RNA Silencing Pathways and Ribosomal RNA Gene Inactivation in Arabidposis

Date of Award

Spring 5-15-2010

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Arabidopsis small RNA silencing pathways are essential for regulating growth and maintaining genome integrity. There are at least five RNA silencing pathways, including the micro-RNA (miRNA), trans-acting small-interfering RNA (ta-siRNA), viral defense/transgene siRNA, natural cis-antisense siRNA (nat-siRNA), and heterochromatic siRNA pathways. The colocalization of the main components of these pathways in Cajal Bodies suggests that these nucleolus-associated bodies act as an intersection for multiple small RNA silencing pathways, possibly facilitating redundancy within the system. In addition to silencing retrotransposons and pericentric repeats, the heterochromatic siRNA pathway is responsible for establishing a repressive chromatin state at ribosomal RNA genes subjected to the epigenetic phenomena, nucleolar dominance. In this phenomenon, one parental set of rRNA genes is specifically silenced in a genetic hybrid. HISTONE DEACETYALSE 6 (HDA6) and METHYLCYTOSINE BINDING DOMAIN PROTEIN 6 (MBD6) are required for maintaining the repressed state of the silenced rRNA genes in the allotetraploid hybrid A. suecica. HDA6 and MBD6 are also required for maintaining rRNA gene silencing in A. thaliana. By mass spectrometric analysis of affinity purified HDA6, a novel AT-hook motif protein that interacts with HDA6 was identified. We named this protein AT-hook domain Protein interacts with HDA6 (APH). Whereas HDA6 is unable to bind to DNA or chromatin, APH can bind DNA and recruit HDA6 into a ternary complex. Analysis of aph mutants indicates a role for this protein in silencing a subset of HDA6-dependent loci.


English (en)

Chair and Committee

Craig Pikaard

Committee Members

Douglas L. Chalker, Sarah R. Elgin, Susana Gonzalo, Tim B. Schedl, Heather L. True-Krob


Permanent URL: https://doi.org/10.7936/K7542KJ4

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