-
1
-
-
78751580443
-
Differentiation of epigenetic modifications between transposons and genes
-
[1] Saze, H., Kakutani, T., Differentiation of epigenetic modifications between transposons and genes. Curr. Opin. Plant Biol. 14 (2011), 81–87.
-
(2011)
Curr. Opin. Plant Biol.
, vol.14
, pp. 81-87
-
-
Saze, H.1
Kakutani, T.2
-
2
-
-
0037154275
-
Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude
-
[2] Fu, H., Zheng, Z., Dooner, H.K., Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. U. S. A. 99 (2002), 1082–1087.
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 1082-1087
-
-
Fu, H.1
Zheng, Z.2
Dooner, H.K.3
-
3
-
-
36249023071
-
A unified classification system for eukaryotic transposable elements
-
[3] Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., Schulman, A.H., A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8 (2007), 973–982.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 973-982
-
-
Wicker, T.1
Sabot, F.2
Hua-Van, A.3
Bennetzen, J.L.4
Capy, P.5
Chalhoub, B.6
Flavell, A.7
Leroy, P.8
Morgante, M.9
Panaud, O.10
Paux, E.11
SanMiguel, P.12
Schulman, A.H.13
-
4
-
-
84872051484
-
Spreading of heterochromatin is limited to specific families of maize retrotransposons
-
e1003127
-
[4] Eichten, S.R., Ellis, N.A., Makarevitch, I., Yeh, C.T., Gent, J.I., Guo, L., McGinnis, K.M., Zhang, X., Schnable, P.S., Vaughn, M.W., Dawe, R.K., Springer, N.M., Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genet., 8, 2012, e1003127.
-
(2012)
PLoS Genet.
, vol.8
-
-
Eichten, S.R.1
Ellis, N.A.2
Makarevitch, I.3
Yeh, C.T.4
Gent, J.I.5
Guo, L.6
McGinnis, K.M.7
Zhang, X.8
Schnable, P.S.9
Vaughn, M.W.10
Dawe, R.K.11
Springer, N.M.12
-
5
-
-
84875741680
-
The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
-
[5] Zemach, A., Kim, M.Y., Hsieh, P.H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., Harmer, S.L., Zilberman, D., The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153 (2013), 193–205.
-
(2013)
Cell
, vol.153
, pp. 193-205
-
-
Zemach, A.1
Kim, M.Y.2
Hsieh, P.H.3
Coleman-Derr, D.4
Eshed-Williams, L.5
Thao, K.6
Harmer, S.L.7
Zilberman, D.8
-
6
-
-
84922208635
-
Genetic perturbation of the maize methylome
-
[6] Li, Q., Eichten, S.R., Hermanson, P.J., Zaunbrecher, V.M., Song, J., Wendt, J., Rosenbaum, H., Madzima, T.F., Sloan, A.E., Huang, J., Burgess, D.L., Richmond, T.A., McGinnis, K.M., Meeley, R.B., Danilevskaya, O.N., Vaughn, M.W., Kaeppler, S.M., Jeddeloh, J.A., Springer, N.M., Genetic perturbation of the maize methylome. Plant Cell 26 (2014), 4602–4616.
-
(2014)
Plant Cell
, vol.26
, pp. 4602-4616
-
-
Li, Q.1
Eichten, S.R.2
Hermanson, P.J.3
Zaunbrecher, V.M.4
Song, J.5
Wendt, J.6
Rosenbaum, H.7
Madzima, T.F.8
Sloan, A.E.9
Huang, J.10
Burgess, D.L.11
Richmond, T.A.12
McGinnis, K.M.13
Meeley, R.B.14
Danilevskaya, O.N.15
Vaughn, M.W.16
Kaeppler, S.M.17
Jeddeloh, J.A.18
Springer, N.M.19
-
7
-
-
0013630297
-
Nested retrotransposons in the intergenic regions of the maize genome
-
[7] SanMiguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., Avramova, Z., Bennetzen, J.L., Nested retrotransposons in the intergenic regions of the maize genome. Science 274 (1996), 765–768.
-
(1996)
Science
, vol.274
, pp. 765-768
-
-
SanMiguel, P.1
Tikhonov, A.2
Jin, Y.K.3
Motchoulskaia, N.4
Zakharov, D.5
Melake-Berhan, A.6
Springer, P.S.7
Edwards, K.J.8
Lee, M.9
Avramova, Z.10
Bennetzen, J.L.11
-
8
-
-
84986194435
-
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
-
[8] Willing, E., Rawat, V., Mandáková, T., Maumus, F., James, G.V., Nordström, K.J.V., Becker, C., Warthmann, N., Chica, C., Szarzynska, B., Zytnicki, M., Albani, M.C., Kiefer, C., Bergonzi, S., Castaings, L., Mateos, J.L., Berns, M.C., Bujdoso, N., Piofczyk, T., de Lorenzo, L., Barrero-Sicilia, C., Mateos, I., Piednoël, M., Hagmann, J., Chen-Min-Tao, R., Iglesias-Fernández, R., Schuster, S.C., Alonso-Blanco, C., Roudier, F., Carbonero, P., Paz-Ares, J., Davis, S.J., Pecinka, A., Quesneville, H., Colot, V., Lysak, M.A., Weigel, D., Coupland, G., Schneeberger, K., Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat. Plants, 1, 2015, 14023.
-
(2015)
Nat. Plants
, vol.1
, pp. 14023
-
-
Willing, E.1
Rawat, V.2
Mandáková, T.3
Maumus, F.4
James, G.V.5
Nordström, K.J.V.6
Becker, C.7
Warthmann, N.8
Chica, C.9
Szarzynska, B.10
Zytnicki, M.11
Albani, M.C.12
Kiefer, C.13
Bergonzi, S.14
Castaings, L.15
Mateos, J.L.16
Berns, M.C.17
Bujdoso, N.18
Piofczyk, T.19
de Lorenzo, L.20
Barrero-Sicilia, C.21
Mateos, I.22
Piednoël, M.23
Hagmann, J.24
Chen-Min-Tao, R.25
Iglesias-Fernández, R.26
Schuster, S.C.27
Alonso-Blanco, C.28
Roudier, F.29
Carbonero, P.30
Paz-Ares, J.31
Davis, S.J.32
Pecinka, A.33
Quesneville, H.34
Colot, V.35
Lysak, M.A.36
Weigel, D.37
Coupland, G.38
Schneeberger, K.39
more..
-
9
-
-
77952670452
-
Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs
-
[9] Lerat, E., Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity (Edinb) 104 (2010), 520–533.
-
(2010)
Heredity (Edinb)
, vol.104
, pp. 520-533
-
-
Lerat, E.1
-
10
-
-
0034649566
-
Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
[10] Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 2000, 796–815.
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
11
-
-
84892538565
-
Transposable elements: powerful contributors to angiosperm evolution and diversity
-
[11] Oliver, K.R., McComb, J.A., Greene, W.K., Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol. Evol. 5 (2013), 1886–1901.
-
(2013)
Genome Biol. Evol.
, vol.5
, pp. 1886-1901
-
-
Oliver, K.R.1
McComb, J.A.2
Greene, W.K.3
-
12
-
-
70450202132
-
The B73 maize genome: complexity, diversity, and dynamics
-
[12] Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T.A., Minx, P., Reily, A.D., Courtney, L., Kruchowski, S.S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S.M., Belter, E., Du, F., Kim, K., Abbott, R.M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S.M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M.J., McMahan, L., Van Buren, P., Vaughn, M.W., Ying, K., Yeh, C.T., Emrich, S.J., Jia, Y., Kalyanaraman, A., Hsia, A.P., Barbazuk, W.B., Baucom, R.S., Brutnell, T.P., Carpita, N.C., Chaparro, C., Chia, J.M., Deragon, J.M., Estill, J.C., Fu, Y., Jeddeloh, J.A., Han, Y., Lee, H., Li, P., Lisch, D.R., Liu, S., Liu, Z., Nagel, D.H., McCann, M.C., SanMiguel, P., Myers, A.M., Nettleton, D., Nguyen, J., Penning, B.W., Ponnala, L., Schneider, K.L., Schwartz, D.C., Sharma, A., Soderlund, C., Springer, N.M., Sun, Q., Wang, H., Waterman, M., Westerman, R., Wolfgruber, T.K., Yang, L., Yu, Y., Zhang, L., Zhou, S., Zhu, Q., Bennetzen, J.L., Dawe, R.K., Jiang, J., Jiang, N., Presting, G.G., Wessler, S.R., Aluru, S., Martienssen, R.A., Clifton, S.W., McCombie, W.R., Wing, R.A., Wilson, R.K., The B73 maize genome: complexity, diversity, and dynamics. Science 326 (2009), 1112–1115.
