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

    51 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

    ASJC Scopus subject areas

    • Genetics
    • Plant Science
    • Cell Biology

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