-
1
-
-
77955273950
-
A triptych of the evolution of plant transposable elements
-
Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15:471-478.
-
(2010)
Trends Plant Sci
, vol.15
, pp. 471-478
-
-
Tenaillon, M.I.1
Hollister, J.D.2
Gaut, B.S.3
-
2
-
-
66449124318
-
Epigenetic regulation of transposable elements in plants
-
Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43-66.
-
(2009)
Annu Rev Plant Biol
, vol.60
, pp. 43-66
-
-
Lisch, D.1
-
3
-
-
18044393885
-
RNA silencing and genome regulation
-
DOI 10.1016/j.tcb.2005.03.006
-
Almeida R, Allshire RC (2005) RNA silencing and genome regulation. Trends Cell Biol 15:251-258. (Pubitemid 40603894)
-
(2005)
Trends in Cell Biology
, vol.15
, Issue.5
, pp. 251-258
-
-
Almeida, R.1
Allshire, R.C.2
-
4
-
-
42549085238
-
The epigenetic landscape of plants
-
Zhang X (2008) The epigenetic landscape of plants. Science 320:489-492.
-
(2008)
Science
, vol.320
, pp. 489-492
-
-
Zhang, X.1
-
5
-
-
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
-
6
-
-
33947303168
-
Transposable elements and the epigenetic regulation of the genome
-
DOI 10.1038/nrg2072, PII NRG2072
-
Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8:272-285. (Pubitemid 46439291)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.4
, pp. 272-285
-
-
Slotkin, R.K.1
Martienssen, R.2
-
7
-
-
33645775498
-
Meiotically stable natural epialleles of Sadhu, a novel Arabidopsis retroposon
-
Rangwala SH, et al. (2006) Meiotically stable natural epialleles of Sadhu, a novel Arabidopsis retroposon. PLoS Genet 2:e36.
-
(2006)
PLoS Genet
, vol.2
-
-
Rangwala, S.H.1
-
8
-
-
37249026814
-
Genome-wide analysis of DNA methylation patterns
-
DOI 10.1242/dev.001131
-
Zilberman D, Henikoff S (2007) Genome-wide analysis of DNA methylation patterns. Development 134:3959-3965. (Pubitemid 350269413)
-
(2007)
Development
, vol.134
, Issue.22
, pp. 3959-3965
-
-
Zilberman, D.1
Henikoff, S.2
-
9
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, et al. (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
-
10
-
-
73649118150
-
Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs
-
Jia Y, et al. (2009) Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet 5:e1000737.
-
(2009)
PLoS Genet
, vol.5
-
-
Jia, Y.1
-
11
-
-
0037197916
-
A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing
-
DOI 10.1073/pnas.052152199
-
Lisch D, Carey CC, Dorweiler JE, Chandler VL (2002) A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing. Proc Natl Acad Sci USA 99:6130-6135. (Pubitemid 34493277)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.9
, pp. 6130-6135
-
-
Lisch, D.1
Carey, C.C.2
Dorweiler, J.E.3
Chandler, V.L.4
-
12
-
-
70349276670
-
Bursts of retrotransposition reproduced in Arabidopsis
-
Tsukahara S, et al. (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461:423-426.
-
(2009)
Nature
, vol.461
, pp. 423-426
-
-
Tsukahara, S.1
-
13
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
DOI 10.1038/nature02651
-
Lippman Z, et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-476. (Pubitemid 38987911)
-
(2004)
Nature
, vol.430
, Issue.6998
, 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.B.10
Carrington, J.C.11
Doerge, R.W.12
Colot, V.13
Martienssen, R.14
-
14
-
-
34248340993
-
Role of RNA polymerase IV in plant small RNA metabolism
-
DOI 10.1073/pnas.0611456104
-
Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE (2007) Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci USA 104:4536-4541. (Pubitemid 47186260)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.11
, pp. 4536-4541
-
-
Zhang, X.1
Henderson, I.R.2
Lu, C.3
Green, P.J.4
Jacobsen, S.E.5
-
16
-
-
10044244768
-
SiRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis
-
DOI 10.1101/gad.1217304
-
Liu J, He Y, Amasino R, Chen X (2004) siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev 18:2873-2878. (Pubitemid 39602306)
-
(2004)
Genes and Development
, vol.18
, Issue.23
, pp. 2873-2878
-
-
Liu, J.1
He, Y.2
Amasino, R.3
Chen, X.4
-
17
-
-
45349108094
-
Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading
-
DOI 10.1101/gad.1667808
-
Henderson IR, Jacobsen SE (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev 22:1597-1606. (Pubitemid 351846840)
-
(2008)
Genes and Development
, vol.22
, Issue.12
, pp. 1597-1606
-
-
Henderson, I.R.1
Jacobsen, S.E.2
-
18
-
-
1642515876
-
One-Way Control of FWA Imprinting in Arabidopsis Endosperm by DNA Methylation
-
DOI 10.1126/science.1089835
-
Kinoshita T, et al. (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303:521-523. (Pubitemid 38120849)
-
(2004)
Science
, vol.303
, Issue.5657
, 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
-
19
-
-
68149144366
-
Epigenetic silencing of transposable elements: A tradeoff between reduced transposition and deleterious effects on neighboring gene expression
-
Hollister JD, Gaut BS (2009) Epigenetic silencing of transposable elements: a tradeoff between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 19:1419-1428.