-
(2009)
Science
, vol.326
, pp. 1112-1115
-
-
Schnable, P.S.1
Ware, D.2
Fulton, R.S.3
Stein, J.C.4
Wei, F.5
Pasternak, S.6
Liang, C.7
Zhang, J.8
Fulton, L.9
Graves, T.A.10
Minx, P.11
Reily, A.D.12
Courtney, L.13
Kruchowski, S.S.14
Tomlinson, C.15
Strong, C.16
Delehaunty, K.17
Fronick, C.18
Courtney, B.19
Rock, S.M.20
Belter, E.21
Du, F.22
Kim, K.23
Abbott, R.M.24
Cotton, M.25
Levy, A.26
Marchetto, P.27
Ochoa, K.28
Jackson, S.M.29
Gillam, B.30
Chen, W.31
Yan, L.32
Higginbotham, J.33
Cardenas, M.34
Waligorski, J.35
Applebaum, E.36
Phelps, L.37
Falcone, J.38
Kanchi, K.39
Thane, T.40
Scimone, A.41
Thane, N.42
Henke, J.43
Wang, T.44
Ruppert, J.45
Shah, N.46
Rotter, K.47
Hodges, J.48
Ingenthron, E.49
Cordes, M.50
Kohlberg, S.51
Sgro, J.52
Delgado, B.53
Mead, K.54
Chinwalla, A.55
Leonard, S.56
Crouse, K.57
Collura, K.58
Kudrna, D.59
Currie, J.60
He, R.61
Angelova, A.62
Rajasekar, S.63
Mueller, T.64
Lomeli, R.65
Scara, G.66
Ko, A.67
Delaney, K.68
Wissotski, M.69
Lopez, G.70
Campos, D.71
Braidotti, M.72
Ashley, E.73
Golser, W.74
Kim, H.75
Lee, S.76
Lin, J.77
Dujmic, Z.78
Kim, W.79
Talag, J.80
Zuccolo, A.81
Fan, C.82
Sebastian, A.83
Kramer, M.84
Spiegel, L.85
Nascimento, L.86
Zutavern, T.87
Miller, B.88
Ambroise, C.89
Muller, S.90
Spooner, W.91
Narechania, A.92
Ren, L.93
Wei, S.94
Kumari, S.95
Faga, B.96
Levy, M.J.97
McMahan, L.98
Van Buren, P.99
Vaughn, M.W.100
Ying, K.101
Yeh, C.T.102
Emrich, S.J.103
Jia, Y.104
Kalyanaraman, A.105
Hsia, A.P.106
Barbazuk, W.B.107
Baucom, R.S.108
Brutnell, T.P.109
Carpita, N.C.110
Chaparro, C.111
Chia, J.M.112
Deragon, J.M.113
Estill, J.C.114
Fu, Y.115
Jeddeloh, J.A.116
Han, Y.117
Lee, H.118
Li, P.119
Lisch, D.R.120
Liu, S.121
Liu, Z.122
Nagel, D.H.123
McCann, M.C.124
SanMiguel, P.125
Myers, A.M.126
Nettleton, D.127
Nguyen, J.128
Penning, B.W.129
Ponnala, L.130
Schneider, K.L.131
Schwartz, D.C.132
Sharma, A.133
Soderlund, C.134
Springer, N.M.135
Sun, Q.136
Wang, H.137
Waterman, M.138
Westerman, R.139
Wolfgruber, T.K.140
Yang, L.141
Yu, Y.142
Zhang, L.143
Zhou, S.144
Zhu, Q.145
Bennetzen, J.L.146
Dawe, R.K.147
Jiang, J.148
Jiang, N.149
Presting, G.G.150
Wessler, S.R.151
Aluru, S.152
Martienssen, R.A.153
Clifton, S.W.154
McCombie, W.R.155
Wing, R.A.156
Wilson, R.K.157
more..
-
13
-
-
74549221016
-
Genome sequence of the palaeopolyploid soybean
-
[13] Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J., Xu, D., Hellsten, U., May, G.D., Yu, Y., Sakurai, T., Umezawa, T., Bhattacharyya, M.K., Sandhu, D., Valliyodan, B., Lindquist, E., Peto, M., Grant, D., Shu, S., Goodstein, D., Barry, K., Futrell-Griggs, M., Abernathy, B., Du, J., Tian, Z., Zhu, L., Gill, N., Joshi, T., Libault, M., Sethuraman, A., Zhang, X.C., Shinozaki, K., Nguyen, H.T., Wing, R.A., Cregan, P., Specht, J., Grimwood, J., Rokhsar, D., Stacey, G., Shoemaker, R.C., Jackson, S.A., Genome sequence of the palaeopolyploid soybean. Nature 463 (2010), 178–183.
-
(2010)
Nature
, vol.463
, pp. 178-183
-
-
Schmutz, J.1
Cannon, S.B.2
Schlueter, J.3
Ma, J.4
Mitros, T.5
Nelson, W.6
Hyten, D.L.7
Song, Q.8
Thelen, J.J.9
Cheng, J.10
Xu, D.11
Hellsten, U.12
May, G.D.13
Yu, Y.14
Sakurai, T.15
Umezawa, T.16
Bhattacharyya, M.K.17
Sandhu, D.18
Valliyodan, B.19
Lindquist, E.20
Peto, M.21
Grant, D.22
Shu, S.23
Goodstein, D.24
Barry, K.25
Futrell-Griggs, M.26
Abernathy, B.27
Du, J.28
Tian, Z.29
Zhu, L.30
Gill, N.31
Joshi, T.32
Libault, M.33
Sethuraman, A.34
Zhang, X.C.35
Shinozaki, K.36
Nguyen, H.T.37
Wing, R.A.38
Cregan, P.39
Specht, J.40
Grimwood, J.41
Rokhsar, D.42
Stacey, G.43
Shoemaker, R.C.44
Jackson, S.A.45
more..
-
14
-
-
73649140264
-
Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome
-
e1000732
-
[14] Baucom, R.S., Estill, J.C., Chaparro, C., Upshaw, N., Jogi, A., Deragon, J.M., Westerman, R.P., Sanmiguel, P.J., Bennetzen, J.L., Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet., 5, 2009, e1000732.
-
(2009)
PLoS Genet.
, vol.5
-
-
Baucom, R.S.1
Estill, J.C.2
Chaparro, C.3
Upshaw, N.4
Jogi, A.5
Deragon, J.M.6
Westerman, R.P.7
Sanmiguel, P.J.8
Bennetzen, J.L.9
-
15
-
-
84947967022
-
RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome
-
[15] Li, Q., Gent, J.I., Zynda, G., Song, J., Makarevitch, I., Hirsch, C.D., Hirsch, C.N., Dawe, R.K., Madzima, T.F., McGinnis, K.M., Lisch, D., Schmitz, R.J., Vaughn, M.W., Springer, N.M., RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc. Natl. Acad. Sci. U. S. A., 2015.
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
-
-
Li, Q.1
Gent, J.I.2
Zynda, G.3
Song, J.4
Makarevitch, I.5
Hirsch, C.D.6
Hirsch, C.N.7
Dawe, R.K.8
Madzima, T.F.9
McGinnis, K.M.10
Lisch, D.11
Schmitz, R.J.12
Vaughn, M.W.13
Springer, N.M.14
-
16
-
-
84883130171
-
Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin
-
[16] Saze, H., Kitayama, J., Takashima, K., Miura, S., Harukawa, Y., Ito, T., Kakutani, T., Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin. Nat. Commun., 4, 2013, 2301.
-
(2013)
Nat. Commun.
, vol.4
, pp. 2301
-
-
Saze, H.1
Kitayama, J.2
Takashima, K.3
Miura, S.4
Harukawa, Y.5
Ito, T.6
Kakutani, T.7
-
17
-
-
84905970505
-
Genomic distribution of H3K9me2 and DNA methylation in a maize genome
-
e105267
-
[17] West, P.T., Li, Q., Ji, L., Eichten, S.R., Song, J., Vaughn, M.W., Schmitz, R.J., Springer, N.M., Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS One, 9, 2014, e105267.
