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47 Publications


2023 | Journal Article | IST-REx-ID: 12672 | OA
Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons
D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).
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2022 | Book Chapter | IST-REx-ID: 12294
An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis
R. Kumar, M. Reichelt, N.C. Bisht, in:, J. Jez (Ed.), Biochemical Pathways and Environmental Responses in Plants: Part A, Elsevier, 2022, pp. 49–69.
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2021 | Journal Article | IST-REx-ID: 10533 | OA
Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin
J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).
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2021 | Journal Article | IST-REx-ID: 9877 | OA
Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting
J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).
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2020 | Journal Article | IST-REx-ID: 9526 | OA
DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts
J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77 (2020) 310–323.e7.
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2019 | Journal Article | IST-REx-ID: 9460 | OA
DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm
M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
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2019 | Journal Article | IST-REx-ID: 9530 | OA
DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development
K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).
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2018 | Journal Article | IST-REx-ID: 9471 | OA
FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis
J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.
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2017 | Journal Article | IST-REx-ID: 9445 | OA
DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
D.B. Lyons, D. Zilberman, ELife 6 (2017).
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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).
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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.
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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.
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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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