Roles of DNA mobile elements in primate genomes

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DNA mobile elements, also called transposable elements or transposons, are DNA elements that can move or copy from one location to another in the genomes. They exist in the genomes of most organisms from bacteria to humans, and constitute as much as 85% in some plant and animal genomes. In the human genome, more than 50% of the DNA sequences are comprised of mobile elements, which are represented by more than 5 million individual elements from many families and subfamilies of mobile elements. Although once considered as “Junk DNA”, mobile elements are now known to play important roles in shaping the genome evolution of species and in contributing to specific gene functions through a plethora of molecular mechanisms. However, much is still unknown about the degree of their impact on genome evolution and gene function, as well as their specific mechanisms, especially in a species-specific fashion. ******In the next five years, we aim to further our understanding of mobile elements using primates, especially human, as models. As the best-studied organism with the best quality of a reference genome and gene annotation, as well as the availability of a large number of personal genomes, the human serves as an ideal model for our research questions. The genome sequences of many other primate species closely related to human have also become available recently. This permits us to perform both inter- and intra-species comparative genomic studies. Specifically, we will first examine the differences in mobile element compositions, location, and potential impact on gene functions in a species-specific fashion for at least eight primate species through a comparative genomic approach. We will then study the mobile elements in the human genome in detail to examine their profile changes during human evolution, contribution to genetic polymorphism among human individuals, and participation in the human transcriptomes. We will continue to maintain/update our flagship dbRIP database, which documents the genetic polymorphisms derived from mobile element insertions. Further, we aim to provide complete sequence characterization of mobile element variants in humans and develop bioinformatics resources to provide more streamlined and accurate personal genome analysis.******While addressing these important biological questions, the proposed studies will also build valuable resources for the genomics/genetic research communities. They will also develop multi-disciplinary collaborations and provide HQP training in the highly demanded areas of genomics and bioinformatics.