-
(2014)
PLoS One
, vol.9
-
-
West, P.T.1
Li, Q.2
Ji, L.3
Eichten, S.R.4
Song, J.5
Vaughn, M.W.6
Schmitz, R.J.7
Springer, N.M.8
-
18
-
-
84878420758
-
The Norway spruce genome sequence and conifer genome evolution
-
[18] Nystedt, B., Street, N.R., Wetterbom, A., Zuccolo, A., Lin, Y.C., Scofield, D.G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstrand, M., Gramzow, L., Holmberg, K., Hallman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Kaller, M., Luthman, J., Lysholm, F., Niittyla, T., Olson, A., Rilakovic, N., Ritland, C., Rossello, J.A., Sena, J., Svensson, T., Talavera-Lopez, C., Theissen, G., Tuominen, H., Vanneste, K., Wu, Z.Q., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R., Bohlmann, J., Bousquet, J., Garcia Gil, R., Hvidsten, T.R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Thompson, S.L., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P.K., Lundeberg, J., Jansson, S., The Norway spruce genome sequence and conifer genome evolution. Nature 497 (2013), 579–584.
-
(2013)
Nature
, vol.497
, pp. 579-584
-
-
Nystedt, B.1
Street, N.R.2
Wetterbom, A.3
Zuccolo, A.4
Lin, Y.C.5
Scofield, D.G.6
Vezzi, F.7
Delhomme, N.8
Giacomello, S.9
Alexeyenko, A.10
Vicedomini, R.11
Sahlin, K.12
Sherwood, E.13
Elfstrand, M.14
Gramzow, L.15
Holmberg, K.16
Hallman, J.17
Keech, O.18
Klasson, L.19
Koriabine, M.20
Kucukoglu, M.21
Kaller, M.22
Luthman, J.23
Lysholm, F.24
Niittyla, T.25
Olson, A.26
Rilakovic, N.27
Ritland, C.28
Rossello, J.A.29
Sena, J.30
Svensson, T.31
Talavera-Lopez, C.32
Theissen, G.33
Tuominen, H.34
Vanneste, K.35
Wu, Z.Q.36
Zhang, B.37
Zerbe, P.38
Arvestad, L.39
Bhalerao, R.40
Bohlmann, J.41
Bousquet, J.42
Garcia Gil, R.43
Hvidsten, T.R.44
de Jong, P.45
MacKay, J.46
Morgante, M.47
Ritland, K.48
Sundberg, B.49
Thompson, S.L.50
Van de Peer, Y.51
Andersson, B.52
Nilsson, O.53
Ingvarsson, P.K.54
Lundeberg, J.55
Jansson, S.56
more..
-
19
-
-
84978008054
-
Evolutionary patterns of genic DNA methylation vary across land plants
-
[19] Takuno, S., Ran, J., Gaut, B.S., Evolutionary patterns of genic DNA methylation vary across land plants. Nat. Plants, 2, 2016, 15222.
-
(2016)
Nat. Plants
, vol.2
, pp. 15222
-
-
Takuno, S.1
Ran, J.2
Gaut, B.S.3
-
20
-
-
12544254467
-
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
-
[20] Tran, R.K., Henikoff, J.G., Zilberman, D., Ditt, R.F., Jacobsen, S.E., Henikoff, S., DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15 (2005), 154–159.
-
(2005)
Curr. Biol.
, vol.15
, pp. 154-159
-
-
Tran, R.K.1
Henikoff, J.G.2
Zilberman, D.3
Ditt, R.F.4
Jacobsen, S.E.5
Henikoff, S.6
-
21
-
-
33748629119
-
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
-
[21] Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., Ecker, J.R., Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126 (2006), 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
-
22
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
-
[22] Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T., Henikoff, S., Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39 (2007), 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
-
23
-
-
84992127120
-
On the Origin and Evolutionary Consequences of Gene Body DNA Methylation
-
[23] Bewick, A.J., Ji, L., Niederhuth, C.E., Willing, E., Hofmeisterb, B.T., Shia, X., Wang, L., Lua, Z., Rohra, N.A., Hartwig, B., Kiefer, C., Deal, R.B., Schmutz, J., Grimwood, J., Stroud, H., Jacobsen, S.E., Schneeberger, K., Zhang, X., Schmitz, R.J., On the Origin and Evolutionary Consequences of Gene Body DNA Methylation. Biorxiv, 2016, 10.1101/045542.
-
(2016)
Biorxiv
-
-
Bewick, A.J.1
Ji, L.2
Niederhuth, C.E.3
Willing, E.4
Hofmeisterb, B.T.5
Shia, X.6
Wang, L.7
Lua, Z.8
Rohra, N.A.9
Hartwig, B.10
Kiefer, C.11
Deal, R.B.12
Schmutz, J.13
Grimwood, J.14
Stroud, H.15
Jacobsen, S.E.16
Schneeberger, K.17
Zhang, X.18
Schmitz, R.J.19
-
24
-
-
85006792035
-
Widespread natural variation of DNA methylation within angiosperms
-
[24] Niederhuth, C.E., Bewick, A.J., Ji, L., Alabady, M.S., Kim, K.D., Page, J.T., Li, Q., Rohr, N.A., Rambani, A., Burke, J.M., Udall, J.A., Egesi, C., Schmutz, J., Grimwood, J., Jackson, S.A., Springer, N.M., Schmitz, R.J., Widespread natural variation of DNA methylation within angiosperms. Biorxiv, 2016, 10.1101/045880.
-
(2016)
Biorxiv
-
-
Niederhuth, C.E.1
Bewick, A.J.2
Ji, L.3
Alabady, M.S.4
Kim, K.D.5
Page, J.T.6
Li, Q.7
Rohr, N.A.8
Rambani, A.9
Burke, J.M.10
Udall, J.A.11
Egesi, C.12
Schmutz, J.13
Grimwood, J.14
Jackson, S.A.15
Springer, N.M.16
Schmitz, R.J.17
-
25
-
-
84939139239
-
A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean
-
[25] Kim, K.D., El Baidouri, M., Abernathy, B., Iwata-Otsubo, A., Chavarro, C., Gonzales, M., Libault, M., Grimwood, J., Jackson, S.A., A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean. Plant Physiol. 168 (2015), 1433–1447.
-
(2015)
Plant Physiol.
, vol.168
, pp. 1433-1447
-
-
Kim, K.D.1
El Baidouri, M.2
Abernathy, B.3
Iwata-Otsubo, A.4
Chavarro, C.5
Gonzales, M.6
Libault, M.7
Grimwood, J.8
Jackson, S.A.9
-
26
-
-
84930216292
-
Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana
-
[26] Le, T.N., Miyazaki, Y., Takuno, S., Saze, H., Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana. Nucleic Acids Res. 43 (2015), 3911–3921.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 3911-3921
-
-
Le, T.N.1
Miyazaki, Y.2
Takuno, S.3
Saze, H.4
-
27
-
-
84889855598
-
Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat
-
(209–2229–13-209)
-
[27] Khan, A.R., Enjalbert, J., Marsollier, A.C., Rousselet, A., Goldringer, I., Vitte, C., Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat. BMC Plant Biol., 13, 2013 (209–2229–13-209).
-
(2013)
BMC Plant Biol.
, vol.13
-
-
Khan, A.R.1
Enjalbert, J.2
Marsollier, A.C.3
Rousselet, A.4
Goldringer, I.5
Vitte, C.6
-
28
-
-
84873027817
-
Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes
-
(71–2164–14-71)
-
[28] Han, Y., Qin, S., Wessler, S.R., Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes. BMC Genomics, 14, 2013 (71–2164–14-71).
-
(2013)
BMC Genomics
, vol.14
-
-
Han, Y.1
Qin, S.2
Wessler, S.R.3
-
29
-
-
40449136688
-
Chromodomains direct integration of retrotransposons to heterochromatin
-
[29] Gao, X., Hou, Y., Ebina, H., Levin, H.L., Voytas, D.F., Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 18 (2008), 359–369.
-
(2008)
Genome Res.
, vol.18
, pp. 359-369
-
-
Gao, X.1
Hou, Y.2
Ebina, H.3
Levin, H.L.4
Voytas, D.F.5
-
30
-
-
84929501317
-
Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration
-
[30] Bridier-Nahmias, A., Tchalikian-Cosson, A., Baller, J.A., Menouni, R., Fayol, H., Flores, A., Saib, A., Werner, M., Voytas, D.F., Lesage, P., Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration. Science 348 (2015), 585–588.
-
(2015)
Science
, vol.348
, pp. 585-588
-
-
Bridier-Nahmias, A.1
Tchalikian-Cosson, A.2
Baller, J.A.3
Menouni, R.4
Fayol, H.5
Flores, A.6
Saib, A.7
Werner, M.8
Voytas, D.F.9
Lesage, P.10
-
31
-
-
0025576260
-
Insertion of Mu1 elements in the first intron of the Adh1-S gene of maize results in novel RNA processing events
-
[31] Luehrsen, K.R., Walbot, V., Insertion of Mu1 elements in the first intron of the Adh1-S gene of maize results in novel RNA processing events. Plant Cell 2 (1990), 1225–1238.
