hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures Santiago Moreno-Va´zquez 1 , Jianchang Ning 2 and Blake C. Meyers 2,3, * 1 Departamento de Biologı´a Vegetal, E.T.S. Ingenieros Agro ´nomos, Universidad Polite´cnica de Madrid, 28040, Ciudad Universitaria Madrid, Spain; 2 Delaware Biotechnology Institute, University of Delaware, 19711, Newark, DE, USA; 3 Department of Plant and Soil Sciences, University of Delaware, 19714, Newark, DE, USA (*author for correspondence; e-mail meyers@dbi.udel.edu) Received 14 March 2005; accepted in revised form 1 June 2005 Key words: MITE, mobile element, rice, transposase, transposon Abstract We identified a 178 bp mobile DNA element in lettuce with characteristic CGAGC/GCTCG repeats in the subterminal regions. This element has terminal inverted repeats and 8-bp target site duplications typical of the hAT superfamily of class II mobile elements, but its small size and potential to form a single-stranded stable hairpin-like secondary structure suggest that it is related to MITE elements. In silico searches for related elements identified 252 plant sequences with 8-bp target site duplications and sequence similarity in their terminal and subterminal regions. Some of these sequences were predicted to encode transposases and may be autonomous elements; these constituted a separate clade within the phylogram of hAT transpos- ases. We demonstrate that the CGAGC/GCTCG pentamer maximizes the hairpin stability compared to any other pentamer with the same C+G content, and the secondary structures of these elements are more stable than for most MITEs. We named these elements collectively as hATpin elements because of the hAT similarity and their hairpin structures. The nearly complete rice genome sequence and the highly advanced genome annotation allowed us to localize most rice elements and to deduce insertion preferences. hATpin elements are distributed on all chromosomes, but with significant bias for chromosomes 1 and 10 and in regions of moderate gene density. This family of class II mobile elements is found primarily in monocot species, but is also present in dicot species. Introduction There are two major classes of DNA mobile elements, the class I elements that transpose via RNA intermediates and can reach high copy number, and the class II elements that move without transposition intermediates and are com- monly found at a relative low copy number. Class II elements in plants are commonly subdivided into five superfamilies (hAT, CACTA/En/Spm, IS5/PIF/Pong/Harbinger/Tourist-like, IS256/Mutator and IS630/Tc1/Mariner/Stowaway-like) according to their terminal inverted repeat sequences (TIRs) and the length of the target site duplication (TSD) produce by the insertion (Feschotte et al., 2002a; Ouyang and Buell, 2004). Superfamilies are sub- divided into families. Each family is comprised of closely related elements usually found within a single species. Members of the hAT superfamily are charac- terized by a target site duplication of eight nucleotides (Streck et al., 1986; Frank et al., 1998). These elements commonly have two distinctive cis-acting motifs required for transpo- Plant Molecular Biology (2005) 58:869–886 Ó Springer 2005 DOI 10.1007/s11103-005-8271-8