Transposable elements (TEs) are interspersed repetitive sequences that are present in most genomes. Miniature inverted repeat transposable elements (MITEs) are the most numerous Class II elements in higher eukaryotes. Little is known about their origin, transposition and function. In this study, three novel MITE families (Kiddo, MDM1 and MDM2) were identified in the rice genome. They bear terminal inverted repeats (TIRs) and show target site duplications (TSDs) at the insertion sites. Each family is present in hundreds of copies with length that range from 200 bp to 400 bp. An evolutionary relationship between Mutator elements and MDM1 and MDM2 family was established. The absence of an observed transposition event, together with the mutated ancestral elements identified by in silico analysis, led to a conclusion that Kiddo and its autonomous elements are not presently active. To overcome laborious and time consuming manual analysis of MITEs on a genomic scale, MAK, a computational tool kit, was developed to automatically retrieve MITE sequences, their neighboring genes and ancestral elements from genome sequences. MAK has been functionally tested and is now available to the research community. Studies on the effect of MITE (Kiddo and MDM1) insertions into a rice ubiquitin (rubq2) promoter revealed a two-edged role of MITEs on gene regulation. While Kiddo and MDM1 contribute ~40% to rubq2 promoter activity, they also induce progressive silencing of this promoter. The evolutionary implications of the two-edged role of MITEs in gene regulation are discussed.

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