-
(1990)
Plant Cell
, vol.2
, pp. 1225-1238
-
-
Luehrsen, K.R.1
Walbot, V.2
-
32
-
-
84866182526
-
Transposon insertion in a cinnamyl alcohol dehydrogenase gene is responsible for a brown midrib1 mutation in maize
-
[32] Chen, W., VanOpdorp, N., Fitzl, D., Tewari, J., Friedemann, P., Greene, T., Thompson, S., Kumpatla, S., Zheng, P., Transposon insertion in a cinnamyl alcohol dehydrogenase gene is responsible for a brown midrib1 mutation in maize. Plant Mol. Biol. 80 (2012), 289–297.
-
(2012)
Plant Mol. Biol.
, vol.80
, pp. 289-297
-
-
Chen, W.1
VanOpdorp, N.2
Fitzl, D.3
Tewari, J.4
Friedemann, P.5
Greene, T.6
Thompson, S.7
Kumpatla, S.8
Zheng, P.9
-
33
-
-
0034872980
-
Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation
-
[33] Papa, C.M., Springer, N.M., Muszynski, M.G., Meeley, R., Kaeppler, S.M., Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13 (2001), 1919–1928.
-
(2001)
Plant Cell
, vol.13
, pp. 1919-1928
-
-
Papa, C.M.1
Springer, N.M.2
Muszynski, M.G.3
Meeley, R.4
Kaeppler, S.M.5
-
34
-
-
0026885574
-
Alternative splicing induced by insertion of retrotransposons into the maize waxy gene
-
[34] Varagona, M.J., Purugganan, M., Wessler, S.R., Alternative splicing induced by insertion of retrotransposons into the maize waxy gene. Plant Cell 4 (1992), 811–820.
-
(1992)
Plant Cell
, vol.4
, pp. 811-820
-
-
Varagona, M.J.1
Purugganan, M.2
Wessler, S.R.3
-
35
-
-
84942540296
-
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
-
[35] Ong-Abdullah, M., Ordway, J.M., Jiang, N., Ooi, S.E., Kok, S.Y., Sarpan, N., Azimi, N., Hashim, A.T., Ishak, Z., Rosli, S.K., Malike, F.A., Bakar, N.A., Marjuni, M., Abdullah, N., Yaakub, Z., Amiruddin, M.D., Nookiah, R., Singh, R., Low, E.T., Chan, K.L., Azizi, N., Smith, S.W., Bacher, B., Budiman, M.A., Van Brunt, A., Wischmeyer, C., Beil, M., Hogan, M., Lakey, N., Lim, C.C., Arulandoo, X., Wong, C.K., Choo, C.N., Wong, W.C., Kwan, Y.Y., Alwee, S.S., Sambanthamurthi, R., Martienssen, R.A., Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525 (2015), 533–537.
-
(2015)
Nature
, vol.525
, pp. 533-537
-
-
Ong-Abdullah, M.1
Ordway, J.M.2
Jiang, N.3
Ooi, S.E.4
Kok, S.Y.5
Sarpan, N.6
Azimi, N.7
Hashim, A.T.8
Ishak, Z.9
Rosli, S.K.10
Malike, F.A.11
Bakar, N.A.12
Marjuni, M.13
Abdullah, N.14
Yaakub, Z.15
Amiruddin, M.D.16
Nookiah, R.17
Singh, R.18
Low, E.T.19
Chan, K.L.20
Azizi, N.21
Smith, S.W.22
Bacher, B.23
Budiman, M.A.24
Van Brunt, A.25
Wischmeyer, C.26
Beil, M.27
Hogan, M.28
Lakey, N.29
Lim, C.C.30
Arulandoo, X.31
Wong, C.K.32
Choo, C.N.33
Wong, W.C.34
Kwan, Y.Y.35
Alwee, S.S.36
Sambanthamurthi, R.37
Martienssen, R.A.38
more..
-
36
-
-
84941931731
-
Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats
-
e111959
-
[36] Zabala, G., Vodkin, L.O., Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS One, 9, 2014, e111959.
-
(2014)
PLoS One
, vol.9
-
-
Zabala, G.1
Vodkin, L.O.2
-
37
-
-
84884695071
-
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
-
[37] Regulski, M., Lu, Z., Kendall, J., Donoghue, M.T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W.R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R.A., The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res. 23 (2013), 1651–1662.
-
(2013)
Genome Res.
, vol.23
, pp. 1651-1662
-
-
Regulski, M.1
Lu, Z.2
Kendall, J.3
Donoghue, M.T.4
Reinders, J.5
Llaca, V.6
Deschamps, S.7
Smith, A.8
Levy, D.9
McCombie, W.R.10
Tingey, S.11
Rafalski, A.12
Hicks, J.13
Ware, D.14
Martienssen, R.A.15
-
38
-
-
33745394130
-
Alternative splicing and RNA selection pressure–evolutionary consequences for eukaryotic genomes
-
[38] Xing, Y., Lee, C., Alternative splicing and RNA selection pressure–evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 7 (2006), 499–509.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 499-509
-
-
Xing, Y.1
Lee, C.2
-
39
-
-
84922237555
-
Transposable element-driven transcript diversification and its relevance to genetic disorders
-
[39] Ayarpadikannan, S., Lee, H.E., Han, K., Kim, H.S., Transposable element-driven transcript diversification and its relevance to genetic disorders. Gene 558 (2015), 187–194.
-
(2015)
Gene
, vol.558
, pp. 187-194
-
-
Ayarpadikannan, S.1
Lee, H.E.2
Han, K.3
Kim, H.S.4
-
40
-
-
0036192047
-
Maize Mu transposons are targeted to the 5' untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome
-
[40] Dietrich, C.R., Cui, F., Packila, M.L., Li, J., Ashlock, D.A., Nikolau, B.J., Schnable, P.S., Maize Mu transposons are targeted to the 5' untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome. Genetics 160 (2002), 697–716.
-
(2002)
Genetics
, vol.160
, pp. 697-716
-
-
Dietrich, C.R.1
Cui, F.2
Packila, M.L.3
Li, J.4
Ashlock, D.A.5
Nikolau, B.J.6
Schnable, P.S.7
-
41
-
-
84884335747
-
RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1
-
[41] Wang, X., Duan, C.G., Tang, K., Wang, B., Zhang, H., Lei, M., Lu, K., Mangrauthia, S.K., Wang, P., Zhu, G., Zhao, Y., Zhu, J.K., RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), 15467–15472.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 15467-15472
-
-
Wang, X.1
Duan, C.G.2
Tang, K.3
Wang, B.4
Zhang, H.5
Lei, M.6
Lu, K.7
Mangrauthia, S.K.8
Wang, P.9
Zhu, G.10
Zhao, Y.11
Zhu, J.K.12
-
42
-
-
33847133819
-
EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels
-
[42] Eulgem, T., Tsuchiya, T., Wang, X.J., Beasley, B., Cuzick, A., Tor, M., Zhu, T., McDowell, J.M., Holub, E., Dangl, J.L., EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels. Plant J. 49 (2007), 829–839.
-
(2007)
Plant J.
, vol.49
, pp. 829-839
-
-
Eulgem, T.1
Tsuchiya, T.2
Wang, X.J.3
Beasley, B.4
Cuzick, A.5
Tor, M.6
Zhu, T.7
McDowell, J.M.8
Holub, E.9
Dangl, J.L.10
-
43
-
-
84883796284
-
An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication
-
[43] Tsuchiya, T., Eulgem, T., An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), E3535–E3543.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. E3535-E3543
-
-
Tsuchiya, T.1
Eulgem, T.2
-
44
-
-
84902531824
-
The PHD-finger module of the Arabidopsis thaliana defense regulator EDM2 can recognize triply modified histone H3 peptides
-
e29202
-
[44] Tsuchiya, T., Eulgem, T., The PHD-finger module of the Arabidopsis thaliana defense regulator EDM2 can recognize triply modified histone H3 peptides. Plant Signal. Behav., 9, 2014, e29202.
-
(2014)
Plant Signal. Behav.
, vol.9
-
-
Tsuchiya, T.1
Eulgem, T.2
-
45
-
-
84891958894
-
Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns
-
[45] Lei, M., La, H., Lu, K., Wang, P., Miki, D., Ren, Z., Duan, C.G., Wang, X., Tang, K., Zeng, L., Yang, L., Zhang, H., Nie, W., Liu, P., Zhou, J., Liu, R., Zhong, Y., Liu, D., Zhu, J.K., Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 527–532.
