title: hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures.
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 transposases. 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.
authors.affiliation: Departamento de Biología Vegetal, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28040, Madrid, Spain.
authors.forename: Santiago
authors.initials: S
authors.lastname: Moreno-Vázquez
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, 19711, Newark, DE, USA.
authors.forename: Jianchang
authors.initials: J
authors.lastname: Ning
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, 19711, Newark, DE, USA. meyers@dbi.udel.edu.|Department of Plant and Soil Sciences, University of Delaware, 19714, Newark, DE, USA. meyers@dbi.udel.edu.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry* / Q000235:genetics*; D030541:Databases, Genetic; D018745:Genome, Plant; D018545:Lactuca / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics; D013816:Thermodynamics
chemical_list: D018744:DNA, Plant; D018626:Retroelements