This project investigates a biological mechanism, called paramutation, which is responsible for turning selected genes "on" and "off" in highly predictable ways and for passing these "on" and "off" states to future generations. Similar to the well-known process of mutation, paramutation generates heritable biological variation that impacts evolutionary success. Unlike mutations, however, paramutations occur without changes to the DNA code. The project thus addresses an exception to an established rule of modern genetics by asking how regulatory information is altered and transmitted to offspring in the absence of DNA changes. The work will be carried out in corn, the preeminent model for studying the paramutation mechanism because the "on" and "off" states of genes responsible for plant color are visually tracked, controlled matings are simple to perform, and detailed multigenerational pedigrees can be generated and evaluated. A working model for paramutation has been proposed based on research and this project tests specific aspects of that model. The project will also identify novel molecules and chromosome structures responsible for the "on" and "off" switching during paramutations. Because paramutation occurs in both plants and animals, the results of this research could have broad biological impact, ranging from increased understanding of reproductive biology and genetics to development of novel strategies for improving agriculture or animal health. Educational materials such as colorful corn ears will be generated and made available through existing outreach programs for teaching both basic and advanced genetic concepts in the classroom. The activities integrate the training of young scientists at undergraduate and graduate levels as well as provide research experiences for high school students.
Paramutation describes a behavior in which specific trans-homolog interactions result in meiotically-heritable regulatory alterations. This behavior is potentially mediated by small RNAs but the mechanism remain largely unknown. A model system was developed using plant and flower color to define the molecular mechanism of paramutation occurring in maize. Expression of the purple plant1 gene is monitored with visible pigments. A strong purple state of the Pl1-Rhoades (Pl1-Rh) allele can change to weaker expression states referred to as Pl'. When purple types (Pl/Pl) are mated with weakly pigmented plants (Pl/Pl'), only weakly pigmented progeny - from which only Pl' states are sexually transmitted - are obtained; this is a classic example of paramutation. Forward genetics identifies important cis-acting regions and fifteen loci whose functions are required to maintain repression (rmr) of Pl' states. Prior projects helped identify five RMR proteins acting in a presumed small RNA-directed DNA methylation pathway and led to the discovery of a co-transcriptional repression mechanism operating to maintain meiotically-heritable regulatory states established by paramutation. This project builds on this emerging mechanistic understanding by combining forward genetics, molecular profiling, and mutant analyses to specifically 1) test working models of the paramutation mechanism by profiling transcription, small RNA levels, and cytosine methylation patterns during paramutation events, 2) functionally define cis-acting sequences responsible for paramutation behaviors through structural characterizations of mutant Pl1-Rh alleles, and 3) discover additional molecular components governing paramutations through positional-based cloning of additional rmr loci. Training and outreach opportunities are integrated in these efforts to provide a greater understanding of fundamental eukaryotic genetics and genome biology.
This project is jointly funded by the Genetics Mechanisms Cluster in the Division of Molecular and Cellular Biosciences and the Plant Genome Research Program in the Division of Integrative Organismal Systems.