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.111
, pp. 527-532
-
-
Lei, M.1
La, H.2
Lu, K.3
Wang, P.4
Miki, D.5
Ren, Z.6
Duan, C.G.7
Wang, X.8
Tang, K.9
Zeng, L.10
Yang, L.11
Zhang, H.12
Nie, W.13
Liu, P.14
Zhou, J.15
Liu, R.16
Zhong, Y.17
Liu, D.18
Zhu, J.K.19
-
46
-
-
0037301560
-
Origin of a substantial fraction of human regulatory sequences from transposable elements
-
[46] Jordan, I.K., Rogozin, I.B., Glazko, G.V., Koonin, E.V., Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19 (2003), 68–72.
-
(2003)
Trends Genet.
, vol.19
, pp. 68-72
-
-
Jordan, I.K.1
Rogozin, I.B.2
Glazko, G.V.3
Koonin, E.V.4
-
47
-
-
5044251591
-
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos
-
[47] Peaston, A.E., Evsikov, A.V., Graber, J.H., de Vries, W.N., Holbrook, A.E., Solter, D., Knowles, B.B., Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7 (2004), 597–606.
-
(2004)
Dev. Cell
, vol.7
, pp. 597-606
-
-
Peaston, A.E.1
Evsikov, A.V.2
Graber, J.H.3
de Vries, W.N.4
Holbrook, A.E.5
Solter, D.6
Knowles, B.B.7
-
48
-
-
42349096534
-
Transposable elements and the evolution of regulatory networks
-
[48] Feschotte, C., Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9 (2008), 397–405.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 397-405
-
-
Feschotte, C.1
-
49
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
[49] Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., Schroder, K., Cloonan, N., Steptoe, A.L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A.R., Suzuki, H., Hayashizaki, Y., Hume, D.A., Orlando, V., Grimmond, S.M., Carninci, P., The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41 (2009), 563–571.
-
(2009)
Nat. Genet.
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
Wani, S.4
Plessy, C.5
Irvine, K.M.6
Schroder, K.7
Cloonan, N.8
Steptoe, A.L.9
Lassmann, T.10
Waki, K.11
Hornig, N.12
Arakawa, T.13
Takahashi, H.14
Kawai, J.15
Forrest, A.R.16
Suzuki, H.17
Hayashizaki, Y.18
Hume, D.A.19
Orlando, V.20
Grimmond, S.M.21
Carninci, P.22
more..
-
50
-
-
84957535518
-
How retrotransposons shape genome regulation
-
[50] Mita, P., Boeke, J.D., How retrotransposons shape genome regulation. Curr. Opin. Genet. Dev. 37 (2016), 90–100.
-
(2016)
Curr. Opin. Genet. Dev.
, vol.37
, pp. 90-100
-
-
Mita, P.1
Boeke, J.D.2
-
51
-
-
70349847245
-
Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis
-
[51] Yamamoto, Y.Y., Yoshitsugu, T., Sakurai, T., Seki, M., Shinozaki, K., Obokata, J., Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J. 60 (2009), 350–362.
-
(2009)
Plant J.
, vol.60
, pp. 350-362
-
-
Yamamoto, Y.Y.1
Yoshitsugu, T.2
Sakurai, T.3
Seki, M.4
Shinozaki, K.5
Obokata, J.6
-
52
-
-
84907338600
-
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures
-
[52] Morton, T., Petricka, J., Corcoran, D.L., Li, S., Winter, C.M., Carda, A., Benfey, P.N., Ohler, U., Megraw, M., Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. Plant Cell 26 (2014), 2746–2760.
-
(2014)
Plant Cell
, vol.26
, pp. 2746-2760
-
-
Morton, T.1
Petricka, J.2
Corcoran, D.L.3
Li, S.4
Winter, C.M.5
Carda, A.6
Benfey, P.N.7
Ohler, U.8
Megraw, M.9
-
53
-
-
84954442637
-
Core promoter plasticity between maize tissues and genotypes contrasts with predominance of sharp transcription initiation sites
-
[53] Mejia-Guerra, M., Li, W., Galeano, N.F., Vidal Gray, M., A.I., D.J., Grotewold, E., Core promoter plasticity between maize tissues and genotypes contrasts with predominance of sharp transcription initiation sites. Plant Cell, 2015.
-
(2015)
Plant Cell
-
-
Mejia-Guerra, M.1
Li, W.2
Galeano, N.F.3
Vidal Gray, M.4
A.I., D.J.5
Grotewold, E.6
-
54
-
-
0028245837
-
Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage
-
[54] Michaud, E.J., van Vugt, M.J., Bultman, S.J., Sweet, H.O., Davisson, M.T., Woychik, R.P., Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes Dev. 8 (1994), 1463–1472.
-
(1994)
Genes Dev.
, vol.8
, pp. 1463-1472
-
-
Michaud, E.J.1
van Vugt, M.J.2
Bultman, S.J.3
Sweet, H.O.4
Davisson, M.T.5
Woychik, R.P.6
-
55
-
-
0032751471
-
Epigenetic inheritance at the agouti locus in the mouse
-
[55] Morgan, H.D., Sutherland, H.G., Martin, D.I., Whitelaw, E., Epigenetic inheritance at the agouti locus in the mouse. Nat. Genet. 23 (1999), 314–318.
-
(1999)
Nat. Genet.
, vol.23
, pp. 314-318
-
-
Morgan, H.D.1
Sutherland, H.G.2
Martin, D.I.3
Whitelaw, E.4
-
56
-
-
7444264729
-
Complex patterns of transcription at the insertion site of a retrotransposon in the mouse
-
[56] Druker, R., Bruxner, T.J., Lehrbach, N.J., Whitelaw, E., Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic Acids Res. 32 (2004), 5800–5808.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5800-5808
-
-
Druker, R.1
Bruxner, T.J.2
Lehrbach, N.J.3
Whitelaw, E.4
-
57
-
-
84860200867
-
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges
-
[57] Butelli, E., Licciardello, C., Zhang, Y., Liu, J., Mackay, S., Bailey, P., Reforgiato-Recupero, G., Martin, C., Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24 (2012), 1242–1255.
-
(2012)
Plant Cell
, vol.24
, pp. 1242-1255
-
-
Butelli, E.1
Licciardello, C.2
Zhang, Y.3
Liu, J.4
Mackay, S.5
Bailey, P.6
Reforgiato-Recupero, G.7
Martin, C.8
-
58
-
-
0026353505
-
Inactivation of Maize Transposon Mu Suppresses a Mutant Phenotype by Activating an Outward-Reading Promoter Near the End of Mu1
-
[58] Barkan, A., Martienssen, R., Inactivation of Maize Transposon Mu Suppresses a Mutant Phenotype by Activating an Outward-Reading Promoter Near the End of Mu1. PNAS 88 (1991), 3502–3506.
-
(1991)
PNAS
, vol.88
, pp. 3502-3506
-
-
Barkan, A.1
Martienssen, R.2
-
59
-
-
0035155845
-
Duplication and suppression of chloroplast protein translocation genes in maize
-
[59] Settles, A.M., Baron, A., Barkan, A., Martienssen, R.A., Duplication and suppression of chloroplast protein translocation genes in maize. Genetics 157 (2001), 349–360.
-
(2001)
Genetics
, vol.157
, pp. 349-360
-
-
Settles, A.M.1
Baron, A.2
Barkan, A.3
Martienssen, R.A.4
-
60
-
-
0026042289
-
Identification of a regulatory transposon that controls the Mutator transposable element system in maize
-
[60] Chomet, P., Lisch, D., Hardeman, K.J., Chandler, V.L., Freeling, M., Identification of a regulatory transposon that controls the Mutator transposable element system in maize. Genetics 129 (1991), 261–270.
-
(1991)
Genetics
, vol.129
, pp. 261-270
-
-
Chomet, P.1
Lisch, D.2
Hardeman, K.J.3
Chandler, V.L.4
Freeling, M.5
-
61
-
-
0031128280
-
Tam3 produces a suppressible allele of the DAG locus of Antirrhinum majus similar to Mu-suppressible alleles of maize
-
[61] Chatterjee, M., Martin, C., Tam3 produces a suppressible allele of the DAG locus of Antirrhinum majus similar to Mu-suppressible alleles of maize. Plant J. 11 (1997), 759–771.
-
(1997)
Plant J.
, vol.11
, pp. 759-771
-
-
Chatterjee, M.1
Martin, C.2
-
62
-
-
0032124749
-
A porphyrin pathway impairment is responsible for the phenotype of a dominant disease lesion mimic mutant of maize
-
[62] Hu, G., Yalpani, N., Briggs, S.P., Johal, G.S., A porphyrin pathway impairment is responsible for the phenotype of a dominant disease lesion mimic mutant of maize. Plant Cell 10 (1998), 1095–1105.
