The LORE1 insertion mutant resource

Anna Małolepszy, Terry Mun, Niels Sandal, Vikas Gupta, Manu Dubin, Dorian Urbański, Niraj Shah, Asger Bachmann, Eigo Fukai, Hideki Hirakawa, Satoshi Tabata, Marcin Nadzieja, Katharina Markmann, Junyi Su, Yosuke Umehara, Takashi Soyano, Akira Miyahara, Shusei Sato, Makoto Hayashi, Jens StougaardStig U. Andersen

Research output: Contribution to journalArticlepeer-review

87 Citations (Scopus)

Abstract

Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.

Original languageEnglish
Pages (from-to)306-317
Number of pages12
JournalPlant Journal
Volume88
Issue number2
DOIs
Publication statusPublished - 2016 Oct 1

Keywords

  • DNA methylation
  • Long terminal repeat retrotransposon
  • Lotus japonicus
  • mutagenesis
  • palindrome

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