-
(2009)
Genome Res
, vol.19
, pp. 1419-1428
-
-
Hollister, J.D.1
Gaut, B.S.2
-
20
-
-
77952734605
-
Conservation and divergence of methylation patterning in plants and animals
-
Feng S, et al. (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107:8689-8694.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 8689-8694
-
-
Feng, S.1
-
21
-
-
77952355762
-
Genome-wide evolutionary analysis of eukaryotic DNA methylation
-
Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916-919.
-
(2010)
Science
, vol.328
, pp. 916-919
-
-
Zemach, A.1
McDaniel, I.E.2
Silva, P.3
Zilberman, D.4
-
22
-
-
74849090833
-
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
-
Ossowski S, et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92-94.
-
(2010)
Science
, vol.327
, pp. 92-94
-
-
Ossowski, S.1
-
23
-
-
78649817356
-
Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana
-
Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci USA 107:18724-18728.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 18724-18728
-
-
Beilstein, M.A.1
Nagalingum, N.S.2
Clements, M.D.3
Manchester, S.R.4
Mathews, S.5
-
24
-
-
33751014556
-
The ABC's of comparative genomics in the Brassicaceae: Building blocks of crucifer genomes
-
DOI 10.1016/j.tplants.2006.09.002, PII S1360138506002482
-
Schranz ME, Lysak MA, Mitchell-Olds T (2006) The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535-542. (Pubitemid 44740519)
-
(2006)
Trends in Plant Science
, vol.11
, Issue.11
, pp. 535-542
-
-
Schranz, M.E.1
Lysak, M.A.2
Mitchell-Olds, T.3
-
25
-
-
20444394144
-
Breakdown of self-incompatibility in the perennial Arabidopsis lyrata (Brassicaceae) and its genetic consequences
-
Mable BK, Robertson AV, Dart S, Di Berardo C, Witham L (2005) Breakdown of self-incompatibility in the perennial Arabidopsis lyrata (Brassicaceae) and its genetic consequences. Evolution 59:1437-1448. (Pubitemid 41102229)
-
(2005)
Evolution
, vol.59
, Issue.7
, pp. 1437-1448
-
-
Mable, B.K.1
Robertson, A.V.2
Dart, S.3
Berardo, C.D.I.4
Witham, L.5
-
26
-
-
0033288975
-
Transposon dynamics and the breeding system
-
Wright SI, Schoen DJ (1999) Transposon dynamics and the breeding system. Genetica 107:139-148. (Pubitemid 129574960)
-
(1999)
Genetica
, vol.107
, Issue.1-3
, pp. 139-148
-
-
Wright, S.I.1
Schoen, D.J.2
-
27
-
-
0034945229
-
Transposable element number in mixed mating populations
-
Morgan MT (2001) Transposable element number in mixed mating populations. Genet Res 77:261-275.
-
(2001)
Genet Res
, vol.77
, pp. 261-275
-
-
Morgan, M.T.1
-
28
-
-
0034924455
-
Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis
-
Wright SI, Le QH, Schoen DJ, Bureau TE (2001) Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis.. Genetics 158:1279-1288. (Pubitemid 32672877)
-
(2001)
Genetics
, vol.158
, Issue.3
, pp. 1279-1288
-
-
Wright, S.I.1
Le, Q.H.2
Schoen, D.J.3
Bureau, T.E.4
-
29
-
-
77649301731
-
The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata
-
Lockton S, Gaut BS (2010) The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol 10:10.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 10
-
-
Lockton, S.1
Gaut, B.S.2
-
30
-
-
77953217767
-
Arabidopsis lyrata small RNAs: Transient MIRNA and small interfering RNA loci within the Arabidopsis genus
-
Ma Z, Coruh C, Axtell MJ (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22:1090-1103.
-
(2010)
Plant Cell
, vol.22
, pp. 1090-1103
-
-
Ma, Z.1
Coruh, C.2
Axtell, M.J.3
-
31
-
-
77953214518
-
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
-
Fahlgren N, et al. (2010) MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 22:1074-1089.
