Daniel Zilberman
Chromatin
Associate Professor
211 Koshland Hall
Berkeley, CA 94720
Phone 510.642.8151
Lab Phone 510.642.9550
Fax 510.642.4995

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

Research

Chromatin Biology

Biotin-tagged histone H2A.Z (Green)
Biotin-tagged histone H2A.Z (green) and DNA (blue) in an Arabidopsis root nucleus.

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.

Genome

Recent Publications

Jason T. Huff and Daniel Zilberman. (2014) "Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes." Cell, 156: 1286-1297. PDF

M. Yvonne Kim and Daniel Zilberman. (2014) "DNA methylation as a system of plant genomic immunity." Trends in Plant Science, http://dx.doi.org/10.1016/j.tplants.2014.01.014. PDF  

Jessica A. Rodrigues, Randy Ruan, Toshiro Nishimura, Manoj Sharma, Rita Sharma, Pamela C. Ronald, Robert L. Fischer, and Daniel Zilberman. (2013) “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm.” PNAS, 110: 7934-7939. PDF

Assaf Zemach, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. (2013) "The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin." Cell, 153: 193-205. PDF  
    Preview in Molecular Cell, 49: 1021-1022. PDF

Xiaoqi Feng, Daniel Zilberman and Hugh Dickinson (2013) “A conversation across generations: soma-germ cell crosstalk in plants.” Developmental Cell, 24: 215-225. PDF

Devin Coleman-Derr and Daniel Zilberman (2012) “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology, 77: 147-154. PDF

Devin Coleman-Derr and Daniel Zilberman (2012) “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes.” PLoS Genetics, 8(10): e1002988. PDF

Christian A. Ibarra, Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, Nina Chumak, Adriana Machlicova, Toshiro Nishimura, Denisse Rojas, Robert L. Fischer, Hisashi Tamaru, and Daniel Zilberman (2012) “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.” Science, 337: 1360-1364. PDF

Sang Yeol Kim, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman*, and Z. Renee Sung* (2012) “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development.” PLoS Genetics, 8(3): e1002512. *Corresponding authors. PDF

Jason T. Huff and Daniel Zilberman (2012) “Regulation of biological accuracy, precision, and memory by plant chromatin organization.” Current Opinion in Genetics and Development, 22: 132-138. PDF

Daniel Zilberman (2011) “Balancing parental contributions in plant embryonic gene activation.” Developmental Cell, 20: 735-736. PDF

Tzung-Fu Hsieh, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, Ryan C. Kirkbride, John J. Harada, Daniel Zilberman*, and Robert L. Fischer*. (2011) “Regulation of imprinted gene expression in Arabidopsis endosperm.” PNAS, 108: 1755-1762. *Corresponding authors. PDF

Assaf Zemach, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. (2010) “Local DNA hypomethylation activates genes in rice endosperm.” PNAS, 107: 18729-18734. PDF

Assaf Zemach and Daniel Zilberman. (2010) “Evolution of eukaryotic DNA methylation and the pursuit of safer sex.” Current Biology, 20: R780-785. PDF

Assaf Zemach, Ivy E. McDaniel, Pedro Silva and Daniel Zilberman. (2010) "Genome-wide evolutionary analysis of eukaryotic DNA methylation." Science, 328: 916-919. PDF  
    Nature news, research highlights in Science, 328: 837-838. PDF and PNAS, 107: 9027-9028. PDF

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
    Research highlights in Nature, 459: 893. PDF,  Current Biology, 19: R649-R651. PDF   and Genome Biology, 10: 232. 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

Honors and Awards

Young Investigator Award - Arnold & Mabel Beckman Foundation - 2009
Fellowship - Leukemia & Lymphoma Society - 2005
Chancellor's Fellowship - UCLA - 1999