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Friday, May 6, 2016 at 11:15am
Daniel Zilberman
Associate Professor, University of California Berkley
Research: Chromatin Biology
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.
Abstract: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Through a comprehensive analysis of DNA methylation in the genome of Arabidopsis thaliana, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation, and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin. Together, DDM1 and RdDM mediate nearly all transposon methylation, and collaborate to repress transposition and regulate the methylation and expression of genes. Our results suggest that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.
Tara Reed
607.255.2131
Daniel Zilberman Ph.D.
University of California Berkley
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