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Title of Journal: Plant Mol Biol

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Abbravation: Plant Molecular Biology

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Springer Netherlands

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DOI

10.1016/j.bbrc.2008.07.050

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ISSN

1573-5028

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Emphasis Type="Italic"hATpin/Emphasis a Famil

Authors: Santiago MorenoVázquez Jianchang Ning Blake C Meyers
Publish Date: 2005/08/01
Volume: 58, Issue: 6, Pages: 869-886
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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 8bp target site duplications typical of the hAT superfamily of class II mobile elements but its small size and potential to form a singlestranded stable hairpinlike secondary structure suggest that it is related to MITE elements In silico searches for related elements identified 252 plant sequences with 8bp 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

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