-
(1998)
Plant Cell
, vol.10
, pp. 1095-1105
-
-
Hu, G.1
Yalpani, N.2
Briggs, S.P.3
Johal, G.S.4
-
63
-
-
0037297505
-
Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize
-
[63] Cui, X., Hsia, A.P., Liu, F., Ashlock, D.A., Wise, R.P., Schnable, P.S., Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize. Genetics 163 (2003), 685–698.
-
(2003)
Genetics
, vol.163
, pp. 685-698
-
-
Cui, X.1
Hsia, A.P.2
Liu, F.3
Ashlock, D.A.4
Wise, R.P.5
Schnable, P.S.6
-
64
-
-
0141593573
-
Maize-targeted mutagenesis: A knockout resource for maize
-
[64] May, B.P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P.D., Roh, D., Pan, X., Stein, L., Freeling, M., Alexander, D., Martienssen, R., Maize-targeted mutagenesis: A knockout resource for maize. Proc. Natl. Acad. Sci. U. S. A. 100 (2003), 11541–11546.
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 11541-11546
-
-
May, B.P.1
Liu, H.2
Vollbrecht, E.3
Senior, L.4
Rabinowicz, P.D.5
Roh, D.6
Pan, X.7
Stein, L.8
Freeling, M.9
Alexander, D.10
Martienssen, R.11
-
65
-
-
0033978502
-
Mutator-suppressible alleles of rough sheath1 and liguleless3 in maize reveal multiple mechanisms for suppression
-
[65] Girard, L., Freeling, M., Mutator-suppressible alleles of rough sheath1 and liguleless3 in maize reveal multiple mechanisms for suppression. Genetics 154 (2000), 437–446.
-
(2000)
Genetics
, vol.154
, pp. 437-446
-
-
Girard, L.1
Freeling, M.2
-
66
-
-
84873507928
-
Transposable elements re-wire and fine-tune the transcriptome
-
e1003234
-
[66] Cowley, M., Oakey, R.J., Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet., 9, 2013, e1003234.
-
(2013)
PLoS Genet.
, vol.9
-
-
Cowley, M.1
Oakey, R.J.2
-
67
-
-
84871329875
-
How important are transposons for plant evolution?
-
[67] Lisch, D., How important are transposons for plant evolution?. Nat. Rev. Genet. 14 (2013), 49–61.
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 49-61
-
-
Lisch, D.1
-
68
-
-
84957899695
-
Retrotransposons as regulators of gene expression
-
[68] Elbarbary, R.A., Lucas, B.A., Maquat, L.E., Retrotransposons as regulators of gene expression. Science, 351, 2016, aac7247.
-
(2016)
Science
, vol.351
, pp. aac7247
-
-
Elbarbary, R.A.1
Lucas, B.A.2
Maquat, L.E.3
-
69
-
-
84904645254
-
Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality
-
[69] Hu, L., Li, N., Xu, C., Zhong, S., Lin, X., Yang, J., Zhou, T., Yuliang, A., Wu, Y., Chen, Y.R., Cao, X., Zemach, A., Rustgi, S., von Wettstein, D., Liu, B., Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 10642–10647.
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.111
, pp. 10642-10647
-
-
Hu, L.1
Li, N.2
Xu, C.3
Zhong, S.4
Lin, X.5
Yang, J.6
Zhou, T.7
Yuliang, A.8
Wu, Y.9
Chen, Y.R.10
Cao, X.11
Zemach, A.12
Rustgi, S.13
von Wettstein, D.14
Liu, B.15
-
70
-
-
0028090085
-
Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations
-
[70] Greene, B., Walko, R., Hake, S., Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. Genetics 138 (1994), 1275–1285.
-
(1994)
Genetics
, vol.138
, pp. 1275-1285
-
-
Greene, B.1
Walko, R.2
Hake, S.3
-
71
-
-
0028981075
-
Ectopic expression of the knox homeo box gene rough sheath1 alters cell fate in the maize leaf
-
[71] Schneeberger, R.G., Becraft, P.W., Hake, S., Freeling, M., Ectopic expression of the knox homeo box gene rough sheath1 alters cell fate in the maize leaf. Genes Dev. 9 (1995), 2292–2304.
-
(1995)
Genes Dev.
, vol.9
, pp. 2292-2304
-
-
Schneeberger, R.G.1
Becraft, P.W.2
Hake, S.3
Freeling, M.4
-
72
-
-
0033080483
-
Ectopic expression of the maize homeobox gene liguleless3 alters cell fates in the leaf
-
[72] Muehlbauer, G.J., Fowler, J.E., Girard, L., Tyers, R., Harper, L., Freeling, M., Ectopic expression of the maize homeobox gene liguleless3 alters cell fates in the leaf. Plant Physiol. 119 (1999), 651–662.
-
(1999)
Plant Physiol.
, vol.119
, pp. 651-662
-
-
Muehlbauer, G.J.1
Fowler, J.E.2
Girard, L.3
Tyers, R.4
Harper, L.5
Freeling, M.6
-
73
-
-
2342648914
-
Retrotransposon-induced mutations in grape skin color
-
[73] Kobayashi, S., Goto-Yamamoto, N., Hirochika, H., Retrotransposon-induced mutations in grape skin color. Science, 304, 2004, 982.
-
(2004)
Science
, vol.304
, pp. 982
-
-
Kobayashi, S.1
Goto-Yamamoto, N.2
Hirochika, H.3
-
74
-
-
0029166837
-
Teosinte Branched1 and the Origin of Maize: Evidence for Epistasis and the Evolution of Dominance
-
[74] Doebley, J., Stec, A., Gustus, C., Teosinte Branched1 and the Origin of Maize: Evidence for Epistasis and the Evolution of Dominance. Genetics 141 (1995), 333–346.
-
(1995)
Genetics
, vol.141
, pp. 333-346
-
-
Doebley, J.1
Stec, A.2
Gustus, C.3
-
75
-
-
80054968887
-
Identification of a functional transposon insertion in the maize domestication gene tb1
-
[75] Studer, A., Zhao, Q., Ross-Ibarra, J., Doebley, J., Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43 (2011), 1160–1163.
-
(2011)
Nat. Genet.
, vol.43
, pp. 1160-1163
-
-
Studer, A.1
Zhao, Q.2
Ross-Ibarra, J.3
Doebley, J.4
-
76
-
-
84885829511
-
CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize
-
[76] Yang, Q., Li, Z., Li, W., Ku, L., Wang, C., Ye, J., Li, K., Yang, N., Li, Y., Zhong, T., Li, J., Chen, Y., Yan, J., Yang, X., Xu, M., CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), 16969–16974.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 16969-16974
-
-
Yang, Q.1
Li, Z.2
Li, W.3
Ku, L.4
Wang, C.5
Ye, J.6
Li, K.7
Yang, N.8
Li, Y.9
Zhong, T.10
Li, J.11
Chen, Y.12
Yan, J.13
Yang, X.14
Xu, M.15
-
77
-
-
34547398400
-
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize
-
[77] Salvi, S., Sponza, G., Morgante, M., Tomes, D., Niu, X., Fengler, K.A., Meeley, R., Ananiev, E.V., Svitashev, S., Bruggemann, E., Li, B., Hainey, C.F., Radovic, S., Zaina, G., Rafalski, J.A., Tingey, S.V., Miao, G.H., Phillips, R.L., Tuberosa, R., Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc. Natl. Acad. Sci. U. S. A. 104 (2007), 11376–11381.
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 11376-11381
-
-
Salvi, S.1
Sponza, G.2
Morgante, M.3
Tomes, D.4
Niu, X.5
Fengler, K.A.6
Meeley, R.7
Ananiev, E.V.8
Svitashev, S.9
Bruggemann, E.10
Li, B.11
Hainey, C.F.12
Radovic, S.13
Zaina, G.14
Rafalski, J.A.15
Tingey, S.V.16
Miao, G.H.17
Phillips, R.L.18
Tuberosa, R.19
-
78
-
-
85044690181
-
A MITE Transposon Insertion Is Associated with Differential Methylation at the Maize Flowering Time QTL Vgt1
-
[78] Castelletti, S., Tuberosa, R., Pindo, M., Salvi, S., A MITE Transposon Insertion Is Associated with Differential Methylation at the Maize Flowering Time QTL Vgt1. G3 (Bethesda), 2014.
-
(2014)
G3 (Bethesda)
-
-
Castelletti, S.1
Tuberosa, R.2
Pindo, M.3
Salvi, S.4
-
79
-
-
68149144366
-
Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression
-
[79] Hollister, J.D., Gaut, B.S., Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19 (2009), 1419–1428.
