-
1
-
-
33748623819
-
Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis.
-
10.1016/j.cell.2006.09.002, 16990127
-
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW-L, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 2006, 126:1025-1028. 10.1016/j.cell.2006.09.002, 16990127.
-
(2006)
Cell
, vol.126
, pp. 1025-1028
-
-
Zhang, X.1
Yazaki, J.2
Sundaresan, A.3
Cokus, S.4
Chan, S.W.-.L.5
Chen, H.6
Henderson, I.R.7
Shinn, P.8
Pellegrini, M.9
Jacobsen, S.E.10
Ecker, J.R.11
-
2
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.
-
10.1038/ng1929, 17128275
-
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 2007, 39:61-69. 10.1038/ng1929, 17128275.
-
(2007)
Nat Genet
, vol.39
, pp. 61-69
-
-
Zilberman, D.1
Gehring, M.2
Tran, R.K.3
Ballinger, T.4
Henikoff, S.5
-
3
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
-
10.1038/nature06745, 2377394, 18278030
-
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219. 10.1038/nature06745, 2377394, 18278030.
-
(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
-
4
-
-
42549090878
-
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression.
-
10.1105/tpc.107.056879, 2276441, 18263775
-
Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Terzaghi W, Li S, Deng XW. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 2008, 20:259-276. 10.1105/tpc.107.056879, 2276441, 18263775.
-
(2008)
Plant Cell
, vol.20
, pp. 259-276
-
-
Li, X.1
Wang, X.2
He, K.3
Ma, Y.4
Su, N.5
He, H.6
Stolc, V.7
Tongprasit, W.8
Jin, W.9
Jiang, J.10
Terzaghi, W.11
Li, S.12
Deng, X.W.13
-
5
-
-
0030885667
-
DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa.
-
10.1101/gad.11.18.2383, 316521, 9308966
-
Rountree MR, Selker EU. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev 1997, 11:2383-2395. 10.1101/gad.11.18.2383, 316521, 9308966.
-
(1997)
Genes Dev
, vol.11
, pp. 2383-2395
-
-
Rountree, M.R.1
Selker, E.U.2
-
6
-
-
0027215524
-
Methylation induced premeiotically in Ascobolus: coextension with DNA repeat lengths and effect on transcript elongation.
-
10.1073/pnas.90.10.4557, 46551, 8506299
-
Barry C, Faugeron G, Rossignol JL. Methylation induced premeiotically in Ascobolus: coextension with DNA repeat lengths and effect on transcript elongation. Proc Natl Acad Sci USA 1993, 90:4557-4561. 10.1073/pnas.90.10.4557, 46551, 8506299.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 4557-4561
-
-
Barry, C.1
Faugeron, G.2
Rossignol, J.L.3
-
7
-
-
0029738385
-
Methylation of coding region alone inhibits gene expression in plant protoplasts.
-
10.1073/pnas.93.16.8334, 38671, 8710871
-
Hohn T, Corsten S, Rieke S, Muller M, Rothnie H. Methylation of coding region alone inhibits gene expression in plant protoplasts. Proc Natl Acad Sci USA 1996, 93:8334-8339. 10.1073/pnas.93.16.8334, 38671, 8710871.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 8334-8339
-
-
Hohn, T.1
Corsten, S.2
Rieke, S.3
Muller, M.4
Rothnie, H.5
-
8
-
-
7544231794
-
Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells.
-
10.1038/nsmb840, 15467727
-
Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 2004, 11:1068-1075. 10.1038/nsmb840, 15467727.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 1068-1075
-
-
Lorincz, M.C.1
Dickerson, D.R.2
Schmitt, M.3
Groudine, M.4
-
9
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.
-
10.1038/nature05632, 17392789
-
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 2007, 446:572-576. 10.1038/nature05632, 17392789.
-
(2007)
Nature
, vol.446
, pp. 572-576
-
-
Albert, I.1
Mavrich, T.N.2
Tomsho, L.P.3
Qi, J.4
Zanton, S.J.5
Schuster, S.C.6
Pugh, B.F.7
-
10
-
-
43749099875
-
Nucleosome organization in the Drosophila genome.
-
10.1038/nature06929, 2735122, 18408708
-
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF. Nucleosome organization in the Drosophila genome. Nature 2008, 453:358-362. 10.1038/nature06929, 2735122, 18408708.
-
(2008)
Nature
, vol.453
, pp. 358-362
-
-
Mavrich, T.N.1
Jiang, C.2
Ioshikhes, I.P.3
Li, X.4
Venters, B.J.5
Zanton, S.J.6
Tomsho, L.P.7
Qi, J.8
Glaser, R.L.9
Schuster, S.C.10
Gilmour, D.S.11
Albert, I.12
Pugh, B.F.13
-
11
-
-
33749153628
-
Nucleosome positions predicted through comparative genomics.
