-
2
-
-
84881510549
-
Epigenetic variation, inheritance, and selection in plant populations
-
Hirsch S, Baumberger R, Grossniklaus U. Epigenetic variation, inheritance, and selection in plant populations. Cold SpringHarb Symp Quant Biol 2012;77:97-104.
-
(2012)
Cold SpringHarb Symp Quant Biol
, vol.77
, pp. 97-104
-
-
Hirsch, S.1
Baumberger, R.2
Grossniklaus, U.3
-
4
-
-
84858071017
-
Epigenetic and epigenomic variation in Arabidopsis thaliana
-
Schmitz RJ, Ecker JR. Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci 2012;17:149-54.
-
(2012)
Trends Plant Sci
, vol.17
, pp. 149-154
-
-
Schmitz, R.J.1
Ecker, J.R.2
-
5
-
-
79959899772
-
A comparative analysis of DNA methylation across human embryonic stem cell lines
-
Chen PY, Feng S, Joo JW, et al. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol 2011;12:R62.
-
(2011)
Genome Biol
, vol.12
-
-
Chen, P.Y.1
Feng, S.2
Joo, J.W.3
-
6
-
-
84879663784
-
Global epigenomic reconfiguration during mammalian brain development
-
Lister R, Mukamel EA, Nery JR, et al. Global epigenomic reconfiguration during mammalian brain development. Science 2013;341:1237905.
-
(2013)
Science
, vol.341
, pp. 1237905
-
-
Lister, R.1
Mukamel, E.A.2
Nery, J.R.3
-
7
-
-
77952355762
-
Genome-wide evolutionary analysis of eukaryotic DNA methylation
-
Zemach A, McDaniel IE, Silva P, et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010;328:916-9.
-
(2010)
Science
, vol.328
, pp. 916-919
-
-
Zemach, A.1
McDaniel, I.E.2
Silva, P.3
-
8
-
-
70349278339
-
Selective epigenetic control of retrotransposition in Arabidopsis
-
Mirouze M, Reinders J, Bucher E, et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 2009;461: 427-30.
-
(2009)
Nature
, vol.461
, pp. 427-430
-
-
Mirouze, M.1
Reinders, J.2
Bucher, E.3
-
9
-
-
34250637203
-
Genetic analyses of DNA methyltransferases in Arabidopsis thaliana
-
Zhang X, Jacobsen SE. Genetic analyses of DNA methyltransferases in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol 2006;71:439-47.
-
(2006)
Cold Spring Harb Symp Quant Biol
, vol.71
, pp. 439-447
-
-
Zhang, X.1
Jacobsen, S.E.2
-
10
-
-
65249148019
-
RNA-mediated chromatin-based silencing in plants
-
Matzke M, Kanno T, Daxinger L, et al. RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 2009;21:367-76.
-
(2009)
Curr Opin Cell Biol
, vol.21
, pp. 367-376
-
-
Matzke, M.1
Kanno, T.2
Daxinger, L.3
-
11
-
-
84875741680
-
The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
-
Zemach A, Kim MY, Hsieh PH, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 2013;153: 193-205.
-
(2013)
Cell
, vol.153
, pp. 193-205
-
-
Zemach, A.1
Kim, M.Y.2
Hsieh, P.H.3
-
12
-
-
84883454804
-
Reconstructing de novo silencing of an active plant retrotransposon
-
Mari-Ordonez A, Marchais A, Etcheverry M, et al. Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet 2013;45:1029-39.
-
(2013)
Nat Genet
, vol.45
, pp. 1029-1039
-
-
Mari-Ordonez, A.1
Marchais, A.2
Etcheverry, M.3
-
13
-
-
84898734518
-
Covering your bases: inheritance of DNA methylation in plant genomes
-
Advance Access publication date 22 November 2013, doi: 10.1093/mp/sst165.
-
Chad EN, Robert JS. Covering your bases: inheritance of DNA methylation in plant genomes. Mol Plant 2013. Advance Access publication date 22 November 2013, doi: 10.1093/mp/sst165.
-
Mol Plant 2013
-
-
Chad, E.N.1
Robert, J.S.2
-
14
-
-
33646193822
-
Inherited epigenetic variation-revisiting soft inheritance
-
Richards EJ. Inherited epigenetic variation-revisiting soft inheritance. Nat RevGenet 2006;7:395-401.
-
(2006)
Nat RevGenet
, vol.7
, pp. 395-401
-
-
Richards, E.J.1
-
15
-
-
0033539183
-
An epigenetic mutation responsible for natural variation in floral symmetry
-
Cubas P, Vincent C, Coen E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 1999;401:157-61.
