-
1
-
-
79953680754
-
Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells
-
Angrisano T, Sacchetti S, Natale F, Cerrato A, Pero R, Keller S, Peluso S, Perillo B, Avvedimento VE, Fusco A, et al. 2011. Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells. Nucleic Acids Res 39: 1993-2006.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 1993-2006
-
-
Angrisano, T.1
Sacchetti, S.2
Natale, F.3
Cerrato, A.4
Pero, R.5
Keller, S.6
Peluso, S.7
Perillo, B.8
Avvedimento, V.E.9
Fusco, A.10
-
2
-
-
67349190247
-
Linking DNA methylation and histone modification: Patterns and paradigms
-
Cedar H, Bergman Y. 2009. Linking DNA methylation and histone modification: Patterns and paradigms. Nat Rev Genet 10: 295-304.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 295-304
-
-
Cedar, H.1
Bergman, Y.2
-
3
-
-
0028096611
-
High sensitivity mapping of methylated cytosines
-
Clark SJ, Harrison J, Paul CL, Frommer M. 1994. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22: 2990-2997. (Pubitemid 24260626)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.15
, pp. 2990-2997
-
-
Clark, S.J.1
Harrison, J.2
Paul, C.L.3
Frommer, M.4
-
4
-
-
34547528183
-
DNA methylation: Bisulphite modification and analysis
-
Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M. 2006. DNA methylation: Bisulphite modification and analysis. Nat Protoc 1: 2353-2364.
-
(2006)
Nat Protoc
, vol.1
, pp. 2353-2364
-
-
Clark, S.J.1
Statham, A.2
Stirzaker, C.3
Molloy, P.L.4
Frommer, M.5
-
5
-
-
77954834510
-
The current state of chromatin immunoprecipitation
-
Collas P. 2010. The current state of chromatin immunoprecipitation. Mol Biotechnol 45: 87-100.
-
(2010)
Mol Biotechnol
, vol.45
, pp. 87-100
-
-
Collas, P.1
-
6
-
-
35648937679
-
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: Critical evaluation and improvements
-
doi:10.1093/nar/gkm662
-
Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ. 2007. Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: Critical evaluation and improvements. Nucleic Acids Res 35: e119. doi:10.1093/nar/gkm662.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Coolen, M.W.1
Statham, A.L.2
Gardiner-Garden, M.3
Clark, S.J.4
-
7
-
-
77649271805
-
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
-
Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, et al. 2010. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 12: 235-246.
-
(2010)
Nat Cell Biol
, vol.12
, pp. 235-246
-
-
Coolen, M.W.1
Stirzaker, C.2
Song, J.Z.3
Statham, A.L.4
Kassir, Z.5
Moreno, C.S.6
Young, A.N.7
Varma, V.8
Speed, T.P.9
Cowley, M.10
-
8
-
-
78650985680
-
An assessment of histone-modification antibody quality
-
Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, et al. 2011. An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18: 91-93.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 91-93
-
-
Egelhofer, T.A.1
Minoda, A.2
Klugman, S.3
Lee, K.4
Kolasinska-Zwierz, P.5
Alekseyenko, A.A.6
Cheung, M.S.7
Day, D.S.8
Gadel, S.9
Gorchakov, A.A.10
-
9
-
-
51349105905
-
Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line
-
Gal-Yam EN, Egger G, Iniguez L, Holster H, Einarsson S, Zhang X, Lin JC, Liang G, Jones PA, Tanay A. 2008. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci 105: 12979-12984.
-
(2008)
Proc Natl Acad Sci
, vol.105
, pp. 12979-12984
-
-
Gal-Yam, E.N.1
Egger, G.2
Iniguez, L.3
Holster, H.4
Einarsson, S.5
Zhang, X.6
Lin, J.C.7
Liang, G.8
Jones, P.A.9
Tanay, A.10
-
10
-
-
77449153454
-
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
-
Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. 2010. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7: 133-136.
-
(2010)
Nat Methods
, vol.7
, pp. 133-136
-
-
Gu, H.1
Bock, C.2
Mikkelsen, T.S.3
Jager, N.4
Smith, Z.D.5
Tomazou, E.6
Gnirke, A.7
Lander, E.S.8
Meissner, A.9
-
11
-
-
57749090255
-
Methylation of Polycomb target genes in intestinal cancer is mediated by inflammation
-
Hahn MA, Hahn T, Lee DH, Esworthy RS, Kim BW, Riggs AD, Chu FF, Pfeifer GP. 2008. Methylation of Polycomb target genes in intestinal cancer is mediated by inflammation. Cancer Res 68: 10280-10289.