-
10.1038/ng1878, 16964265
-
Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nat Genet 2006, 38:1210-1215. 10.1038/ng1878, 16964265.
-
(2006)
Nat Genet
, vol.38
, pp. 1210-1215
-
-
Ioshikhes, I.P.1
Albert, I.2
Zanton, S.J.3
Pugh, B.F.4
-
12
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
-
10.1101/gr.078261.108, 2493396, 18550805
-
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008, 18:1073-1083. 10.1101/gr.078261.108, 2493396, 18550805.
-
(2008)
Genome Res
, vol.18
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
Jiang, C.4
Tomsho, L.P.5
Qi, J.6
Schuster, S.C.7
Albert, I.8
Pugh, B.F.9
-
13
-
-
16344367080
-
DNA methylation, nucleosome formation and positioning.
-
10.1093/bfgp/3.4.351, 15814025
-
Pennings S, Allan J, Davey CS. DNA methylation, nucleosome formation and positioning. Brief Funct Genomic Proteomic 2005, 3:351-361. 10.1093/bfgp/3.4.351, 15814025.
-
(2005)
Brief Funct Genomic Proteomic
, vol.3
, pp. 351-361
-
-
Pennings, S.1
Allan, J.2
Davey, C.S.3
-
14
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome.
-
10.1016/j.cell.2008.02.022, 18329373
-
Schones DE, Cui K, Cuddapah S, Roh T-Y, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132:887-898. 10.1016/j.cell.2008.02.022, 18329373.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.-.Y.4
Barski, A.5
Wang, Z.6
Wei, G.7
Zhao, K.8
-
15
-
-
34147168036
-
Transcription through chromatin by RNA polymerase II: histone displacement and exchange.
-
1924643, 17313961
-
Kulaeva OI, Gaykalova D, Studitsky VM. Transcription through chromatin by RNA polymerase II: histone displacement and exchange. Mutat Res 2007, 618:116-129. 1924643, 17313961.
-
(2007)
Mutat Res
, vol.618
, pp. 116-129
-
-
Kulaeva, O.I.1
Gaykalova, D.2
Studitsky, V.M.3
-
16
-
-
33747500567
-
A genomic code for nucleosome positioning.
-
10.1038/nature04979, 2623244, 16862119
-
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JZ, Widom J. A genomic code for nucleosome positioning. Nature 2006, 442:772-778. 10.1038/nature04979, 2623244, 16862119.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thastrom, A.4
Field, Y.5
Moore, I.K.6
Wang, J.Z.7
Widom, J.8
-
17
-
-
34047116826
-
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.
-
10.1038/ng1990, 17334365
-
Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007, 39:457-466. 10.1038/ng1990, 17334365.
-
(2007)
Nat Genet
, vol.39
, pp. 457-466
-
-
Weber, M.1
Hellmann, I.2
Stadler, M.B.3
Ramos, L.4
Pääbo, S.5
Rebhan, M.6
Schübeler, D.7
-
18
-
-
0032575756
-
DNA structure in human RNA polymerase II promoters.
-
10.1006/jmbi.1998.1972, 9710538
-
Pedersen AG, Baldi P, Chauvin Y, Brunak S. DNA structure in human RNA polymerase II promoters. J Mol Biol 1998, 281:663-673. 10.1006/jmbi.1998.1972, 9710538.
-
(1998)
J Mol Biol
, vol.281
, pp. 663-673
-
-
Pedersen, A.G.1
Baldi, P.2
Chauvin, Y.3
Brunak, S.4
-
19
-
-
34250775905
-
The pattern and evolution of yeast promoter bendability.
-
10.1016/j.tig.2007.03.015, 17418911
-
Tirosh I, Berman J, Barkai N. The pattern and evolution of yeast promoter bendability. Trends Genet 2007, 23:318-321. 10.1016/j.tig.2007.03.015, 17418911.
-
(2007)
Trends Genet
, vol.23
, pp. 318-321
-
-
Tirosh, I.1
Berman, J.2
Barkai, N.3
-
20
-
-
0029039118
-
Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
-
398274, 7737131
-
Brukner I, Sánchez R, Suck D, Pongor S. Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J 1995, 14:1812-1818. 398274, 7737131.
-
(1995)
EMBO J
, vol.14
, pp. 1812-1818
-
-
Brukner, I.1
Sánchez, R.2
Suck, D.3
Pongor, S.4
-
21
-
-
30044441988
-
The human SWI/SNF subunit Brm is a regulator of alternative splicing.