-
(1999)
Nature
, vol.401
, pp. 157-161
-
-
Cubas, P.1
Vincent, C.2
Coen, E.3
-
16
-
-
0028885673
-
Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis
-
Bender J, Fink GR. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 1995;83:725-34.
-
(1995)
Cell
, vol.83
, pp. 725-734
-
-
Bender, J.1
Fink, G.R.2
-
17
-
-
33746513103
-
A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening
-
Manning K, Tor M, Poole M, et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 2006;38:948-52.
-
(2006)
Nat Genet
, vol.38
, pp. 948-952
-
-
Manning, K.1
Tor, M.2
Poole, M.3
-
18
-
-
0027303886
-
Arabidopsis thaliana DNA methylation mutants
-
Vongs A, Kakutani T, Martienssen RA, et al. Arabidopsis thaliana DNA methylation mutants. Science 1993;260: 1926-8.
-
(1993)
Science
, vol.260
, pp. 1926-1928
-
-
Vongs, A.1
Kakutani, T.2
Martienssen, R.A.3
-
19
-
-
78951493642
-
Tissue cultureinduced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize
-
Rhee Y, Sekhon RS, Chopra S, et al. Tissue cultureinduced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize. Genetics 2010;186: 843-55.
-
(2010)
Genetics
, vol.186
, pp. 843-855
-
-
Rhee, Y.1
Sekhon, R.S.2
Chopra, S.3
-
20
-
-
84873587727
-
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
-
Zhong S, Fei Z, Chen YR, et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 2013; 31:154-9.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 154-159
-
-
Zhong, S.1
Fei, Z.2
Chen, Y.R.3
-
21
-
-
33748629119
-
Genome-wide highresolution mapping and functional analysis of DNA methylation in Arabidopsis
-
Zhang X, Yazaki J, Sundaresan A, et al. Genome-wide highresolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 2006;126:1189-201.
-
(2006)
Cell
, vol.126
, pp. 1189-1201
-
-
Zhang, X.1
Yazaki, J.2
Sundaresan, A.3
-
22
-
-
74849090833
-
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
-
Ossowski S, Schneeberger K, Lucas-Lledo JI, et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 2010;327:92-4.
-
(2010)
Science
, vol.327
, pp. 92-94
-
-
Ossowski, S.1
Schneeberger, K.2
Lucas-Lledo, J.I.3
-
23
-
-
80054718602
-
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
-
Becker C, Hagmann J, Muller J, et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 2011;480:245-9.
-
(2011)
Nature
, vol.480
, pp. 245-249
-
-
Becker, C.1
Hagmann, J.2
Muller, J.3
-
24
-
-
80054837794
-
Transgenerational epigenetic instability is a source of novel methylation variants
-
Schmitz RJ, Schultz MD, Lewsey MG, et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 2011;334:369-73.
-
(2011)
Science
, vol.334
, pp. 369-373
-
-
Schmitz, R.J.1
Schultz, M.D.2
Lewsey, M.G.3
-
25
-
-
0036456019
-
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers
-
Cervera MT, Ruiz-Garcia L, Martinez-Zapater JM. Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. MolGenetGenomics 2002;268:543-52.
-
(2002)
MolGenetGenomics
, vol.268
, pp. 543-552
-
-
Cervera, M.T.1
Ruiz-Garcia, L.2
Martinez-Zapater, J.M.3
-
26
-
-
34248145207
-
Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.)
-
Keyte AL, Percifield R, Liu B, et al. Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). JHered 2006;97:444-50.
-
(2006)
JHered
, vol.97
, pp. 444-450
-
-
Keyte, A.L.1
Percifield, R.2
Liu, B.3
-
27
-
-
36148957919
-
Brassica oleracea displays a high level of DNA methylation polymorphism
-
Salmon A, Clotault J, Jenczewski E, et al. Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Science 2008;174:61-70.
-
(2008)
Plant Science
, vol.174
, pp. 61-70
-
-
Salmon, A.1
Clotault, J.2
Jenczewski, E.3
-
28
-
-
84884697475
-
Epigenetic and genetic influences on DNA methylation variation in maize populations
-
Eichten SR, Briskine R, Song J, et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 2013;25:2783-97.
-
(2013)
Plant Cell
, vol.25
, pp. 2783-2797
-
-
Eichten, S.R.1
Briskine, R.2
Song, J.3
-
29
-
-
77249137168
-
Principles and challenges of genomewide DNA methylation analysis
-
Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010;11:191-203.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 191-203
-
-
Laird, P.W.1
-
30
-
-
79955091504
-
High-throughput approaches for plant epigenomic studies
-
Schmitz RJ, Zhang X. High-throughput approaches for plant epigenomic studies. Curr Opin Plant Biol 2011;14: 130-6.
