-
1
-
-
53749085372
-
The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana
-
Aceituno FF, Moseyko N, Rhee SY, Gutierrez RA (2008) The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics 9: 438-451.
-
(2008)
BMC Genomics
, vol.9
, pp. 438-451
-
-
Aceituno, F.F.1
Moseyko, N.2
Rhee, S.Y.3
Gutierrez, R.A.4
-
2
-
-
33746807366
-
Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation
-
Agius F, Kapoor A, Zhu JK (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103: 11796-11801.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 11796-11801
-
-
Agius, F.1
Kapoor, A.2
Zhu, J.K.3
-
3
-
-
64349091471
-
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
-
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27: 361-368.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 361-368
-
-
Ball, M.P.1
Li, J.B.2
Gao, Y.3
Lee, J.H.4
Leproust, E.M.5
Park, I.H.6
Xie, B.7
Daley, G.Q.8
Church, G.M.9
-
4
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
-
(2002)
Genes Dev
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
5
-
-
27744577727
-
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription
-
Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581-592.
-
(2005)
Cell
, vol.123
, pp. 581-592
-
-
Carrozza, M.J.1
Li, B.2
Florens, L.3
Suganuma, T.4
Swanson, S.K.5
Lee, K.K.6
Shia, W.J.7
Anderson, S.8
Yates, J.9
Washburn, M.P.10
Workman, J.L.11
-
6
-
-
17744364327
-
Gardening the genome: DNA methylation in Arabidopsisthaliana
-
Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsisthaliana. Nat Rev Genet 6: 351-360.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 351-360
-
-
Chan, S.W.1
Henderson, I.R.2
Jacobsen, S.E.3
-
7
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
Chen, Z.4
Merriman, B.5
Haudenschild, C.D.6
Pradhan, S.7
Nelson, S.F.8
Pellegrini, M.9
Jacobsen, S.E.10
-
8
-
-
33751505540
-
DNA methylation profiling of human chromosomes 6, 20 and 22
-
Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378-1385.
-
(2006)
Nat Genet
, vol.38
, pp. 1378-1385
-
-
Eckhardt, F.1
Lewin, J.2
Cortese, R.3
Rakyan, V.K.4
Attwood, J.5
Burger, M.6
Burton, J.7
Cox, T.V.8
Davies, R.9
Down, T.A.10
Haefliger, C.11
Horton, R.12
Howe, K.13
Jackson, D.K.14
Kunde, J.15
Koenig, C.16
Liddle, J.17
Niblett, D.18
Otto, T.19
Pettett, R.20
Seemann, S.21
Thompson, C.22
West, T.23
Rogers, J.24
Olek, A.25
Berlin, K.26
Beck, S.27
more..
-
9
-
-
32044470027
-
DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation
-
Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495-506.
-
(2006)
Cell
, vol.124
, pp. 495-506
-
-
Gehring, M.1
Huh, J.H.2
Hsieh, T.F.3
Penterman, J.4
Choi, Y.5
Harada, J.J.6
Goldberg, R.B.7
Fischer, R.L.8
-
10
-
-
67149086996
-
Extensive demethylation of repetitive elements during seed development underlies gene imprinting
-
Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451.
-
(2009)
Science
, vol.324
, pp. 1447-1451
-
-
Gehring, M.1
Bubb, K.L.2
Henikoff, S.3
-
11
-
-
34249330696
-
Epigenetic inheritance in plants
-
Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447: 418-424.
-
(2007)
Nature
, vol.447
, pp. 418-424
-
-
Henderson, I.R.1
Jacobsen, S.E.2
-
12
-
-
67149119197
-
Genome-wide demethylation of Arabidopsis endosperm
-
Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324: 1451-1454.
-
(2009)
Science
, vol.324
, pp. 1451-1454
-
-
Hsieh, T.F.1
Ibarra, C.A.2
Silva, P.3
Zemach, A.4
Eshed-Williams, L.5
Fischer, R.L.6
Zilberman, D.7
-
13
-
-
27744587302
-
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex
-
Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593-605.
