Miniature Inverted‐Repeat Transposable Elements and Their Relationship to Established DNA Transposons

Abstract

With the advent of genome sequencing projects, vast amounts of DNA sequence, from a wide variety of plant and animal species, have become available for analysis. Miniature inverted-repeat transposable elements (MITEs), with their high copy number, distinct structural features (target site duplications [TSDs] and terminal inverted repeats [TIRs]), and compact stature, are relatively easy to mine from DNA sequence databases. Comparison of the transposase-encoding Tc elements and the numerous MITE families suggested possible scenarios for the origin of MITEs in Caenorhabditis elegans. Several groups independently discovered an abundant family of short (80-bp) palindromic elements, called Mrs or Made1. The TIRs are 80 to 100% similar to those of mariner-like elements (MLEs) that are dispersed in the genome. These were the first MLEs identified in mammals and were subsequently grouped into the Hsmar1 family. Plant MITEs related to pogo-like transposons have only been identified in Arabidopsis. Phylogenetic analyses of over 100 plant MLE transposase sequences revealed the existence of multiple and divergent lineages of MLE transposases. Together these results provide an explanation for the proliferation, diversity, and success of Stowaway MITEs in plant genomes. P instability factor (PIF) is an active DNA element family first discovered as multiple mutagenic insertions into the maize R gene. Several MITE families described from plants, animals, and fungi do not share any structural or sequence features with known DNA transposon families. The proliferation of nonautonomous elements has been hypothesized to lead to the extinction of the cognate autonomous element through titration of active transposase.