-
(2011)
Curr Opin Plant Biol
, vol.14
, pp. 130-136
-
-
Schmitz, R.J.1
Zhang, X.2
-
31
-
-
37249026814
-
Genome-wide analysis of DNA methylation patterns
-
Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. Development 2007;134:3959-65.
-
(2007)
Development
, vol.134
, pp. 3959-3965
-
-
Zilberman, D.1
Henikoff, S.2
-
32
-
-
42649089780
-
The methylome: approaches for global DNA methylation profiling
-
Beck S, Rakyan VK. The methylome: approaches for global DNA methylation profiling. TrendsGenet 2008;24:231-7.
-
(2008)
TrendsGenet
, vol.24
, pp. 231-237
-
-
Beck, S.1
Rakyan, V.K.2
-
33
-
-
66449121652
-
Finding the fifth base: genome-wide sequencing of cytosine methylation
-
Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 2009;19: 959-66.
-
(2009)
Genome Res
, vol.19
, pp. 959-966
-
-
Lister, R.1
Ecker, J.R.2
-
35
-
-
77957937011
-
Quantitative comparison of genome-wide DNA methylation mapping technologies
-
Bock C, Tomazou EM, Brinkman AB, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010;28:1106-14.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1106-1114
-
-
Bock, C.1
Tomazou, E.M.2
Brinkman, A.B.3
-
36
-
-
77957932941
-
Comparison of sequencing- based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
-
Harris RA, Wang T, Coarfa C, et al. Comparison of sequencing- based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010;28:1097-105.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1097-1105
-
-
Harris, R.A.1
Wang, T.2
Coarfa, C.3
-
37
-
-
43049159700
-
Repeated big bangs and the expanding universe: Directionality in plant genome size evolution
-
Hawkins JS, Grover CE, Wendel JF. Repeated big bangs and the expanding universe: Directionality in plant genome size evolution. Plant Science 2008;174:557-62.
-
(2008)
Plant Science
, vol.174
, pp. 557-562
-
-
Hawkins, J.S.1
Grover, C.E.2
Wendel, J.F.3
-
38
-
-
77956811011
-
Recent insights into mechanisms of genome size change in plants
-
Article ID 382732.
-
Grover CE, Wendel JF. Recent insights into mechanisms of genome size change in plants. J Bot 2010; 2010. Article ID 382732.
-
(2010)
J Bot 2010
-
-
Grover, C.E.1
Wendel, J.F.2
-
39
-
-
77449127799
-
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
-
Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2010;38:391-9.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 391-399
-
-
Serre, D.1
Lee, B.H.2
Ting, A.H.3
-
40
-
-
46949098742
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
-
Down TA, Rakyan VK, Turner DJ, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008;26:779-85.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 779-785
-
-
Down, T.A.1
Rakyan, V.K.2
Turner, D.J.3
-
41
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, O'Malley RC, Tonti-Filippini J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008;133:523-36.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
-
42
-
-
0017841507
-
Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis
-
Bird AP, Southern EM. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. JMol Biol 1978;118: 27-47.
-
(1978)
J Mol Biol
, vol.118
, pp. 27-47
-
-
Bird, A.P.1
Southern, E.M.2
-
43
-
-
0023181267
-
Use of restriction enzymes to detect potential gene sequences in mammalian DNA
-
Lindsay S, Bird AP. Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature 1987; 327:336-8.
-
(1987)
Nature
, vol.327
, pp. 336-338
-
-
Lindsay, S.1
Bird, A.P.2
-
44
-
-
0026052179
-
A genomic scanning method for higher organisms using restriction sites as landmarks
-
Hatada I, Hayashizaki Y, Hirotsune S, et al. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 1991;88: 9523-7.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 9523-9527
-
-
Hatada, I.1
Hayashizaki, Y.2
Hirotsune, S.3
-
45
-
-
0024215214
-
The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases-a review
-
McClelland M, Nelson M. The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases-a review. Gene 1988;74: 291-304.
-
(1988)
Gene
, vol.74
, pp. 291-304
-
-
McClelland, M.1
Nelson, M.2
-
46
-
-
0028060576
-
Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases
-
McClelland M, Nelson M, Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1994;22: 3640-59.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3640-3659
-
-
McClelland, M.1
Nelson, M.2
Raschke, E.3
-
47
-
-
0026634757
-
McrBC: a multisubunit GTP-dependent restriction endonuclease
-
Sutherland E, Coe L, Raleigh EA. McrBC: a multisubunit GTP-dependent restriction endonuclease. J Mol Biol 1992; 225:327-48.
