hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures - PubMed (original) (raw)

hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures

Santiago Moreno-Vázquez et al. Plant Mol Biol. 2005 Aug.

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.

PubMed Disclaimer

Cited by

Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome.
Lin L, Sharma A, Yu Q. Lin L, et al. BMC Plant Biol. 2021 Sep 18;21(1):424. doi: 10.1186/s12870-021-03194-0. BMC Plant Biol. 2021. PMID: 34537020 Free PMC article.
A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome.
Macko-Podgórni A, Machaj G, Grzebelus D. Macko-Podgórni A, et al. Genes (Basel). 2021 Jun 3;12(6):859. doi: 10.3390/genes12060859. Genes (Basel). 2021. PMID: 34205210 Free PMC article.
Amplification of miniature inverted-repeat transposable elements and the associated impact on gene regulation and alternative splicing in mulberry (Morus notabilis).
Xin Y, Ma B, Xiang Z, He N. Xin Y, et al. Mob DNA. 2019 Jun 25;10:27. doi: 10.1186/s13100-019-0169-0. eCollection 2019. Mob DNA. 2019. PMID: 31289464 Free PMC article.
Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla).
Zhou M, Tao G, Pi P, Zhu Y, Bai Y, Meng X. Zhou M, et al. Planta. 2016 Oct;244(4):775-87. doi: 10.1007/s00425-016-2544-0. Epub 2016 May 9. Planta. 2016. PMID: 27160169
Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation.
Wang L, Peng Q, Zhao J, Ren F, Zhou H, Wang W, Liao L, Owiti A, Jiang Q, Han Y. Wang L, et al. Plant Mol Biol. 2016 May;91(1-2):179-91. doi: 10.1007/s11103-016-0454-y. Epub 2016 Mar 3. Plant Mol Biol. 2016. PMID: 26941188

References

1. Mol Gen Genet. 1997 Apr 16;254(3):219-30 - PubMed
1. Cell. 1991 Aug 9;66(3):465-71 - PubMed
1. Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1699-704 - PubMed
1. Insect Mol Biol. 1999 Nov;8(4):571-4 - PubMed
1. Cell. 1983 Nov;35(1):235-42 - PubMed

hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures - PubMed (original) (raw)