The maize required to maintain repression6 locus and its control of epigenotypes

While virtually all cells in a given multicellular organism contain an identical and complete complement of genes, variation in the expression of these genes produces the distinct tissues and organs that make up that organism. The information encoded in an organism's DNA comprises its "genotype," while the organizers that determine how and when that information is expressed act to specify distinct "epigenotypes". Together with environmental factors, the genotype and epigenotype determine the phenotype, the physical and biochemical characteristics of a tissue or organism. While the factors contributing to the genotype appear well understood, the molecules and mechanisms determining distinct epigenotypes are less clear.;Paramutation-induced repression of specific maize purple plant1 (pl1) alleles provides a model system in which to investigate mechanisms responsible for epigenetic change. Several trans-acting factors that are required for maintenance of epigentically repressed Pl1-Rhoades alleles have been isolated in mutant screens. One, mediator of paramutation1 (mop1) encodes a putative RNA-dependent RNA polymerase, while another, required to maintain repression1 (rmr1) encodes a Snf2-like protein. A third factor, encoded by the rmr6 locus, is required for meiotically heritable transcriptional repression of specific epigenetic states of certain alleles. The identity and function of rmr6 is of particular interest because loss of its function leads to various developmental abnormalities. My thesis research shows that most of the phenotypes documented in rmr6 mutants resemble those of plants deficient in the production or function of specific microRNAs. This finding, along with the similarity of RMR1 and MOP1 to molecules functioning in Arabidopsis RNA-directed DNA methylation, suggest that rmr6 maintains repressive chromatin conformations induced by non-coding RNA molecules.;My thesis research results show that rmr6 contributes directly to the epigenotype because it is required to maintain tissue-specific expression of factors that affect key developmental processes. Efforts to determine the molecular identity of rmr6 through positional cloning resulted in the delineation of a small physical interval from which potential candidate genes can be selected for sequencing and analysis. A collection of rmr6 mutant alleles was isolated for the identification of molecular lesions in candidate genes. The identification of the rmr6 gene product will contribute novel information to a growing body of knowledge about chromosome structure and function as it is related to defining the epigenotype.