Dr. Dafang Wang
Dynamic epigenetic control of transposon silencing
Transposable elements (TEs) are ubiquitous mobile genetic elements in all eukaryotes that are generally considered to be “parasitic” DNA sequences because they can replicate themselves and insert into new locations within genomes, which can cause deleterious mutations. All branches of life have evolved strategies to repress TE activity. TE silencing in plants and animals share many similarities. Therefore, discoveries in plants can advance our understanding of TE silencing in animal systems, which is directly related to human health. We propose to use maize to study the initiation and maintenance of TE silencing. We have developed a novel model system in which a naturally active Mutator element can be silenced by a silencing trigger that is a source of small RNAs. This makes it possible for us to trigger and then monitor the initiation of silencing in various tissues and at various time points. We have observed a novel silencing phenotype from this system and have obtained high throughput sequencing data of mRNA and small RNA in different tissues at different developmental stages. This provides us with unique advantages in the investigation of the dynamic epigenetic control of transposons during development. We propose to analyze these data to determine the genes involved in this novel silencing mechanism, and to use our TE silencing system to examine how these changes are associated with changes in the initiation of TE silencing. In addition, plants can serve as a powerful tool for understanding the role that DNA methylation plays in adaptation, a topic of considerable interest among biologists investigating epigenetics in both plant and animal systems. We have obtained bisulfite sequencing data from several modern maize lines and their ancestor, teosinte, and have developed an in-house algorithm that can effectively estimate the patterns of selection on DNA methylation using a methylation site frequency spectrum (mSFS). By applying the algorithm, we can investigate the evolutionary forces acting on methylation variation of transposons in maize and identify epigenetic selection signatures during maize domestication. A key feature of our proposed activities involves training. Undergraduate students will be trained to analyze high throughput sequencing data. A hands-on bioinformatics workshop will also be hosted to local high school students to promote STEM education for our community.