-
(2008)
Cancer Res
, vol.68
, pp. 10280-10289
-
-
Hahn, M.A.1
Hahn, T.2
Lee, D.H.3
Esworthy, R.S.4
Kim, B.W.5
Riggs, A.D.6
Chu, F.F.7
Pfeifer, G.P.8
-
12
-
-
77953809032
-
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
-
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, et al. 2010. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6: 479-491.
-
(2010)
Cell Stem Cell
, vol.6
, pp. 479-491
-
-
Hawkins, R.D.1
Hon, G.C.2
Lee, L.K.3
Ngo, Q.4
Lister, R.5
Pelizzola, M.6
Edsall, L.E.7
Kuan, S.8
Luu, Y.9
Klugman, S.10
-
13
-
-
44349131472
-
Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation
-
DOI 10.1038/ng.159, PII NG159
-
Kondo Y, Shen L, Cheng AS, Ahmed S, Boumber Y, Charo C, Yamochi T, Urano T, Furukawa K, Kwabi-Addo B, et al. 2008. Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nat Genet 40: 741-750. (Pubitemid 351748874)
-
(2008)
Nature Genetics
, vol.40
, Issue.6
, pp. 741-750
-
-
Kondo, Y.1
Shen, L.2
Cheng, A.S.3
Ahmed, S.4
Boumber, Y.5
Charo, C.6
Yamochi, T.7
Urano, T.8
Furukawa, K.9
Kwabi-Addo, B.10
Gold, D.L.11
Sekido, Y.12
Huang, T.H.-M.13
Issa, J.-P.J.14
-
14
-
-
77249137168
-
Principles and challenges of genomewide DNA methylation analysis
-
LairdPW. 2010. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 3: 191-203.
-
(2010)
Nat Rev Genet
, vol.3
, pp. 191-203
-
-
Laird, P.W.1
-
15
-
-
77649267695
-
Dynamic changes in the human methylome during differentiation
-
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, et al. 2010. Dynamic changes in the human methylome during differentiation. Genome Res 20: 320-331.
-
(2010)
Genome Res
, vol.20
, pp. 320-331
-
-
Laurent, L.1
Wong, E.2
Li, G.3
Huynh, T.4
Tsirigos, A.5
Ong, C.T.6
Low, H.M.7
Kin Sung, K.W.8
Rigoutsos, I.9
Loring, J.10
-
16
-
-
80054736583
-
Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis
-
Li Y, Tollefsbol TO. 2011. Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis. Methods Mol Biol 791: 239-251.
-
(2011)
Methods Mol Biol
, vol.791
, pp. 239-251
-
-
Li, Y.1
Tollefsbol, T.O.2
-
17
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
18
-
-
70450217879
-
Human DNA methylomes at base resolutionshowwidespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. 2009. Human DNA methylomes at base resolutionshowwidespread epigenomic differences. Nature 462: 315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
-
19
-
-
6344256774
-
In vivo analysis of DNA methylation patterns recognized by specific proteins: Coupling ChIP and bisulfite analysis
-
Matarazzo MR, Lembo F, Angrisano T, Ballestar E, Ferraro M, Pero R, De Bonis ML, Bruni CB, Esteller M, D'Esposito M et al. 2004. In vivo analysis of DNA methylation patterns recognized by specific proteins: Coupling CHIP and bisulfite analysis. BioTechniques 37: 666-673. (Pubitemid 39391183)
-
(2004)
BioTechniques
, vol.37
, Issue.4
, pp. 666-673
-
-
Matarazzo, M.R.1
Lembo, F.2
Angrisano, T.3
Ballestar, E.4
Ferraro, M.5
Pero, R.6
De Bonis, M.L.7
Bruni, C.B.8
Esteller, M.9
D'Esposito, M.10
Chiariotti, L.11
-
20
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.E.8
Nusbaum, C.9
Jaffe, D.B.10
-
21
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
DOI 10.1038/nature06008, PII NATURE06008
-
Mikkelsen TS, KuM, Jaffe DB, Issac B, Lieberman E, GiannoukosG, Alvarez P, Brockman W, Kim TK, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560. (Pubitemid 47206934)
-
(2007)
Nature
, vol.448
, Issue.7153
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.-K.9
Koche, R.P.10
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
22
-
-
51649129596
-
Lineage-specific Polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors
-
Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schubeler D. 2008. Lineage-specific Polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30: 755-766.
-
(2008)
Mol Cell
, vol.30
, pp. 755-766
-
-
Mohn, F.1
Weber, M.2
Rebhan, M.3
Roloff, T.C.4
Richter, J.5
Stadler, M.B.6
Bibel, M.7
Schubeler, D.8
-
23
-
-
33846569960
-
A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing
-
Ohm JE, McGarvey KM, Yu X, Cheng L, Schuebel KE, Cope L, Mohammad HP, Chen W, Daniel VC, Yu W, et al. 2007. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet 39: 237-242.