-
(1992)
J Mol Biol
, vol.225
, pp. 327-348
-
-
Sutherland, E.1
Coe, L.2
Raleigh, E.A.3
-
48
-
-
23744484912
-
Profiling DNA methylation patterns using genomic tiling microarrays
-
Lippman Z, Gendrel AV, Colot V, et al. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2005;2:219-24.
-
(2005)
Nat Methods
, vol.2
, pp. 219-224
-
-
Lippman, Z.1
Gendrel, A.V.2
Colot, V.3
-
49
-
-
33746756014
-
Comparative isoschizomer profiling of cytosine methylation: the HELP assay
-
Khulan B, Thompson RF, Ye K, et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 2006;16:1046-55.
-
(2006)
Genome Res
, vol.16
, pp. 1046-1055
-
-
Khulan, B.1
Thompson, R.F.2
Ye, K.3
-
50
-
-
43149098062
-
Comprehensive high-throughput arrays for relative methylation (CHARM)
-
Irizarry RA, Ladd-Acosta C, Carvalho B, et al. Comprehensive high-throughput arrays for relative methylation (CHARM). GenomeRes 2008;18:780-90.
-
(2008)
GenomeRes
, vol.18
, pp. 780-790
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Carvalho, B.3
-
51
-
-
65549107163
-
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
-
Brunner AL, Johnson DS, Kim SW, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 2009;19:1044-56.
-
(2009)
Genome Res
, vol.19
, pp. 1044-1056
-
-
Brunner, A.L.1
Johnson, D.S.2
Kim, S.W.3
-
52
-
-
67651149735
-
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
-
Oda M, Glass JL, Thompson RF, et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res 2009;37:3829-39.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 3829-3839
-
-
Oda, M.1
Glass, J.L.2
Thompson, R.F.3
-
53
-
-
66149176899
-
Genome-wide and organspecific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize
-
Wang X, Elling AA, Li X, et al. Genome-wide and organspecific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009;21:1053-69.
-
(2009)
Plant Cell
, vol.21
, pp. 1053-1069
-
-
Wang, X.1
Elling, A.A.2
Li, X.3
-
54
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
Lippman Z, Gendrel AV, Black M, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004;430:471-6.
-
(2004)
Nature
, vol.430
, pp. 471-476
-
-
Lippman, Z.1
Gendrel, A.V.2
Black, M.3
-
55
-
-
12544254467
-
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
-
Tran RK, Henikoff JG, Zilberman D, et al. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol 2005;15:154-9.
-
(2005)
Curr Biol
, vol.15
, pp. 154-159
-
-
Tran, R.K.1
Henikoff, J.G.2
Zilberman, D.3
-
56
-
-
34347327677
-
Epigenetic natural variation in Arabidopsis thaliana
-
Vaughn MW, Tanurdzic M, Lippman Z, et al. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 2007;5: e174.
-
(2007)
PLoS Biol
, vol.5
-
-
Vaughn, M.W.1
Tanurdzic, M.2
Lippman, Z.3
-
57
-
-
42549090878
-
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression
-
Li X, Wang X, He K, et al. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 2008;20:259-76.
-
(2008)
Plant Cell
, vol.20
, pp. 259-276
-
-
Li, X.1
Wang, X.2
He, K.3
-
58
-
-
84891713248
-
Epigenomic consequences of immortalized plant cell suspension culture
-
Tanurdzic M, Vaughn MW, Jiang H, et al. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol 2008;6:2880-95.
-
(2008)
PLoS Biol
, vol.6
, pp. 2880-2895
-
-
Tanurdzic, M.1
Vaughn, M.W.2
Jiang, H.3
-
59
-
-
77950346035
-
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids
-
He G, Zhu X, Elling AA, et al. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 2010;22:17-33.
-
(2010)
Plant Cell
, vol.22
, pp. 17-33
-
-
He, G.1
Zhu, X.2
Elling, A.A.3
-
60
-
-
0027495467
-
Dissection of the methyl- CpG binding domain from the chromosomal protein MeCP2
-
Nan X, Meehan RR, Bird A. Dissection of the methyl- CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 1993;21:4886-92.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 4886-4892
-
-
Nan, X.1
Meehan, R.R.2
Bird, A.3
-
61
-
-
0026747761
-
Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA
-
Lewis JD, Meehan RR, Henzel WJ, et al. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 1992; 69:905-14.