-
(2010)
Plant Cell
, vol.22
, pp. 1074-1089
-
-
Fahlgren, N.1
-
32
-
-
0031707062
-
The paleontology of intergene retrotransposons of maize
-
DOI 10.1038/1695
-
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43-45. (Pubitemid 28410341)
-
(1998)
Nature Genetics
, vol.20
, Issue.1
, pp. 43-45
-
-
SanMiguel, P.1
Gaut, B.S.2
Tikhonov, A.3
Nakajima, Y.4
Bennetzen, J.L.5
-
33
-
-
52949131888
-
Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata
-
Lockton S, Ross-Ibarra J, Gaut BS (2008) Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. Proc Natl Acad Sci USA 105:13965-13970.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 13965-13970
-
-
Lockton, S.1
Ross-Ibarra, J.2
Gaut, B.S.3
-
34
-
-
70350515004
-
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
-
Naito K, et al. (2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461:1130-1134.
-
(2009)
Nature
, vol.461
, pp. 1130-1134
-
-
Naito, K.1
-
35
-
-
76949127123
-
Chromosome organization and genic expression
-
McClintock B (1951) Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol 16:13-47.
-
(1951)
Cold Spring Harb Symp Quant Biol
, vol.16
, pp. 13-47
-
-
McClintock, B.1
-
36
-
-
0023056233
-
Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus
-
Coen ES, Carpenter R, Martin C (1986) Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus. Cell 47:285-296.
-
(1986)
Cell
, vol.47
, pp. 285-296
-
-
Coen, E.S.1
Carpenter, R.2
Martin, C.3
-
37
-
-
84887212541
-
The effect of transposable element insertions on gene expression evolution in rodents
-
Pereira V, Enard D, Eyre-Walker A (2009) The effect of transposable element insertions on gene expression evolution in rodents. PLoS ONE 4:e4321.
-
(2009)
PLoS ONE
, vol.4
-
-
Pereira, V.1
Enard, D.2
Eyre-Walker, A.3
-
38
-
-
77955000272
-
Transposable elements: Insertion pattern and impact on gene expression evolution in hominids
-
Warnefors M, Pereira V, Eyre-Walker A (2010) Transposable elements: insertion pattern and impact on gene expression evolution in hominids. Mol Biol Evol 27:1955-1962.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1955-1962
-
-
Warnefors, M.1
Pereira, V.2
Eyre-Walker, A.3
-
39
-
-
35848941492
-
Population and evolutionary dynamics of helitron transposable elements in Arabidopsis thaliana
-
DOI 10.1093/molbev/msm197
-
Hollister JD, Gaut BS (2007) Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana. Mol Biol Evol 24:2515-2524. (Pubitemid 350060458)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.11
, pp. 2515-2524
-
-
Hollister, J.D.1
Gaut, B.S.2
-
40
-
-
20044378849
-
Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication
-
DOI 10.1038/ng1576
-
Slotkin RK, Freeling M, Lisch D (2005) Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 37:641-644. (Pubitemid 40770421)
-
(2005)
Nature Genetics
, vol.37
, Issue.6
, pp. 641-644
-
-
Slotkin, R.K.1
Freeling, M.2
Lisch, D.3
-
41
-
-
33749392949
-
Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
-
DOI 10.1101/gr.5290206
-
Piegu B, et al. (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262-1269. (Pubitemid 44506959)
-
(2006)
Genome Research
, vol.16
, Issue.10
, pp. 1262-1269
-
-
Piegu, B.1
Guyot, R.2
Picault, N.3
Roulin, A.4
Saniyal, A.5
Kim, H.6
Collura, K.7
Brar, D.S.8
Jackson, S.9
Wing, R.A.10
Panaud, O.11
-
42
-
-
33749389724
-
Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
-
DOI 10.1101/gr.5282906
-
Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16:1252-1261. (Pubitemid 44506958)
-
(2006)
Genome Research
, vol.16
, Issue.10
, pp. 1252-1261
-
-
Hawkins, J.S.1
Kim, H.2
Nason, J.D.3
Wing, R.A.4
Wendel, J.F.5
-
44
-
-
57149099394
-
Sequencing of natural strains of Arabidopsis thaliana with short reads
-
Ossowski S, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024-2033.
-
(2008)
Genome Res
, vol.18
, pp. 2024-2033
-
-
Ossowski, S.1
-
45
-
-
58149114653
-
Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes
-
Naouar N, et al. (2009) Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J 57:184-194.
-
(2009)
Plant J
, vol.57
, pp. 184-194
-
-
Naouar, N.1
-
46
-
-
48249130774
-
At-TAX: A whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
-
Laubinger S, et al. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 9:R112.
-
(2008)
Genome Biol
, vol.9
-
-
Laubinger, S.1
|