Daniel Zilberman

Assistant Professor
Ph.D.  MCD Biology    University of California, Los Angeles, 2004
B.S.   Biology    California Institute of Technology, 1998

211 Koshland Hall
Berkeley, California 94720
danielz@berkeley.edu
office: 510-642-8151   lab: 510-642-9550   fax:  510-642-4995

Web site         Recent publications      People

The genetic material of virtually all eukaryotes exists as chromatin. The basic unit of chromatin is a nucleosome, an octameric complex of histones H2A, H2B, H3 and H4, around which about 150 base pairs of DNA are wrapped. Chromatin is a complex and highly dynamic environment. Nucleosomes are differentiated by variants of histones H2A and H3 and by many histone post-translational modifications, chromatin-associated proteins and linker histones. Nucleosomes are positioned both by the underlying DNA sequence and by remodeling enzymes and histone chaperones that can mobilize, disassemble or replace histone subunits. In most eukaryotes, chromatin is also modified by methylation of cytosine bases in DNA.

Our goal is to understand how chromatin components interrelate and integrate to regulate transcriptional activity. We combine genetics and biochemistry with genomics and computational analysis to study DNA methylation, deposition of histone variants, chromatin associated proteins and nucleosome remodeling. Our primary model organism is Arabidopsis, which has a compact, gene-rich genome with extensive DNA methylation and numerous viable mutants in key chromatin-related proteins. These features provide an exciting opportunity to analyze chromatin on a genome-wide scale.

Tzung-Fu Hsieh, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer and Daniel Zilberman. (2009) "Genome-wide demethylation of Arabidopsis endosperm." Science, 324: 1451-1454. PDF

Daniel Zilberman (2008) “The evolving functions of DNA methylation.” Current Opinion in Plant Biology, 11: 554-559. PDF

Daniel Zilberman*, Devin Coleman-Derr, Tracy Ballinger and Steven Henikoff. (2008) “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks.” Nature, 456: 125-129. *Corresponding author. PDF     Research focus in TIBS, 34: 158-161. PDF

Daniel Zilberman and Steven Henikoff. (2007) “Genome-wide analysis of DNA methylation patterns.” Development, 134: 3959-3965. PDF

Daniel Zilberman (2007) “The human promoter methylome.” Nature Genetics, 39: 442-443. PDF

Jon Penterman, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff and Robert L. Fischer. (2007) “DNA demethylation in the Arabidopsis genome.” PNAS, 104: 6752-6757. PDF

Daniel Zilberman, Mary Gehring, Robert K. Tran, Tracy Ballinger and Steven Henikoff. (2006) “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.” Nature Genetics, 39: 61-69. PDF

Robert K. Tran, Daniel Zilberman, Cecilia De Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, Tom Boyle, Samson Kwong, Terri D. Bryson, Steven E. Jacobsen and Steven Henikoff. (2005) “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis.” Genome Biology, 6: R90. PDF

Daniel Zilberman and Steven Henikoff. (2005) “Epigenetic inheritance in Arabidopsis: selective silence.” Current Opinion in Genetics & Development, 15: 557-562. PDF

Robert K. Tran, Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen and Steven Henikoff. (2005) “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.” Current Biology, 15: 154-159. PDF

Daniel Zilberman and Steven Henikoff. (2004) “Silencing transposons: kick them when they’re down.” Genome Biology, 5: 249-253. PDF

Daniel Zilberman, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington and Steven E. Jacobsen. (2004) “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.” Current Biology, 14: 1214-1220. PDF

Zhixin Xie, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen and James C. Carrington. (2004) “Genetic and functional diversification of small RNA pathways in plants.” PLoS Biology, 2: 644-652. PDF

Simon W.-L. Chan, Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James C. Carrington and Steven E. Jacobsen. (2004) “RNA silencing genes control de novo DNA methylation.” Science, 303: 1336. PDF

Xiaofeng Cao, Werner Aufsatz, Daniel Zilberman, M. Florian Mette, Michael S. Huang, Marjori Matzke and Steven E. Jacobsen. (2003) “Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation.” Current Biology, 13: 2212–2217. PDF

Daniel Zilberman, Xiaofeng Cao and Steven E. Jacobsen. (2003) “ARGONAUTE4 control of locus specific siRNA accumulation and DNA and histone methylation.” Science, 299: 716-719. PDF

Anders Lindroth, Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff and Steven E. Jacobsen. (2001) “Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.” Science, 292: 2077-2080. PDF