-
(1992)
Cell
, vol.69
, pp. 905-914
-
-
Lewis, J.D.1
Meehan, R.R.2
Henzel, W.J.3
-
62
-
-
23044514626
-
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
-
Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005;37:853-62.
-
(2005)
Nat Genet
, vol.37
, pp. 853-862
-
-
Weber, M.1
Davies, J.J.2
Wittig, D.3
-
63
-
-
31744433660
-
Evidence for an instructive mechanism of de novo methylation in cancer cells
-
Keshet I, Schlesinger Y, Farkash S, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 2006;38:149-53.
-
(2006)
Nat Genet
, vol.38
, pp. 149-153
-
-
Keshet, I.1
Schlesinger, Y.2
Farkash, S.3
-
64
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
Cokus SJ, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008;452:215-9.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
-
65
-
-
33748055105
-
MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells
-
Rauch T, Li H, Wu X, et al. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 2006;66:7939-47.
-
(2006)
Cancer Res
, vol.66
, pp. 7939-7947
-
-
Rauch, T.1
Li, H.2
Wu, X.3
-
67
-
-
77955433253
-
Whole genome DNA methylation analysis based on high throughput sequencing technology
-
Li N, Ye M, Li Y, et al. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 2010;52:203-12.
-
(2010)
Methods
, vol.52
, pp. 203-212
-
-
Li, N.1
Ye, M.2
Li, Y.3
-
68
-
-
78650058320
-
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation
-
Robinson MD, Stirzaker C, Statham AL, et al. Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res 2010;20:1719-29.
-
(2010)
Genome Res
, vol.20
, pp. 1719-1729
-
-
Robinson, M.D.1
Stirzaker, C.2
Statham, A.L.3
-
69
-
-
0026546877
-
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
-
Frommer M, McDonald LE, Millar DS, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad SciUSA 1992;89:1827-31.
-
(1992)
Proc Natl Acad SciUSA
, vol.89
, pp. 1827-1831
-
-
Frommer, M.1
McDonald, L.E.2
Millar, D.S.3
-
70
-
-
34547528183
-
DNA methylation: bisulphite modification and analysis
-
Clark SJ, Statham A, Stirzaker C, et al. DNA methylation: bisulphite modification and analysis. Nat Protoc 2006;1: 2353-64.
-
(2006)
Nat Protoc
, vol.1
, pp. 2353-2364
-
-
Clark, S.J.1
Statham, A.2
Stirzaker, C.3
-
71
-
-
77449144498
-
Accurate sodium bisulfite sequencing in plants
-
Henderson IR, Chan SR, Cao X, et al. Accurate sodium bisulfite sequencing in plants. Epigenetics 2010;5:47-9.
-
(2010)
Epigenetics
, vol.5
, pp. 47-49
-
-
Henderson, I.R.1
Chan, S.R.2
Cao, X.3
-
72
-
-
33644649616
-
High-throughput DNA methylation profiling using universal bead arrays
-
Bibikova M, Lin Z, Zhou L, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006;16:383-93.
-
(2006)
Genome Res
, vol.16
, pp. 383-393
-
-
Bibikova, M.1
Lin, Z.2
Zhou, L.3
-
73
-
-
84856306090
-
Genome-wide DNA methylation profiling using Infinium(R) assay
-
Bibikova M, Le J, Barnes B, et al. Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics 2009;1:177-200.
-
(2009)
Epigenomics
, vol.1
, pp. 177-200
-
-
Bibikova, M.1
Le, J.2
Barnes, B.3
-
74
-
-
67649854923
-
High-throughput bisulfite sequencing in mammalian genomes
-
Smith ZD, Gu H, Bock C, et al. High-throughput bisulfite sequencing in mammalian genomes. Methods 2009;48:226-32.
-
(2009)
Methods
, vol.48
, pp. 226-232
-
-
Smith, Z.D.1
Gu, H.2
Bock, C.3
-
75
-
-
79952788617
-
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
-
Gu H, Smith ZD, Bock C, et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011;6:468-81.
-
(2011)
Nat Protoc
, vol.6
, pp. 468-481
-
-
Gu, H.1
Smith, Z.D.2
Bock, C.3
-
76
-
-
27144500218
-
Reduced representation bisulfite sequencing for comparative highresolution DNA methylation analysis
-
Meissner A, Gnirke A, Bell GW, et al. Reduced representation bisulfite sequencing for comparative highresolution DNA methylation analysis. Nucleic Acids Res 2005;33:5868-77.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5868-5877
-
-
Meissner, A.1
Gnirke, A.2
Bell, G.W.3
-
77
-
-
77957948773
-
Taking the measure of the methylome
-
Beck S. Taking the measure of the methylome. Nat Biotechnol 2010;28:1026-8.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1026-1028
-
-
Beck, S.1
-
78
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008;454:766-70.