-
(2007)
Nat Genet
, vol.39
, pp. 237-242
-
-
Ohm, J.E.1
McGarvey, K.M.2
Yu, X.3
Cheng, L.4
Schuebel, K.E.5
Cope, L.6
Mohammad, H.P.7
Chen, W.8
Daniel, V.C.9
Yu, W.10
-
24
-
-
84555189994
-
Epigenetic Analysis: ChIP-chip and ChIP-seq
-
Pellegrini M, Ferrari R. 2012. Epigenetic Analysis: ChIP-chip and ChIP-seq. Methods Mol Biol 802: 377-387.
-
(2012)
Methods Mol Biol
, vol.802
, pp. 377-387
-
-
Pellegrini, M.1
Ferrari, R.2
-
25
-
-
24044468413
-
Headloop suppression PCR and its application to selective amplification of methylated DNA sequences
-
doi: 10.1093/nar/gni120
-
Rand KN, Ho T, Qu W, Mitchell SM, White R, Clark SJ, Molloy PL. 2005. Headloop suppression PCR and its application to selective amplification of methylated DNA sequences. Nucleic Acids Res 33: e127. doi: 10.1093/nar/gni120.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Rand, K.N.1
Ho, T.2
Qu, W.3
Mitchell, S.M.4
White, R.5
Clark, S.J.6
Molloy, P.L.7
-
26
-
-
33846649587
-
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer
-
DOI 10.1038/ng1950, PII NG1950
-
Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, Eden E, Yakhini Z, Ben-Shushan E, Reubinoff BE, et al. 2007. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 39: 232-236. (Pubitemid 46184355)
-
(2007)
Nature Genetics
, vol.39
, Issue.2
, pp. 232-236
-
-
Schlesinger, Y.1
Straussman, R.2
Keshet, I.3
Farkash, S.4
Hecht, M.5
Zimmerman, J.6
Eden, E.7
Yakhini, Z.8
Ben-Shushan, E.9
Reubinoff, B.E.10
Bergman, Y.11
Simon, I.12
Cedar, H.13
-
27
-
-
85047695221
-
Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells
-
DOI 10.1038/sj/onc/1205153
-
Song JZ, Stirzaker C, Harrison J, Melki JR, Clark SJ. 2002. Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene 21: 1048-1061. (Pubitemid 34174517)
-
(2002)
Oncogene
, vol.21
, Issue.7
, pp. 1048-1061
-
-
Song, J.Z.1
Stirzaker, C.2
Harrison, J.3
Melki, J.R.4
Clark, S.J.5
-
28
-
-
77954205689
-
Repitools: An R package for the analysis of enrichment-based epigenomic data
-
Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ, Robinson MD. 2010. Repitools: An R package for the analysis of enrichment-based epigenomic data. Bioinformatics 26: 1662-1663.
-
(2010)
Bioinformatics
, vol.26
, pp. 1662-1663
-
-
Statham, A.L.1
Strbenac, D.2
Coolen, M.W.3
Stirzaker, C.4
Clark, S.J.5
Robinson, M.D.6
-
29
-
-
43749098985
-
DNA methylation landscapes: Provocative insights from epigenomics
-
DOI 10.1038/nrg2341, PII NRG2341
-
Suzuki MM, Bird A. 2008. DNA methylation landscapes: Provocative insights from epigenomics. Nat Rev Genet 9: 465-476. (Pubitemid 351693975)
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.6
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
30
-
-
70350069495
-
The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands
-
Takeshima H, Yamashita S, Shimazu T, Niwa T, Ushijima T. 2009. The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res 19: 1974-1982.
-
(2009)
Genome Res
, vol.19
, pp. 1974-1982
-
-
Takeshima, H.1
Yamashita, S.2
Shimazu, T.3
Niwa, T.4
Ushijima, T.5
-
31
-
-
33846576622
-
Epigenetic stem cell signature in cancer
-
DOI 10.1038/ng1941, PII NG1941
-
Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, et al. 2007. Epigenetic stem cell signature in cancer. Nat Genet 39: 157-158. (Pubitemid 46184343)
-
(2007)
Nature Genetics
, vol.39
, Issue.2
, pp. 157-158
-
-
Widschwendter, M.1
Fiegl, H.2
Egle, D.3
Mueller-Holzner, E.4
Spizzo, G.5
Marth, C.6
Weisenberger, D.J.7
Campan, M.8
Young, J.9
Jacobs, I.10
Laird, P.W.11
|