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48 Publications


2017 | Journal Article | IST-REx-ID: 9506 | OA
An evolutionary case for functional gene body methylation in plants and animals
D. Zilberman, Genome Biology 18 (2017).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 

2016 | Journal Article | IST-REx-ID: 9456 | OA
Mechanism for DNA transposons to generate introns on genomic scales
J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2016 | Journal Article | IST-REx-ID: 9477 | OA
DNA demethylation is initiated in the central cells of Arabidopsis and rice
K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.
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2016 | Journal Article | IST-REx-ID: 9473 | OA
Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues
P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
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2015 | Journal Article | IST-REx-ID: 9532 | OA
Evolution and function of genomic imprinting in plants
J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 

2014 | Journal Article | IST-REx-ID: 9519
DNA methylation as a system of plant genomic immunity
M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
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2014 | Journal Article | IST-REx-ID: 9458 | OA
Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes
J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
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2014 | Journal Article | IST-REx-ID: 9479 | OA
The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes
Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.
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2013 | Journal Article | IST-REx-ID: 9459 | OA
The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
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2013 | Journal Article | IST-REx-ID: 9481 | OA
Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm
J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.
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2013 | Journal Article | IST-REx-ID: 9520 | OA
A conversation across generations: Soma-germ cell crosstalk in plants
X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
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2012 | Journal Article | IST-REx-ID: 9451 | OA
Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes
C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
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2012 | Journal Article | IST-REx-ID: 9535 | OA
DNA methylation, H2A.Z, and the regulation of constitutive expression
D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.
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2012 | Journal Article | IST-REx-ID: 9499 | OA
EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development
S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2012 | Journal Article | IST-REx-ID: 9497 | OA
Deposition of histone variant H2A.Z within gene bodies regulates responsive genes
D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2012 | Journal Article | IST-REx-ID: 9528
Regulation of biological accuracy, precision, and memory by plant chromatin organization
J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.
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2011 | Journal Article | IST-REx-ID: 9483 | OA
Regulation of imprinted gene expression in Arabidopsis endosperm
T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2011 | Other Publication | IST-REx-ID: 9522 | OA
Balancing parental contributions in plant embryonic gene activation
D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011.
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2010 | Journal Article | IST-REx-ID: 9485 | OA
Local DNA hypomethylation activates genes in rice endosperm
A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2010 | Journal Article | IST-REx-ID: 9489 | OA
Evolution of eukaryotic DNA methylation and the pursuit of safer sex
A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2010 | Journal Article | IST-REx-ID: 9452
Genome-wide evolutionary analysis of eukaryotic DNA methylation
A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.
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2009 | Journal Article | IST-REx-ID: 9453 | OA
Genome-wide demethylation of Arabidopsis endosperm
T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer, D. Zilberman, Science 324 (2009) 1451–1454.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2008 | Journal Article | IST-REx-ID: 9537
The evolving functions of DNA methylation
D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.
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2008 | Journal Article | IST-REx-ID: 9457 | OA
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2007 | Journal Article | IST-REx-ID: 9487 | OA
DNA demethylation in the Arabidopsis genome
J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2007 | Other Publication | IST-REx-ID: 9504
The human promoter methylome
D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.
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2007 | Journal Article | IST-REx-ID: 9524 | OA
Genome-wide analysis of DNA methylation patterns
D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2006 | Journal Article | IST-REx-ID: 9505
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.
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2005 | Journal Article | IST-REx-ID: 9491 | OA
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2005 | Journal Article | IST-REx-ID: 9514 | OA
Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis
R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2005 | Journal Article | IST-REx-ID: 9529
Epigenetic inheritance in Arabidopsis: Selective silence
D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562.
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2004 | Journal Article | IST-REx-ID: 9493 | OA
Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats
D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2004 | Journal Article | IST-REx-ID: 9517 | OA
Genetic and functional diversification of small RNA pathways in plants
Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.
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2004 | Journal Article | IST-REx-ID: 9511 | OA
Silencing of transposons in plant genomes: kick them when they're down
D. Zilberman, S. Henikoff, Genome Biology 5 (2004).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 

2004 | Journal Article | IST-REx-ID: 9454
RNA silencing genes control de novo DNA methylation
S.W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.
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2003 | Journal Article | IST-REx-ID: 9495 | OA
Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation
X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E. Jacobsen, Current Biology 13 (2003) 2212–2217.
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2003 | Journal Article | IST-REx-ID: 9455
ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation
D. Zilberman, Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719.
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2001 | Journal Article | IST-REx-ID: 9444
Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation
A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff, S.E. Jacobsen, Science 292 (2001) 2077–2080.
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