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
-
79
-
-
77449153454
-
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
-
Gu H, Bock C, Mikkelsen TS, et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. NatMethods 2010;7:133-6.
-
(2010)
NatMethods
, vol.7
, pp. 133-136
-
-
Gu, H.1
Bock, C.2
Mikkelsen, T.S.3
-
80
-
-
79960926264
-
Dynamic CpG island methylation landscape in oocytes and preimplantation embryos
-
Smallwood SA, Tomizawa S, Krueger F, et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 2011;43:811-4.
-
(2011)
Nat Genet
, vol.43
, pp. 811-814
-
-
Smallwood, S.A.1
Tomizawa, S.2
Krueger, F.3
-
81
-
-
84867053720
-
Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA
-
Calarco JP, Borges F, Donoghue MT, et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012;151:194-205.
-
(2012)
Cell
, vol.151
, pp. 194-205
-
-
Calarco, J.P.1
Borges, F.2
Donoghue, M.T.3
-
82
-
-
84874991260
-
Patterns of population epigenomic diversity
-
Schmitz RJ, Schultz MD, Urich MA, et al. Patterns of population epigenomic diversity. Nature 2013;495:193-8.
-
(2013)
Nature
, vol.495
, pp. 193-198
-
-
Schmitz, R.J.1
Schultz, M.D.2
Urich, M.A.3
-
83
-
-
0034051419
-
CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer
-
Yan PS, Perry MR, Laux DE, et al. CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer. Clin Cancer Res 2000;6:1432-8.
-
(2000)
Clin Cancer Res
, vol.6
, pp. 1432-1438
-
-
Yan, P.S.1
Perry, M.R.2
Laux, D.E.3
-
84
-
-
0037728813
-
Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation
-
Shi H, Wei SH, Leu YW, et al. Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res 2003;63:2164-71.
-
(2003)
Cancer Res
, vol.63
, pp. 2164-2171
-
-
Shi, H.1
Wei, S.H.2
Leu, Y.W.3
-
86
-
-
23444432370
-
Epigenomic mapping in Arabidopsis using tiling microarrays
-
Martienssen RA, Doerge RW, Colot V. Epigenomic mapping in Arabidopsis using tiling microarrays. ChromosomeRes 2005;13:299-308.
-
(2005)
ChromosomeRes
, vol.13
, pp. 299-308
-
-
Martienssen, R.A.1
Doerge, R.W.2
Colot, V.3
-
87
-
-
10644247621
-
Applications of DNA tiling arrays for whole-genome analysis
-
Mockler TC, Chan S, Sundaresan A, et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005;85:1-15.
-
(2005)
Genomics
, vol.85
, pp. 1-15
-
-
Mockler, T.C.1
Chan, S.2
Sundaresan, A.3
-
88
-
-
34848925793
-
Mapping the genome landscape using tiling array technology
-
Yazaki J, Gregory BD, Ecker JR. Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol 2007;10:534-42.
-
(2007)
Curr Opin Plant Biol
, vol.10
, pp. 534-542
-
-
Yazaki, J.1
Gregory, B.D.2
Ecker, J.R.3
-
89
-
-
38949196698
-
Utilizing tiling microarrays for whole-genome analysis in plants
-
Gregory BD, Yazaki J, Ecker JR. Utilizing tiling microarrays for whole-genome analysis in plants. PlantJ 2008;53: 636-44.
-
(2008)
PlantJ
, vol.53
, pp. 636-644
-
-
Gregory, B.D.1
Yazaki, J.2
Ecker, J.R.3
-
91
-
-
84859117267
-
Advances in plant genome sequencing
-
Hamilton JP, Buell CR. Advances in plant genome sequencing. PlantJ 2012;70:177-90.
-
(2012)
PlantJ
, vol.70
, pp. 177-190
-
-
Hamilton, J.P.1
Buell, C.R.2
-
92
-
-
84857730786
-
Trans chromosomal methylation in Arabidopsis hybrids
-
Greaves IK, Groszmann M, Ying H, et al. Trans chromosomal methylation in Arabidopsis hybrids. ProcNatl Acad Sci USA 2012;109:3570-5.
-
(2012)
ProcNatl Acad Sci USA
, vol.109
, pp. 3570-3575
-
-
Greaves, I.K.1
Groszmann, M.2
Ying, H.3
-
93
-
-
84860109530
-
Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids
-
Shen H, He H, Li J, et al. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 2012;24:875-92.