-
(2009)
Genome Res.
, vol.19
, pp. 1419-1428
-
-
Hollister, J.D.1
Gaut, B.S.2
-
80
-
-
84903156536
-
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana
-
[80] Maumus, F., Quesneville, H., Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat. Commun., 5, 2014, 4104.
-
(2014)
Nat. Commun.
, vol.5
, pp. 4104
-
-
Maumus, F.1
Quesneville, H.2
-
81
-
-
79961001437
-
Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis
-
[81] Ahmed, I., Sarazin, A., Bowler, C., Colot, V., Quesneville, H., Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res. 39 (2011), 6919–6931.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6919-6931
-
-
Ahmed, I.1
Sarazin, A.2
Bowler, C.3
Colot, V.4
Quesneville, H.5
-
82
-
-
34547747862
-
Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1
-
[82] Saze, H., Kakutani, T., Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J. 26 (2007), 3641–3652.
-
(2007)
EMBO J.
, vol.26
, pp. 3641-3652
-
-
Saze, H.1
Kakutani, T.2
-
83
-
-
70350504436
-
A transposon-induced epigenetic change leads to sex determination in melon
-
[83] Martin, A., Troadec, C., Boualem, A., Rajab, M., Fernandez, R., Morin, H., Pitrat, M., Dogimont, C., Bendahmane, A., A transposon-induced epigenetic change leads to sex determination in melon. Nature 461 (2009), 1135–1138.
-
(2009)
Nature
, vol.461
, pp. 1135-1138
-
-
Martin, A.1
Troadec, C.2
Boualem, A.3
Rajab, M.4
Fernandez, R.5
Morin, H.6
Pitrat, M.7
Dogimont, C.8
Bendahmane, A.9
-
84
-
-
84904959077
-
Transposable Element Insertion and Epigenetic Modification Cause the Multiallelic Variation in the Expression of FAE1 in Sinapis alba
-
[84] Zeng, F., Cheng, B., Transposable Element Insertion and Epigenetic Modification Cause the Multiallelic Variation in the Expression of FAE1 in Sinapis alba. Plant Cell 26 (2014), 2648–2659.
-
(2014)
Plant Cell
, vol.26
, pp. 2648-2659
-
-
Zeng, F.1
Cheng, B.2
-
85
-
-
84949968449
-
Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat
-
e1005142
-
[85] Williams, B.P., Pignatta, D., Henikoff, S., Gehring, M., Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. PLoS Genet., 11, 2015, e1005142.
-
(2015)
PLoS Genet.
, vol.11
-
-
Williams, B.P.1
Pignatta, D.2
Henikoff, S.3
Gehring, M.4
-
86
-
-
84925379649
-
Regulatory link between DNA methylation and active demethylation in Arabidopsis
-
[86] Lei, M., Zhang, H., Julian, R., Tang, K., Xie, S., Zhu, J.K., Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), 3553–3557.
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. 3553-3557
-
-
Lei, M.1
Zhang, H.2
Julian, R.3
Tang, K.4
Xie, S.5
Zhu, J.K.6
-
87
-
-
1642515876
-
One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation
-
[87] Kinoshita, T., Miura, A., Choi, Y., Kinoshita, Y., Cao, X., Jacobsen, S.E., Fischer, R.L., Kakutani, T., One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303 (2004), 521–523.
-
(2004)
Science
, vol.303
, pp. 521-523
-
-
Kinoshita, T.1
Miura, A.2
Choi, Y.3
Kinoshita, Y.4
Cao, X.5
Jacobsen, S.E.6
Fischer, R.L.7
Kakutani, T.8
-
88
-
-
0033637356
-
The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene
-
[88] Soppe, W.J., Jacobsen, S.E., Alonso-Blanco, C., Jackson, J.P., Kakutani, T., Koornneef, M., Peeters, A.J., The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 6 (2000), 791–802.
-
(2000)
Mol. Cell
, vol.6
, pp. 791-802
-
-
Soppe, W.J.1
Jacobsen, S.E.2
Alonso-Blanco, C.3
Jackson, J.P.4
Kakutani, T.5
Koornneef, M.6
Peeters, A.J.7
-
89
-
-
33845621109
-
Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats
-
[89] Kinoshita, Y., Saze, H., Kinoshita, T., Miura, A., Soppe, W.J., Koornneef, M., Kakutani, T., Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. 49 (2007), 38–45.
-
(2007)
Plant J.
, vol.49
, pp. 38-45
-
-
Kinoshita, Y.1
Saze, H.2
Kinoshita, T.3
Miura, A.4
Soppe, W.J.5
Koornneef, M.6
Kakutani, T.7
-
90
-
-
67149086996
-
Extensive demethylation of repetitive elements during seed development underlies gene imprinting
-
[90] Gehring, M., Bubb, K.L., Henikoff, S., Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324 (2009), 1447–1451.
-
(2009)
Science
, vol.324
, pp. 1447-1451
-
-
Gehring, M.1
Bubb, K.L.2
Henikoff, S.3
-
91
-
-
67149119197
-
Genome-wide demethylation of Arabidopsis endosperm
-
[91] Hsieh, T.F., Ibarra, C.A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R.L., Zilberman, D., Genome-wide demethylation of Arabidopsis endosperm. Science 324 (2009), 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
-
92
-
-
78049414227
-
Epigenetic reprogramming in plant and animal development
-
[92] Feng, S., Jacobsen, S.E., Reik, W., Epigenetic reprogramming in plant and animal development. Science 330 (2010), 622–627.
-
(2010)
Science
, vol.330
, pp. 622-627
-
-
Feng, S.1
Jacobsen, S.E.2
Reik, W.3
-
93
-
-
84888628324
-
Genomic imprinting: insights from plants
-
[93] Gehring, M., Genomic imprinting: insights from plants. Annu. Rev. Genet. 47 (2013), 187–208.
-
(2013)
Annu. Rev. Genet.
, vol.47
, pp. 187-208
-
-
Gehring, M.1
-
94
-
-
84891701738
-
Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
-
[94] Zhang, M., Xie, S., Dong, X., Zhao, X., Zeng, B., Chen, J., Li, H., Yang, W., Zhao, H., Wang, G., Chen, Z., Sun, S., Hauck, A., Jin, W., Lai, J., Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize. Genome Res. 24 (2014), 167–176.
-
(2014)
Genome Res.
, vol.24
, pp. 167-176
-
-
Zhang, M.1
Xie, S.2
Dong, X.3
Zhao, X.4
Zeng, B.5
Chen, J.6
Li, H.7
Yang, W.8
Zhao, H.9
Wang, G.10
Chen, Z.11
Sun, S.12
Hauck, A.13
Jin, W.14
Lai, J.15
-
95
-
-
84906325490
-
Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting
-
e03198
-
[95] Pignatta, D., Erdmann, R.M., Scheer, E., Picard, C.L., Bell, G.W., Gehring, M., Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. Elife, 3, 2014, e03198.
-
(2014)
Elife
, vol.3
-
-
Pignatta, D.1
Erdmann, R.M.2
Scheer, E.3
Picard, C.L.4
Bell, G.W.5
Gehring, M.6
-
96
-
-
85003049029
-
DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis
-
(458–014–0458-3)
-
[96] Le, T.N., Schumann, U., Smith, N.A., Tiwari, S., Au, P.C., Zhu, Q.H., Taylor, J.M., Kazan, K., Llewellyn, D.J., Zhang, R., Dennis, E.S., Wang, M.B., DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol., 15, 2014 (458–014–0458-3).
-
(2014)
Genome Biol.
, vol.15
-
-
Le, T.N.1
Schumann, U.2
Smith, N.A.3
Tiwari, S.4
Au, P.C.5
Zhu, Q.H.6
Taylor, J.M.7
Kazan, K.8
Llewellyn, D.J.9
Zhang, R.10
Dennis, E.S.11
Wang, M.B.12
-
97
-
-
84939516199
-
Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
-
[97] Secco, D., Wang, C., Shou, H., Schultz, M.D., Chiarenza, S., Nussaume, L., Ecker, J.R., Whelan, J., Lister, R., Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife, 4, 2015, 10.7554/eLife.09343.
-
(2015)
Elife
, vol.4
-
-
Secco, D.1
Wang, C.2
Shou, H.3
Schultz, M.D.4
Chiarenza, S.5
Nussaume, L.6
Ecker, J.R.7
Whelan, J.8
Lister, R.9
-
98
-
-
0034625265
-
Endless forms: the evolution of gene regulation and morphological diversity
-
[98] Carroll, S.B., Endless forms: the evolution of gene regulation and morphological diversity. Cell 101 (2000), 577–580.
