Computer-assisted discovery and characterization of rice transposable elements including the first active miniature-inverted repeat transposable element (MITE)

Abstract

The availability of draft sequences for the two subspecies of rice (Oryza sativa, japonica cv. Nipponbare and indica cv. 93-11) has significantly accelerated our understanding of transposable elements in the rice genome. The research described in this dissertation was performed with the expanding rice genomic database. First, 30 Mb of rice genomic sequence was analyzed to study the insertion preference of rice miniature inverted-repeat transposable elements (MITEs), numerically the most abundant elements in rice. Among the 6600 MITEs identified, > 10% were present as nested insertions (multimers) with the proportion of multimers differing among MITE families. The data suggest possible mechanisms underlying the formation of MITE multimers. The second part of this dissertation concerns Dasheng, a novel non-autonomous long terminal repeat (LTR) element with over 1000 copies. Two hundred and fifteen elements were mapped to all twelve rice chromosomes, where more than half of the elements were located in the heterochromatic regions around centromeres. By searching 100 Mb rice genomic sequences including the almost completely assembled chromosome 1, Dasheng elements were found to have inserted five times more frequently into pericentromeric regions than other regions. These features suggest Dasheng may serve as molecular markers for this marker-poor region of the genome. Finally, 187 Mb of genomic sequence was analyzed in a computational approach to isolate the first active DNA transposons from rice and the first active MITE from any organism. The 430 bp mPing, a Tourist-like MITE, was shown to be actively transposing in a cell culture line. Database searches identified a family of related transposaseencoding elements (called Pong) that were also activated to transpose in the same cells. Virtually all new insertions of mPing and Pong elements were into low copy regions of the genome. Intriguingly, the mPing MITEs have preferentially amplified since domestication in cultivars adapted to environmental extremes, a situation reminiscent of McClintock's genomic shock theory for transposon activation. The isolation of an active MITE family and putative autonomous elements may provide a valuable tagging population for gene discovery and allow us to address long-standing questions about the mechanisms underlying the birth, spread and death of MITEs.