-
(2012)
Plant Cell
, vol.24
, pp. 875-892
-
-
Shen, H.1
He, H.2
Li, J.3
-
94
-
-
84873156452
-
Gene body methylation is conserved between plant orthologs and is of evolutionary consequence
-
Takuno S, Gaut BS. Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. ProcNatl Acad SciUSA 2013;110:1797-802.
-
(2013)
ProcNatl Acad SciUSA
, vol.110
, pp. 1797-1802
-
-
Takuno, S.1
Gaut, B.S.2
-
95
-
-
84864353941
-
Transcriptome and methylome interactions in rice hybrids
-
Chodavarapu RK, Feng S, Ding B, et al. Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad SciUSA 2012;109:12040-5.
-
(2012)
Proc Natl Acad SciUSA
, vol.109
, pp. 12040-12045
-
-
Chodavarapu, R.K.1
Feng, S.2
Ding, B.3
-
96
-
-
84863103782
-
Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
-
Li X, Zhu J, Hu F, et al. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMCGenomics 2012;13:300.
-
(2012)
BMCGenomics
, vol.13
, pp. 300
-
-
Li, X.1
Zhu, J.2
Hu, F.3
-
97
-
-
84875971371
-
CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
-
Gent JI, Ellis NA, Guo L, et al. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res 2013;23:628-37.
-
(2013)
Genome Res
, vol.23
, pp. 628-637
-
-
Gent, J.I.1
Ellis, N.A.2
Guo, L.3
-
98
-
-
84884695071
-
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
-
Regulski M, Lu Z, Kendall J, et al. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. GenomeRes 2013;23:1651-62.
-
(2013)
GenomeRes
, vol.23
, pp. 1651-1662
-
-
Regulski, M.1
Lu, Z.2
Kendall, J.3
-
99
-
-
84884688892
-
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
-
Schmitz RJ, He Y, Valdes-Lopez O, et al. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. GenomeRes 2013;23:1663-74.
-
(2013)
GenomeRes
, vol.23
, pp. 1663-1674
-
-
Schmitz, R.J.1
He, Y.2
Valdes-Lopez, O.3
-
100
-
-
84891928839
-
Genome-wide analysis of DNA methylation in soybean
-
Song QX, Lu X, Li QT, et al. Genome-wide analysis of DNA methylation in soybean. Mol Plant 2013;6:1961-74.
-
(2013)
Mol Plant
, vol.6
, pp. 1961-1974
-
-
Song, Q.X.1
Lu, X.2
Li, Q.T.3
-
101
-
-
84869092574
-
'Leveling' the playing field for analyses of single-base resolution DNA methylomes
-
Schultz MD, Schmitz RJ, Ecker JR. 'Leveling' the playing field for analyses of single-base resolution DNA methylomes. Trends Genet 2012;28:583-5.
-
(2012)
Trends Genet
, vol.28
, pp. 583-585
-
-
Schultz, M.D.1
Schmitz, R.J.2
Ecker, J.R.3
-
102
-
-
84891701738
-
Genome-wide high resolution parental specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
-
Zhang M, Xie S, Dong X, et al. Genome-wide high resolution parental specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize. Genome Res 2014;24:167-76.
-
(2014)
Genome Res
, vol.24
, pp. 167-176
-
-
Zhang, M.1
Xie, S.2
Dong, X.3
-
103
-
-
67149086996
-
Extensive demethylation of repetitive elements during seed development underlies gene imprinting
-
Gehring M, Bubb KL, Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009;324:1447-51.
-
(2009)
Science
, vol.324
, pp. 1447-1451
-
-
Gehring, M.1
Bubb, K.L.2
Henikoff, S.3
-
104
-
-
84863393179
-
Parent-oforigin effects on gene expression and DNA methylation in the maize endosperm
-
Waters AJ, Makarevitch I, Eichten SR, et al. Parent-oforigin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 2011;23:4221-33.
-
(2011)
Plant Cell
, vol.23
, pp. 4221-4233
-
-
Waters, A.J.1
Makarevitch, I.2
Eichten, S.R.3
-
105
-
-
84855820359
-
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression
-
Vining KJ, Pomraning KR, Wilhelm LJ, et al. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMCGenomics 2012;13:27.
-
(2012)
BMCGenomics
, vol.13
, pp. 27
-
-
Vining, K.J.1
Pomraning, K.R.2
Wilhelm, L.J.3
-
106
-
-
84883766888
-
Variation in DNA methylation patterns is more common among maize inbreds than among tissues
-
Eichten SR, Vaughn MW, Hermanson PJ, et al. Variation in DNA methylation patterns is more common among maize inbreds than among tissues. Plant Genome 2013;6: 1-10.