-
(2005)
Cell
, vol.123
, pp. 593-605
-
-
Keogh, M.C.1
Kurdistani, S.K.2
Morris, S.A.3
Ahn, S.H.4
Podolny, V.5
Collins, S.R.6
Schuldiner, M.7
Chin, K.8
Punna, T.9
Thompson, N.J.10
Boone, C.11
Emili, A.12
Weissman, J.S.13
Hughes, T.R.14
Strahl, B.D.15
Grunstein, M.16
Greenblatt, J.F.17
Buratowski, S.18
Krogan, N.J.19
-
14
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
-
(2004)
Nature
, vol.430
, pp. 471-476
-
-
Lippman, Z.1
Gendrel, A.V.2
Black, M.3
Vaughn, M.W.4
Dedhia, N.5
McCombie, W.R.6
Lavine, K.7
Mittal, V.8
May, B.9
Kasschau, K.D.10
Carrington, J.C.11
Doerge, R.W.12
Colot, V.13
Martienssen, R.14
-
15
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
16
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
Edsall, L.11
Antosiewicz-Bourget, J.12
Stewart, R.13
Ruotti, V.14
Millar, A.H.15
Thomson, J.A.16
Ren, B.17
Ecker, J.R.18
-
17
-
-
65249148019
-
RNA-mediated chromatin-based silencing in plants
-
Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21: 367-376.
-
(2009)
Curr Opin Cell Biol
, vol.21
, pp. 367-376
-
-
Matzke, M.1
Kanno, T.2
Daxinger, L.3
Huettel, B.4
Matzke, A.J.5
-
18
-
-
70349278339
-
Selective epigenetic control of retrotransposition in Arabidopsis
-
Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, Cao J, Weigel D, Paszkowski J, Mathieu O (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461: 427-430.
-
(2009)
Nature
, vol.461
, pp. 427-430
-
-
Mirouze, M.1
Reinders, J.2
Bucher, E.3
Nishimura, T.4
Schneeberger, K.5
Ossowski, S.6
Cao, J.7
Weigel, D.8
Paszkowski, J.9
Mathieu, O.10
-
19
-
-
0035837378
-
Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis
-
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212-214.
-
(2001)
Nature
, vol.411
, pp. 212-214
-
-
Miura, A.1
Yonebayashi, S.2
Watanabe, K.3
Toyama, T.4
Shimada, H.5
Kakutani, T.6
-
20
-
-
65349171662
-
An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites
-
Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, Kakutani T (2009) An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J 28: 1078-1086.
-
(2009)
EMBO J
, vol.28
, pp. 1078-1086
-
-
Miura, A.1
Nakamura, M.2
Inagaki, S.3
Kobayashi, A.4
Saze, H.5
Kakutani, T.6
-
21
-
-
50849112729
-
Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis
-
Oh S, Park S, van Nocker S (2008) Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet 4: e1000077.
-
(2008)
PLoS Genet
, vol.4
-
-
Oh, S.1
Park, S.2
van Nocker, S.3
-
22
-
-
34249853277
-
DNA demethylation in the Arabidopsis genome
-
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104: 6752-6757.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 6752-6757
-
-
Penterman, J.1
Zilberman, D.2
Huh, J.H.3
Ballinger, T.4
Henikoff, S.5
Fischer, R.L.6
-
23
-
-
0346389569
-
Genes and transposons are differentially methylated in plants, but not in mammals
-
Rabinowicz PD, Palmer LE, May BP, Hemann MT, Lowe SW, McCombie WR, Martienssen RA (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res 13: 2658-2664.
-
(2003)
Genome Res
, vol.13
, pp. 2658-2664
-
-
Rabinowicz, P.D.1
Palmer, L.E.2
May, B.P.3
Hemann, M.T.4
Lowe, S.W.5
McCombie, W.R.6
Martienssen, R.A.7
-
24
-
-
25844507235
-
Differential methylation of genes and repeats in land plants
-
Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O'Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA (2005) Differential methylation of genes and repeats in land plants. Genome Res 15: 1431-1440.
-
(2005)
Genome Res
, vol.15
, pp. 1431-1440
-
-
Rabinowicz, P.D.1
Citek, R.2
Budiman, M.A.3
Nunberg, A.4
Bedell, J.A.5
Lakey, N.6
O'Shaughnessy, A.L.7
Nascimento, L.U.8
McCombie, W.R.9
Martienssen, R.A.10
-
25
-
-
38549116060
-
Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana
-
Saze H, Shiraishi A, Miura A, Kakutani T (2008) Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319: 462-465.
-
(2008)
Science
, vol.319
, pp. 462-465
-
-
Saze, H.1
Shiraishi, A.2
Miura, A.3
Kakutani, T.4
-
26
-
-
0242416979
-
The methylated component of the Neurospora crassa genome
-
Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, Bird AP, Freitag M (2003) The methylated component of the Neurospora crassa genome. Nature 422: 893-897.