-
(2000)
Cell
, vol.101
, pp. 577-580
-
-
Carroll, S.B.1
-
99
-
-
0033800838
-
Stress and transposable elements: co-evolution or useful parasites?
-
[99] Capy, P., Gasperi, G., Biemont, C., Bazin, C., Stress and transposable elements: co-evolution or useful parasites?. Heredity (Edinb.) 85:Pt 2 (2000), 101–106.
-
(2000)
Heredity (Edinb.)
, vol.85
, pp. 101-106
-
-
Capy, P.1
Gasperi, G.2
Biemont, C.3
Bazin, C.4
-
100
-
-
23844474398
-
Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae
-
[100] Grandbastien, M.A., Audeon, C., Bonnivard, E., Casacuberta, J.M., Chalhoub, B., Costa, A.P., Le, Q.H., Melayah, D., Petit, M., Poncet, C., Tam, S.M., Van Sluys, M.A., Mhiri, C., Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110 (2005), 229–241.
-
(2005)
Cytogenet. Genome Res.
, vol.110
, pp. 229-241
-
-
Grandbastien, M.A.1
Audeon, C.2
Bonnivard, E.3
Casacuberta, J.M.4
Chalhoub, B.5
Costa, A.P.6
Le, Q.H.7
Melayah, D.8
Petit, M.9
Poncet, C.10
Tam, S.M.11
Van Sluys, M.A.12
Mhiri, C.13
-
101
-
-
84869490320
-
Epigenetic control of transposon transcription and mobility in Arabidopsis
-
[101] Bucher, E., Reinders, J., Mirouze, M., Epigenetic control of transposon transcription and mobility in Arabidopsis. Curr. Opin. Plant Biol. 15 (2012), 503–510.
-
(2012)
Curr. Opin. Plant Biol.
, vol.15
, pp. 503-510
-
-
Bucher, E.1
Reinders, J.2
Mirouze, M.3
-
102
-
-
84877892296
-
Small RNAs and regulation of transposons in plants
-
[102] Ito, H., Small RNAs and regulation of transposons in plants. Genes Genet. Syst. 88 (2013), 3–7.
-
(2013)
Genes Genet. Syst.
, vol.88
, pp. 3-7
-
-
Ito, H.1
-
103
-
-
0031238581
-
Retrotransposons of rice: their regulation and use for genome analysis
-
[103] Hirochika, H., Retrotransposons of rice: their regulation and use for genome analysis. Plant Mol. Biol. 35 (1997), 231–240.
-
(1997)
Plant Mol. Biol.
, vol.35
, pp. 231-240
-
-
Hirochika, H.1
-
104
-
-
0033832279
-
Epigenetic aspects of somaclonal variation in plants
-
[104] Kaeppler, S.M., Kaeppler, H.F., Rhee, Y., Epigenetic aspects of somaclonal variation in plants. Plant Mol. Biol. 43 (2000), 179–188.
-
(2000)
Plant Mol. Biol.
, vol.43
, pp. 179-188
-
-
Kaeppler, S.M.1
Kaeppler, H.F.2
Rhee, Y.3
-
105
-
-
70350515004
-
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
-
[105] Naito, K., Zhang, F., Tsukiyama, T., Saito, H., Hancock, C.N., Richardson, A.O., Okumoto, Y., Tanisaka, T., Wessler, S.R., Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461 (2009), 1130–1134.
-
(2009)
Nature
, vol.461
, pp. 1130-1134
-
-
Naito, K.1
Zhang, F.2
Tsukiyama, T.3
Saito, H.4
Hancock, C.N.5
Richardson, A.O.6
Okumoto, Y.7
Tanisaka, T.8
Wessler, S.R.9
-
106
-
-
84884666640
-
Utilization of transposable element as a novel genetic tool for modification of the stress response in rice
-
[106] Yasuda, K., Ito, M., Sugita, T., Tsukiyama, T., Saito, H., Naito, K., Teraishi, M., Tanisaka, T., Okumoto, Y., Utilization of transposable element as a novel genetic tool for modification of the stress response in rice. Mol. Breed. 32 (2013), 505–516.
-
(2013)
Mol. Breed.
, vol.32
, pp. 505-516
-
-
Yasuda, K.1
Ito, M.2
Sugita, T.3
Tsukiyama, T.4
Saito, H.5
Naito, K.6
Teraishi, M.7
Tanisaka, T.8
Okumoto, Y.9
-
107
-
-
59349118366
-
Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
-
[107] Slotkin, R.K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J.D., Feijo, J.A., Martienssen, R.A., Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136 (2009), 461–472.
-
(2009)
Cell
, vol.136
, pp. 461-472
-
-
Slotkin, R.K.1
Vaughn, M.2
Borges, F.3
Tanurdzic, M.4
Becker, J.D.5
Feijo, J.A.6
Martienssen, R.A.7
-
108
-
-
84962449788
-
Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2
-
e1005902
-
[108] Bire, S., Casteret, S., Piegu, B., Beauclair, L., Moire, N., Arensbuger, P., Bigot, Y., Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2. PLoS Genet., 12, 2016, e1005902.
-
(2016)
PLoS Genet.
, vol.12
-
-
Bire, S.1
Casteret, S.2
Piegu, B.3
Beauclair, L.4
Moire, N.5
Arensbuger, P.6
Bigot, Y.7
-
109
-
-
0001459820
-
Further Studies of Gene-Control Systems in Maize
-
[109] McClintock, B., Further Studies of Gene-Control Systems in Maize. Carnegie Inst. Wash. Yearb. 62 (1963), 486–493.
-
(1963)
Carnegie Inst. Wash. Yearb.
, vol.62
, pp. 486-493
-
-
McClintock, B.1
-
110
-
-
0021715393
-
The significance of responses of the genome to challenge
-
[110] McClintock, B., The significance of responses of the genome to challenge. Science 226 (1984), 792–801.
-
(1984)
Science
, vol.226
, pp. 792-801
-
-
McClintock, B.1
-
112
-
-
79953746026
-
An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress
-
[112] Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., Paszkowski, J., An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472 (2011), 115–119.
-
(2011)
Nature
, vol.472
, pp. 115-119
-
-
Ito, H.1
Gaubert, H.2
Bucher, E.3
Mirouze, M.4
Vaillant, I.5
Paszkowski, J.6
-
113
-
-
84896719193
-
How a retrotransposon exploits the plant's heat stress response for its activation
-
e1004115
-
[113] Cavrak, V.V., Lettner, N., Jamge, S., Kosarewicz, A., Bayer, L.M., Mittelsten Scheid, O., How a retrotransposon exploits the plant's heat stress response for its activation. PLoS Genet., 10, 2014, e1004115.
-
(2014)
PLoS Genet.
, vol.10
-
-
Cavrak, V.V.1
Lettner, N.2
Jamge, S.3
Kosarewicz, A.4
Bayer, L.M.5
Mittelsten Scheid, O.6
-
114
-
-
84955468903
-
Transposable elements contribute to activation of maize genes in response to abiotic stress
-
e1004915
-
[114] Makarevitch, I., Waters, A.J., West, P.T., Stitzer, M., Hirsch, C.N., Ross-Ibarra, J., Springer, N.M., Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet., 11, 2015, e1004915.
-
(2015)
PLoS Genet.
, vol.11
-
-
Makarevitch, I.1
Waters, A.J.2
West, P.T.3
Stitzer, M.4
Hirsch, C.N.5
Ross-Ibarra, J.6
Springer, N.M.7
-
115
-
-
22444439135
-
An Arabidopsis hAT-like transposase is essential for plant development
-
[115] Bundock, P., Hooykaas, P., An Arabidopsis hAT-like transposase is essential for plant development. Nature 436 (2005), 282–284.
-
(2005)
Nature
, vol.436
, pp. 282-284
-
-
Bundock, P.1
Hooykaas, P.2
-
116
-
-
84866913795
-
A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana
-
e1002931
-
[116] Joly-Lopez, Z., Forczek, E., Hoen, D.R., Juretic, N., Bureau, T.E., A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PLoS Genet., 8, 2012, e1002931.
-
(2012)
PLoS Genet.
, vol.8
-
-
Joly-Lopez, Z.1
Forczek, E.2
Hoen, D.R.3
Juretic, N.4
Bureau, T.E.5
-
117
-
-
84883125886
-
Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs
-
[117] McCue, A.D., Nuthikattu, S., Slotkin, R.K., Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs. RNA Biol. 10 (2013), 1379–1395.
-
(2013)
RNA Biol.
, vol.10
, pp. 1379-1395
-
-
McCue, A.D.1
Nuthikattu, S.2
Slotkin, R.K.3
|