-
(2013)
Plant Genome
, vol.6
, pp. 1-10
-
-
Eichten, S.R.1
Vaughn, M.W.2
Hermanson, P.J.3
-
107
-
-
77955482238
-
Paramutation in maize: RNA mediated trans-generational gene silencing
-
Arteaga-Vazquez MA, Chandler VL. Paramutation in maize: RNA mediated trans-generational gene silencing. Curr Opin Genet Dev 2010;20:156-63.
-
(2010)
Curr Opin Genet Dev
, vol.20
, pp. 156-163
-
-
Arteaga-Vazquez, M.A.1
Chandler, V.L.2
-
108
-
-
84869501857
-
Paramutation: a trans-homolog interaction affecting heritable gene regulation
-
Hollick JB. Paramutation: a trans-homolog interaction affecting heritable gene regulation. CurrOpinPlant Biol 2012; 15:536-43.
-
(2012)
CurrOpinPlant Biol
, vol.15
, pp. 536-543
-
-
Hollick, J.B.1
-
109
-
-
0142060823
-
In search of the molecular basis of heterosis
-
Birchler JA, Auger DL, Riddle NC. In search of the molecular basis of heterosis. Plant Cell 2003;15:2236-9.
-
(2003)
Plant Cell
, vol.15
, pp. 2236-2239
-
-
Birchler, J.A.1
Auger, D.L.2
Riddle, N.C.3
-
111
-
-
84878120893
-
Epigenetic variations in plant hybrids and their potential roles in heterosis
-
He G, He H, Deng XW. Epigenetic variations in plant hybrids and their potential roles in heterosis. J Genet Genomics 2013;40:205-10.
-
(2013)
J Genet Genomics
, vol.40
, pp. 205-210
-
-
He, G.1
He, H.2
Deng, X.W.3
-
112
-
-
1642515876
-
One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation
-
Kinoshita T, Miura A, Choi Y, et al. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004;303:521-3.
-
(2004)
Science
, vol.303
, pp. 521-523
-
-
Kinoshita, T.1
Miura, A.2
Choi, Y.3
-
113
-
-
84864360669
-
Epigenetic mechanisms underlying genomic imprinting in plants
-
Kohler C, Wolff P, Spillane C. Epigenetic mechanisms underlying genomic imprinting in plants. Annu Rev Plant Biol 2012;63:331-52.
-
(2012)
Annu Rev Plant Biol
, vol.63
, pp. 331-352
-
-
Kohler, C.1
Wolff, P.2
Spillane, C.3
-
114
-
-
84888628324
-
Genomic imprinting: parental lessons from plants
-
Gehring M. Genomic imprinting: parental lessons from plants. Annu Rev Genet 2013;47:187-208.
-
(2013)
Annu Rev Genet
, vol.47
, pp. 187-208
-
-
Gehring, M.1
-
115
-
-
0037986761
-
Laser capture microdissection of cells from plant tissues
-
Kerk NM, Ceserani T, Tausta SL, et al. Laser capture microdissection of cells from plant tissues. Plant Physiol 2003;132:27-35.
-
(2003)
Plant Physiol
, vol.132
, pp. 27-35
-
-
Kerk, N.M.1
Ceserani, T.2
Tausta, S.L.3
-
116
-
-
80055102335
-
Fluorescence activated cell sorting of plant protoplasts
-
Bargmann BO, Birnbaum KD. Fluorescence activated cell sorting of plant protoplasts. JVis Exp 2010;36:1673.
-
(2010)
JVis Exp
, vol.36
, pp. 1673
-
-
Bargmann, B.O.1
Birnbaum, K.D.2
-
117
-
-
84867474758
-
FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei
-
Borges F, Gardner R, Lopes T, et al. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. PlantMethods 2012;8:44.
-
(2012)
PlantMethods
, vol.8
, pp. 44
-
-
Borges, F.1
Gardner, R.2
Lopes, T.3
-
118
-
-
50649091418
-
Global characterization of cell-specific gene expression through fluorescence- activated sorting of nuclei
-
Zhang C, Barthelson RA, Lambert GM, et al. Global characterization of cell-specific gene expression through fluorescence- activated sorting of nuclei. Plant Physiol 2008;147: 30-40.
-
(2008)
Plant Physiol
, vol.147
, pp. 30-40
-
-
Zhang, C.1
Barthelson, R.A.2
Lambert, G.M.3
|