Control of Ribosomal RNA Genes by Maintenance and de novo Methylation in Arabidopsis thaliana: Molecular Genetics and Evoluation of the Pol IV/Pol V System

Date of Award

Spring 5-15-2010

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Plant & Microbial Biosciences)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Proper gene regulation is critical to life. For example, ribosomal RNA (rRNA) genes are essential and exist in hundreds of copies, only a fraction of which are expressed at any given time. DNA methylation is required for the establishment and maintenance of rRNA gene silencing, but the mechanisms by which this DNA methylation is targeted to select sequences were previously unknown. Using a diverse set of methods including molecular biology techniques and computational analysis, I have investigated the mechanisms by which DNA methylation is targeted to silence specific DNA sequences, particularly rRNA genes, in two different Arabidopsis systems. In Arabidopsis thaliana, the maintenance methylation machinery is essential for silencing an rRNA variant. Alternatively, RNA‐directed de novo methylation, and not maintenance methylation, is required for silencing via nucleolar dominance in the interspecific hybrid A. suecica. This pathway typically involves the alternative RNA polymerases, Pol IV and Pol V. These plant-specific polymerases are made up of a series of subunits derived from those of RNA Pol II in a multi-step process, probably leading to the additive acquisition of functional differences among the three polymerases over evolutionary time. This work shows the wealth and diversity of mechanisms developed through plant evolution to accomplish the large-scale silencing of specific DNA sequences such as rRNA genes.


English (en)

Chair and Committee

Craig Pikaard

Committee Members

Yehuda Ben-Shahar, Douglas L. Chalker, Sarah Elgin, Elaine Mardis, Kenneth Olsen


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