Daniel Zilberman

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
    Daniel Zilberman
    University of California, 211 Koshland Hall, Berkeley, California 94720, USA
    Nature 456:125-9. 2008
  2. doi request reprint Genome-wide demethylation of Arabidopsis endosperm
    Tzung Fu Hsieh
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Science 324:1451-4. 2009
  3. ncbi request reprint Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats
    Daniel Zilberman
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Curr Biol 14:1214-20. 2004
  4. pmc Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm
    Jessica A Rodrigues
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 110:7934-9. 2013
  5. doi request reprint The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
    Assaf Zemach
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 153:193-205. 2013
  6. doi request reprint Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes
    Christian A Ibarra
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Science 337:1360-4. 2012
  7. doi request reprint Genome-wide evolutionary analysis of eukaryotic DNA methylation
    Assaf Zemach
    Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
    Science 328:916-9. 2010
  8. pmc Local DNA hypomethylation activates genes in rice endosperm
    Assaf Zemach
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:18729-34. 2010
  9. pmc Deposition of histone variant H2A.Z within gene bodies regulates responsive genes
    Devin Coleman-Derr
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 8:e1002988. 2012
  10. pmc Regulation of imprinted gene expression in Arabidopsis endosperm
    Tzung Fu Hsieh
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:1755-62. 2011

Collaborators

  • James C Carrington
  • Zhixin Xie
  • Hisashi Tamaru
  • Stacey L Harmer
  • Assaf Zemach
  • Tzung Fu Hsieh
  • Robert L Fischer
  • Xiaoqi Feng
  • Jessica A Rodrigues
  • Christian A Ibarra
  • Toshiro Nishimura
  • Devin Coleman-Derr
  • Jason T Huff
  • Rie Uzawa
  • Pedro Silva
  • Jon Penterman
  • Simon W L Chan
  • Randy Ruan
  • Rita Sharma
  • Manoj K Sharma
  • Hugh Dickinson
  • Pamela C Ronald
  • Adriana Machlicova
  • Denisse Rojas
  • Vera K Schoft
  • Nina Chumak
  • John J Harada
  • Stephanie Cohen
  • Ryan C Kirkbride
  • Meryl Hashimoto
  • Matthew J Bauer
  • Juhyun Shin
  • Leor Eshed-Williams
  • Jin Hoe Huh
  • Tracy Ballinger
  • Steven Henikoff
  • Steven E Jacobsen
  • Lisa K Johansen

Detail Information

Publications17

  1. pmc Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
    Daniel Zilberman
    University of California, 211 Koshland Hall, Berkeley, California 94720, USA
    Nature 456:125-9. 2008
    ..Z leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation...
  2. doi request reprint Genome-wide demethylation of Arabidopsis endosperm
    Tzung Fu Hsieh
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Science 324:1451-4. 2009
    ..Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo...
  3. ncbi request reprint Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats
    Daniel Zilberman
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Curr Biol 14:1214-20. 2004
    ....
  4. pmc Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm
    Jessica A Rodrigues
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 110:7934-9. 2013
    ..Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants...
  5. doi request reprint The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
    Assaf Zemach
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 153:193-205. 2013
    ..Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway...
  6. doi request reprint Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes
    Christian A Ibarra
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Science 337:1360-4. 2012
    ..Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations...
  7. doi request reprint Genome-wide evolutionary analysis of eukaryotic DNA methylation
    Assaf Zemach
    Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
    Science 328:916-9. 2010
    ..Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes...
  8. pmc Local DNA hypomethylation activates genes in rice endosperm
    Assaf Zemach
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:18729-34. 2010
    ..Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops...
  9. pmc Deposition of histone variant H2A.Z within gene bodies regulates responsive genes
    Devin Coleman-Derr
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 8:e1002988. 2012
    ..We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes...
  10. pmc Regulation of imprinted gene expression in Arabidopsis endosperm
    Tzung Fu Hsieh
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:1755-62. 2011
    ..We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development...
  11. pmc DNA demethylation in the Arabidopsis genome
    Jon Penterman
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:6752-7. 2007
    ..Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation...
  12. doi request reprint The evolving functions of DNA methylation
    Daniel Zilberman
    University of California, 211 Koshland Hall, Berkeley, CA 94720, United States
    Curr Opin Plant Biol 11:554-9. 2008
    ..A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more...
  13. doi request reprint Regulation of biological accuracy, precision, and memory by plant chromatin organization
    Jason T Huff
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Curr Opin Genet Dev 22:132-8. 2012
    ..These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory...
  14. doi request reprint Evolution of eukaryotic DNA methylation and the pursuit of safer sex
    Assaf Zemach
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Curr Biol 20:R780-5. 2010
    ..Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries...
  15. ncbi request reprint Genome-wide analysis of DNA methylation patterns
    Daniel Zilberman
    University of California, 211 Koshland Hall, Berkeley, CA 94720, USA
    Development 134:3959-65. 2007
    ..Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests...
  16. ncbi request reprint RNA silencing genes control de novo DNA methylation
    Simon W L Chan
    Department of MCD Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Science 303:1336. 2004
  17. doi request reprint A conversation across generations: soma-germ cell crosstalk in plants
    Xiaoqi Feng
    Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, Berkeley, CA 94720, USA
    Dev Cell 24:215-25. 2013
    ..Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes...