.3
Wadelius, C.4
Komorowski, J.5
-
43
-
-
61349098460
-
Differential chromatin marking of introns and expressed exons by H3K36me3
-
Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376-381 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
-
44
-
-
80455176999
-
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
-
Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74-79 (2011).
-
(2011)
Nature
, vol.479
, pp. 74-79
-
-
Shukla, S.1
-
45
-
-
84861961269
-
Alternative splicing: Decoding an expansive regulatory layer
-
Irimia, M. & Blencowe, B.J. Alternative splicing: decoding an expansive regulatory layer. Curr. Opin. Cell Biol. 3, 323-332 (2012).
-
(2012)
Curr. Opin. Cell Biol.
, vol.3
, pp. 323-332
-
-
Irimia, M.1
Blencowe, B.J.2
-
46
-
-
78650961149
-
Epigenetics in alternative pre-mRNA splicing
-
Luco, R.F., Allo, M., Schor, I.E., Kornblihtt, A.R. & Misteli, T. Epigenetics in alternative pre-mRNA splicing. Cell 144, 16-26 (2011).
-
(2011)
Cell
, vol.144
, pp. 16-26
-
-
Luco, R.F.1
Allo, M.2
Schor, I.E.3
Kornblihtt, A.R.4
Misteli, T.5
-
47
-
-
77954362183
-
Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine
-
Jin, S.-G., Kadam, S. & Pfeifer, G.P. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 38, e125 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Jin, S.-G.1
Kadam, S.2
Pfeifer, G.P.3
-
48
-
-
0030842443
-
Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine
-
Tardy-Planechaud, S., Fujimoto, J., Lin, S.S. & Sowers, L.C. Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine. Nucleic Acids Res. 25, 553-559 (1997).
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 553-559
-
-
Tardy-Planechaud, S.1
Fujimoto, J.2
Lin, S.S.3
Sowers, L.C.4
-
49
-
-
0036714197
-
Crystallization and preliminary crystallographic study of a ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site
-
Larivière, L., Kurzeck, J., Aschke-Sonnenborn, U., Ruger, W. & Morera, S. Crystallization and preliminary crystallographic study of a ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site. Acta Crystallogr. D Biol. Crystallogr. 58, 1484-1486 (2002).
-
(2002)
Acta Crystallogr. D Biol. Crystallogr.
, vol.58
, pp. 1484-1486
-
-
Larivière, L.1
Kurzeck, J.2
Aschke-Sonnenborn, U.3
Ruger, W.4
Morera, S.5
-
50
-
-
84857149341
-
Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site: A concern for DNA modification studies using restriction endonucleases
-
Ichiyanagi, K. Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site: a concern for DNA modification studies using restriction endonucleases. Epigenetics 7, 131-136 (2012).
-
(2012)
Epigenetics
, vol.7
, pp. 131-136
-
-
Ichiyanagi, K.1
-
51
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.C.1
-
52
-
-
19544393076
-
Repeated measures analysis
-
Ch. 8 Springer
-
Vittinghoff, E., Glidden, D.V., Shiboski, S.C. & McCulloch, C.E. Repeated Measures Analysis, in Regression Methods in Biostatistics Ch. 8, 253-290 (Springer, 2005).
-
(2005)
Regression Methods in Biostatistics
, pp. 253-290
-
-
Vittinghoff, E.1
Glidden, D.V.2
Shiboski, S.C.3
McCulloch, C.E.4
|