Dr Daniel Zilberman

Project Leader
Cell and Developmental Biology

Daniel studies cytosine methylation as a mechanism for epigenetic inheritance.

He uses Arabidopsis alongside other evolutionary significant species to understand how the pattern of methylation is both inherited and altered over generations to influence developmental processes such as flowering.

Daniel is working with mathematical modellers to understand how methylation is controlled and how it can subtly manipulate gene expression.

Daniel is also interested in the mechanism of demethylation during genomic imprinting.

  • Cytosine methylation for epigenetic inheritance
  • Patterns of methylation and the influence on plant development
  • The mechanism demethylation during genomic imprinting 


Most of the information that passes from one generation of cells to the next is encoded in the DNA sequence. However, there is increasing appreciation that cells also receive inherited information through other mediums, known collectively as epigenetic. We study cytosine DNA methylation, a key epigenetic mechanism in plant and animal cells.

Cytosine methylation is able to carry epigenetic information because it is precisely copied when the DNA is replicated. Methylation regulates gene expression, and accurate reproduction of DNA methylation patterns during cell division is therefore essential for plant and animal development, efficient agriculture, and human health.

The enzymes that maintain DNA methylation have to work within chromatin, and particularly to contend with nucleosomes – tight complexes of DNA and histone proteins.

Daniel's group combines genetic, genomic and biochemical approaches to understand the maintenance and function of DNA methylation within chromatin using the flowering plant Arabidopsis thaliana as the primary model. They also study a variety of other species to understand the complex evolution of eukaryotic DNA methylation.

Postdoctoral Researchers vacancies

We’re looking for Postdoctoral Researchers to join the Zilberman lab studying the inheritance, function and evolution of DNA methylation.


Tel: 01603 450533

Professor Daniel Zilberman receives Consolidator Grant from the European Research Council

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Selected Publications

Lyons D. B., Zilberman D. (2017)

DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes.

eLife 6

Publisher’s version: 10.7554/eLife.30674

Huff J. T., Zilberman D., Roy S. W. (2016)

Mechanism for DNA transposons to generate introns on genomic scales.

Nature 538 p533-536

Publisher’s version: 10.1038/nature20110

Zemach A., Kim M. Y., Hsieh P. H., Coleman-Derr D., Eshed-Williams L., Thao K., Harmer S. L., Zilberman D. (2013)

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin.

Cell 153 p193-205

Publisher’s version: 10.1016/j.cell.2013.02.033

Ibarra C. A., Feng X., Schoft V. K., Hsieh T. F., Uzawa R., Rodrigues J. A., Zemach A., Chumak N., Machlicova A., Nishimura T., Rojas D., Fischer R. L., Tamaru H., Zilberman D. (2012)

Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.

Science 337 p1360-1364

Publisher’s version: 10.1126/science.1224839

Recent Publications

Frost J. M., Kim M. Y., Park G. T., Hsieh P. H., Nakamura M., Lin S. J. H., Yoo H., Choi J., Ikeda Y., Kinoshita T., Choi Y., Zilberman D., Fischer R. L. (2018)

FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis.

Proceedings of the National Academy of Sciences of the United States of America 115 pE4720-E4729

Publisher’s version: 10.1073/pnas.1713333115

Park K., Kim M. Y., Vickers M., Park J. S., Hyun Y., Okamoto T., Zilberman D., Fischer R. L., Feng X., Choi Y., Scholten S. (2016)

DNA demethylation is initiated in the central cells of Arabidopsis and rice.

Proceedings of the National Academy of Sciences of the United States of America 113 p15138-15143

Publisher’s version: 10.1073/pnas.1619047114

Zemach A., McDaniel I. E., Silva P., Zilberman D. (2010)

Genome-wide evolutionary analysis of eukaryotic DNA methylation.

Science 328 p916-9

Publisher’s version: 10.1126/science.1186366

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Daniel received a B.S with Honours in Biology from the California Institute of Technology, Pasadena, in 1998.  He received his PhD in Molecular and Cell Biology from the University of California, Los Angeles in 2004, working with Dr Steven Jacobsen.  Daniel then worked as a postdoctoral fellow in Chromatin Biology in the Fred Hutchingson Cancer Research Center, Seattle in 2007 with Dr Steven Henikoff.  From 2007-2017 Daniel worked in the Department of Plant and Microbial Biology at the University of California, Berkeley, initially as a Assistant Professor and then as an Associate Professor. In 2017 Daniel started working as a Project Leader in the Department of Cell and Developmental Biology at the John Innes Centre, Norwich UK.



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01603 450962, comms@jic.ac.uk

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