-
10.1038/nsmb1030, 16341228
-
Batsche E, Yaniv M, Muchardt C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol 2006, 13:22-29. 10.1038/nsmb1030, 16341228.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 22-29
-
-
Batsche, E.1
Yaniv, M.2
Muchardt, C.3
-
22
-
-
30044440197
-
Chromatin, transcript elongation and alternative splicing.
-
10.1038/nsmb0106-5, 16395314
-
Kornblihtt AR. Chromatin, transcript elongation and alternative splicing. Nat Struct Mol Biol 2006, 13:5-7. 10.1038/nsmb0106-5, 16395314.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 5-7
-
-
Kornblihtt, A.R.1
-
23
-
-
61349098460
-
Differential chromatin marking of introns and expressed exons by H3K36me3.
-
10.1038/ng.322, 2648722, 19182803
-
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer1 J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 2009, 41:376-381. 10.1038/ng.322, 2648722, 19182803.
-
(2009)
Nat Genet
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
Down, T.2
Latorre, I.3
Liu, T.4
Liu, X.S.5
Ahringer1, J.6
-
24
-
-
61349087243
-
Processing the H3K36me3 signature.
-
10.1038/ng0309-270, 19240748
-
Sims RJ, Reinberg D. Processing the H3K36me3 signature. Nat Genet 2009, 41:270-271. 10.1038/ng0309-270, 19240748.
-
(2009)
Nat Genet
, vol.41
, pp. 270-271
-
-
Sims, R.J.1
Reinberg, D.2
-
25
-
-
84870647022
-
UCSC Genome Browser
-
UCSC Genome Browser. , http://genome.ucsc.edu/
-
-
-
-
26
-
-
49549122021
-
Saccharomyces Genome Database
-
Saccharomyces Genome Database. , http://www.yeastgenome.org/
-
-
-
-
27
-
-
33845223334
-
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
-
10.1073/pnas.0605645103, 1693835, 17101987
-
Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci USA 2006, 103:17846-17851. 10.1073/pnas.0605645103, 1693835, 17101987.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 17846-17851
-
-
Miura, F.1
Kawaguchi, N.2
Sese, J.3
Toyoda, A.4
Hattori, M.5
Morishita, S.6
Ito, T.7
-
28
-
-
76249126345
-
Nucleosome Maps of the Saccharomyces Genome
-
Nucleosome Maps of the Saccharomyces Genome. , http://atlas.bx.psu.edu/yeast-maps/yeast-index.html
-
-
-
-
29
-
-
76249085851
-
Nucleosome Maps of the Drosophila Genome
-
Nucleosome Maps of the Drosophila Genome. , http://atlas.bx.psu.edu/dmel-maps/dmel-index.html
-
-
-
-
30
-
-
76249132574
-
Nucleosome Data for the Human Genome
-
Nucleosome Data for the Human Genome. , http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/hgtcellnucleosomes.html
-
-
-
-
31
-
-
33748055105
-
MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells.
-
10.1158/0008-5472.CAN-06-1888, 16912168
-
Rauch T, Li H, Wu X, Pfeifer GP. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 2006, 66:7939-7947. 10.1158/0008-5472.CAN-06-1888, 16912168.
-
(2006)
Cancer Res
, vol.66
, pp. 7939-7947
-
-
Rauch, T.1
Li, H.2
Wu, X.3
Pfeifer, G.P.4
-
32
-
-
34248361968
-
Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay.
-
10.1073/pnas.0701059104, 1838508, 17369352
-
Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau SK, Kernstine KH, Riggs AD, Pfeifer GP. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci USA 2007, 104:5527-5532. 10.1073/pnas.0701059104, 1838508, 17369352.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 5527-5532
-
-
Rauch, T.1
Wang, Z.2
Zhang, X.3
Zhong, X.4
Wu, X.5
Lau, S.K.6
Kernstine, K.H.7
Riggs, A.D.8
Pfeifer, G.P.9
-
33
-
-
0023216891
-
CpG islands in vertebrate genomes.
-
10.1016/0022-2836(87)90689-9, 3656447
-
Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987, 196:261-282. 10.1016/0022-2836(87)90689-9, 3656447.
-
(1987)
J Mol Biol
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
34
-
-
55549141877
-
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks.
-
10.1038/nature07324, 18815594
-
Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 2008, 456:125-129. 10.1038/nature07324, 18815594.
-
(2008)
Nature
, vol.456
, pp. 125-129
-
-
Zilberman, D.1
Coleman-Derr, D.2
Ballinger, T.3
Henikoff, S.4
|