-
(2003)
Nature
, vol.422
, pp. 893-897
-
-
Selker, E.U.1
Tountas, N.A.2
Cross, S.H.3
Margolin, B.S.4
Murphy, J.G.5
Bird, A.P.6
Freitag, M.7
-
27
-
-
0033582623
-
Nonmethylated transposable elements and methylated genes in a chordate genome
-
Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, Clark VH, Bird A (1999) Nonmethylated transposable elements and methylated genes in a chordate genome. Science 283: 1164-1167.
-
(1999)
Science
, vol.283
, pp. 1164-1167
-
-
Simmen, M.W.1
Leitgeb, S.2
Charlton, J.3
Jones, S.J.4
Harris, B.R.5
Clark, V.H.6
Bird, A.7
-
28
-
-
0035282119
-
Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1)
-
Singer T, Yordan C, Martienssen RA (2001) Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes Dev 15: 591-602.
-
(2001)
Genes Dev
, vol.15
, pp. 591-602
-
-
Singer, T.1
Yordan, C.2
Martienssen, R.A.3
-
29
-
-
33947303168
-
Transposable elements and the epigenetic regulation of the genome
-
Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 272-285
-
-
Slotkin, R.K.1
Martienssen, R.2
-
30
-
-
59349118366
-
Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
-
Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472.
-
(2009)
Cell
, vol.136
, pp. 461-472
-
-
Slotkin, R.K.1
Vaughn, M.2
Borges, F.3
Tanurdzić, M.4
Becker, J.D.5
Feijó, J.A.6
Martienssen, R.A.7
-
31
-
-
43749098985
-
DNA methylation landscapes: Provocative insights from epigenomics
-
Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
32
-
-
34248195006
-
CpG methylation is targeted to transcription units in an invertebrate genome
-
Suzuki MM, Kerr AR, De Sousa D, Bird A (2007) CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 17: 625-631.
-
(2007)
Genome Res
, vol.17
, pp. 625-631
-
-
Suzuki, M.M.1
Kerr, A.R.2
de Sousa, D.3
Bird, A.4
-
33
-
-
70349276670
-
Bursts of retrotransposition reproduced in Arabidopsis
-
Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461: 423-426.
-
(2009)
Nature
, vol.461
, pp. 423-426
-
-
Tsukahara, S.1
Kobayashi, A.2
Kawabe, A.3
Mathieu, O.4
Miura, A.5
Kakutani, T.6
-
34
-
-
0031027468
-
Methylation of genomes and genes at the invertebrate-vertebrate boundary
-
Tweedie S, Charlton J, Clark V, Bird A (1997) Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol Cell Biol 17: 1469-1475.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 1469-1475
-
-
Tweedie, S.1
Charlton, J.2
Clark, V.3
Bird, A.4
-
35
-
-
0031662164
-
Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
-
Walsh CP, Chaillet JR, Bestor TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20: 116-117.
-
(1998)
Nat Genet
, vol.20
, pp. 116-117
-
-
Walsh, C.P.1
Chaillet, J.R.2
Bestor, T.H.3
-
36
-
-
0030840954
-
Cytosine methylation and the ecology of intragenomic parasites
-
Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335-340.
-
(1997)
Trends Genet
, vol.13
, pp. 335-340
-
-
Yoder, J.A.1
Walsh, C.P.2
Bestor, T.H.3
-
37
-
-
33748629119
-
Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis
-
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.
-
(2006)
Cell
, vol.126
, pp. 1189-1201
-
-
Zhang, X.1
Yazaki, J.2
Sundaresan, A.3
Cokus, S.4
Chan, S.W.5
Chen, H.6
Henderson, I.R.7
Shinn, P.8
Pellegrini, M.9
Jacobsen, S.E.10
Ecker, J.R.11
-
38
-
-
73349104113
-
Active DNA demethylation mediated by DNA glycosylases
-
Zhu JK (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43: 143-166.
-
(2009)
Annu Rev Genet
, vol.43
, pp. 143-166
-
-
Zhu, J.K.1
-
39
-
-
55549141877
-
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
-
Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S (2008) Histone H2A. Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456: 125-129.
-
(2008)
Nature
, vol.456
, pp. 125-129
-
-
Zilberman, D.1
Coleman-Derr, D.2
Ballinger, T.3
Henikoff, S.4
-
40
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
-
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69.
-
(2007)
Nat Genet
, vol.39
, pp. 61-69
-
-
Zilberman, D.1
Gehring, M.2
Tran, R.K.3
Ballinger, T.4
Henikoff, S.5
|