| Often during the formation of inter-species hybrids or allopolyploids a complete set of ribosomal RNA genes derived from one of the progenitors of the hybrid becomes transcriptionally repressed in a phenomenon called nucleolar dominance. In the seventy years since this phenomenon was originally observed a satisfying mechanism explaining nucleolar dominance has not been elucidated. The observation that DNA methylation and histone deacetylation are required to maintain repression of rRNA genes subjected to nucleolar dominance suggested that the repression is epigenetic. In the course of investigating nucleolar dominance genetically, molecularly, and cytologically we have provided insight into how rRNA genes are maintained in distinct epigenetic gene expression states. These results demonstrate that repressed rRNA genes are enriched with histone H3 methylated at lysine 9 and have hypermethylated promoter cytosines whereas active rRNA genes are enriched with histone H3 methylated at lysine 4 and have hypomethylated promoter cytosines. Interestingly, switching rRNA genes from a repressed to an active state by inhibiting either DNA methylation or histone deacetylation results in a coordinated loss of DNA methylation and H3 lysine 9 methylation and an enrichment of H3 lysine 4 methylation. These results imply that a concerted histone methylation/DNA methylation switch directs the assembly of rRNA genes into alternative chromatin states. At least two histone deacetylases, HDA6 and HDT1, are key components of this epigenetic switch. |
