<Emphasis Type="Italic">hATpin</Emphasis>, a Family of MITE-like <Emphasis Type="Italic">hAT</Emphasis> Mobile Elements Conserved in Diverse Plant Species that Forms Highly Stable Secondary Structures |
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Authors: | Santiago?Moreno-Vázquez Jianchang?Ning Email author" target="_blank">Blake?C?MeyersEmail author |
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Institution: | (1) Departamento de Biología Vegetal, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28040 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 |
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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 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.
Electronic supplementary material Electronic supplementary material is available for this article at
and accessible for authorised users. |
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Keywords: | MITE mobile element rice transposase transposon |
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