A New Twist on Transposons: The Maize Genome Harbors Helitron Insertion

Transposable elements (transposons or TEs), which are capable of transferring segments of DNA (or of being transferred) from one site to another within a genome, are abundant in eukaryotic genomes. The highly repetitive, largely noncoding sequence that is prevalent in eukaryotic genomes consists largely of TEs. TEs make up nearly half of the human genome (Lander et al., 2001) and an estimated 50 to 80% of some grass genomes, such as that of maize (Meyers et al., 2001). Eukaryotic TEs can be divided into two classes: class-1 elements (retrotransposons) transpose via an RNA intermediate, whereas class-2 elements (DNA transposons) do not (reviewed by Feschotte et al., 2002). There are numerous families of TEs within each class, based on features that include length and target site preference. TEs of both classes are further classified as autonomous or nonautonomous, based on whether or not they encode, within the element, the proteins necessary for their own transposition. Nonautonomous TEs retain specific borders and certain other features characteristic of their families (which may include portions of transposase genes) and are transposed by means of proteins encoded by other, autonomous TEs within the same family. Most TEs found in present-day genomes are nonautonomous and are presumed to be remnants of autonomous TEs that have experienced deletions, inversions, or other rearrangements (Feschotte et al., 2002). Until recently (Kapitonov and Jurka, 2001), all class-2 elements were thought to transpose via a “cut-and-paste” mechanism that results in terminal repeats and target-site duplications flanking the element (Craig, 1995). Kapitonov and Jurka (2001) described a new type of DNA transposon, called a Helitron , that is presumed to transpose as a rolling circle replicon, similar to some known prokaryotic rolling circle transposons. The Helitrons were discovered by computational analysis of genomic sequences from Arabidopsis, rice, and Caenorhabditis elegans . The analysis consisted of searching genomic sequences for DNA repeats (prospective TEs), grouping repeats into distinct categories, and then generating consensus sequences for presumed autonomous elements without the various insertions and deletions present in inactive or nonautonomous copies. The Helitrons discovered in this “in silico”