Most plants have very large genomes due to the presence of huge amounts of repetitive DNA. It has been estimated that up to half of the interspersed repetitive component is derived from mobile DNA, the vast majority of which is no longer capable of transposition. To identify the active mobile component, thirty mutant alleles of the maize waxy gene have been cloned and over half found to contain insertion elements. Five active retro- transposon families have been isolate from these mutant alleles, making this the largest collection available among plants. These elements have led, in turn, to the identification of ancient retro-transposon insertions in thirty one plant genes and to the discovery of the first example of the transduction of a cellular gene by a non-viral retro-element (Bsl). Finally, a waxy mutations led to the discovery of an enormous superfamily of mobile elements (comprised of Tourist and Stowaway elements) found to be associated with over 125 normal genes of flowering plants. This proposal focuses on a detailed characterization of the retro-and Tourist/Stowaway elements because (i) they are still active and (ii) they have in the past, and presumably will continue, to contribute to genome evolution. The first part of the proposal concerns the mechanism of Tourist/Stowaway transposition. Two active subfamilies of Tourist elements have been identified. They will be further characterized with respect to the sequence of subfamily members, the ability to excise from DNA or even RNA, copy number in the wild relatives of maize and possible amplification during 96 generations of long term human selection. A novel strategy will be employed to isolate new insertions, including perhaps an autonomous element or members of other active subfamilies. Elements will be introduced into rice with the goal of studying transposition in an organism that has Tourist elements but lacks this superfamily. With regard to the retro-transposons, we will test the hypothesis that recently identified gene silencing mechanisms are responsible for the degradation of retro-transposon-encoded transcripts. Finally, experiments are proposed to determine whether the long chimeric open reading frame of the Bsl retro elements has been conserved because it has a role in growth and development.
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