Alleles of imprinted genes are expressed differently depending on whether they are inherited from the male or female parent. Imprinting regulates a number of genes essential for normal development in mammals and flowering plants (angiosperms). In mammals, imprinted genes contribute to the control of fetal growth and placental development. The endosperm, one of the products of angiosperm double fertilization, is an important site of imprinting in plants. The endosperm has functions analogous to the placenta and supports seed growth and development. Failure to imprint certain genes results in embryo abortion and seed death. Genetic and molecular studies have shown that epigenetic regulation, particularly parent-specific gene expression (genomic imprinting), plays an essential role in endosperm development, influencing seed size and quality. The model plant Arabidopsis is being used to study how gene imprinting is epigenetically regulated. Epigenetic information resides in chromatin, DNA and its associated proteins, which exists in an open conformation with the genes accessible to transcription factors or in a compacted conformation that silences genes. Two interdependent processes regulate chromatin conformation: Polycomb group proteins methylate histone proteins around which the DNA is wrapped, and the DME DNA glycosylase demethylates DNA. In Arabidopsis, the DME DNA demethylase and Polycomb group proteins (MEA, FIS2) are the primary regulators of gene imprinting. However, very few sites of action of these proteins, and only a handful of imprinted genes, have been identified. This project will implement highly efficient genomic technologies to systematically elucidate the network of imprinted genes in Arabidopsis endosperm. Specifically, the research will identify all imprinted genes, distinguish all imprinted genes demethylated by DME, define imprinted genes regulated by Polycomb group proteins, and functionally analyze imprinted genes. These studies will lead to a comprehensive understanding of the regulation and function of gene imprinting in angiosperms.
Broader Impacts: This research will advance understanding of endosperm, a major component of crop seeds and the site of synthesis and storage of protein, starch, and lipid nutrients that comprise half of the world food supply. Imprinted genes influence seed yield by controlling resource allocation to the endosperm. Understanding this important process will enable new technologies that increase crop yield and food production to feed a growing population and to address the problem of hunger in our society. Because this research combines genetics with genomics and computational analysis, the students who participate will receive invaluable cross-disciplinary training that will enable them to address future questions that require a multifaceted approach. Moreover, the teaching of science to undergraduates will be integrated into the research activities through collaboration with programs designed to promote the success of undergraduate students from groups underrepresented in the biological sciences and by incorporating research results and state-of-the-art genomic and computational approaches into plant biology lecture and laboratory classes.
Our research advanced the understanding of endosperm, a major component of crop seeds and the site of synthesis and storage of protein, starch, and lipid nutrients that comprise half of the world food supply. Imprinted genes influence seed yield by controlling resource allocation to the endosperm. We identified a large number of new imprinted genes in the endosperm of the model plant Arabidopsis thaliana, many of which are likely to regulate gene expression and hormone signaling. Our results demonstrated that imprinted gene expression is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. We also investigated how imprinted genes are regulated. We showed that active removal of a chemical modification of DNA called methylation by the protein DEMETER is required for the proper expression of multiple imprinted genes. We also found that active removal of methylation in the precursor cell of the nutritive endosperm, as well as in an analogous cell in the pollen, is very extensive, affecting thousands of genomic sequences. We found that this process can communicate information to the female and male gametes, contributing to genome stability and gene regulation in the next generation. We believe that our results will enable new technologies that increase crop yield and food production to feed a growing population and to address the problem of hunger in our society.
