Grant: Discovery Grants Program - Individual

DNA transposable elements, also called mobile elements or transposons, are DNA elements that can move or copy from one location to another in genomes. They exist in the genomes of most organisms from bacteria to humans and constitute as much as 85% of the plant and animal genomes. For humans, ~50% the genome comprises of transposable elements in more than two million copies of many classes. Despite once considered as "Junk DNA", transposable elements are now known to play important roles in generating inter- and intra-species genetic diversity and impacting gene function and phenotype through a plethora of molecular mechanisms. However, much is still unknown about the degree of their impact and specific mechanisms, especially in non-model organisms. Our research aims to further our understanding about the roles of transposable elements in genomes using a few organisms as models, including human, other primates, mouse, rhesus monkey, lavender, and grapevine. Specifically, we will study the role of transposable elements in human evolution by comparatively analyzing the genomes of Neanderthals, Denisovans, ancient human samples, and present-day human populations. The results will allow us to re-examine the hot and debated theory of admixture among Homo species/subspecies using transposable elements as superior genetic markers and better understand the human migration pattern and population structure and history. We will expand similar research into rhesus monkey and mouse to provide comprehensive profiling of inter- and intra-species genetic diversity contributed by transposable elements in these species. We will also examine the role of transposable elements in defining chromosomal topological associating domains for their regulatory rules in an evolutionary and development context. In addition, we will perform detailed analysis of long-terminal retrotransposons, the major type of transposable elements in plant genomes, regarding their contribution to gene function in lavender and intra-species genetic diversity in grapevine. Polymorphism data from the research will be shared with the research community via our flagship dbRIP database to expand its coverage to mouse, rhesus monkey, and grapevine. In addition to addressing important biological questions, our research will also generate valuable resources for genomics research communities in forms of databases and genomics/bioinformatics tools. Furthermore, the research program will provide HQP training with highly demanded skills of genomics/bioinformatics/high-throughput data analytics on high performance computing platforms.