The LORE1 insertion mutant resource

Anna Malolepszy; Terry Mun; Niels Sandal; Vikas Gupta; Manu Dubin; Dorian Fabian Urbanski; 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 Stougaard; Stig Uggerhøj Andersen

doi:10.1111/tpj.13243

The LORE1 insertion mutant resource

Anna Malolepszy, Terry Mun, Niels Sandal, Vikas Gupta, Manu Dubin, Dorian Fabian Urbanski, 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 Uggerhøj Andersen

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

95 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 language	English
Journal	The Plant Journal
Volume	88
Issue	2
Pages (from-to)	306-317
Number of pages	12
ISSN	0960-7412
DOIs	https://doi.org/10.1111/tpj.13243
Publication status	Published - 1 Oct 2016

Keywords

DNA methylation
Long terminal repeat retrotransposon
Lotus japonicus
mutagenesis
palindrome

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title = "The LORE1 insertion mutant resource",

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.",

keywords = "DNA methylation, Long terminal repeat retrotransposon, Lotus japonicus, mutagenesis, palindrome",

author = "Anna Malolepszy and Terry Mun and Niels Sandal and Vikas Gupta and Manu Dubin and Urbanski, {Dorian Fabian} and Niraj Shah and Asger Bachmann and Eigo Fukai and Hideki Hirakawa and Satoshi Tabata and Marcin Nadzieja and Katharina Markmann and Junyi Su and Yosuke Umehara and Takashi Soyano and Akira Miyahara and Shusei Sato and Makoto Hayashi and Jens Stougaard and Andersen, {Stig Uggerh{\o}j}",

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AU - Sandal, Niels

AU - Gupta, Vikas

AU - Dubin, Manu

AU - Urbanski, Dorian Fabian

AU - Shah, Niraj

AU - Bachmann, Asger

AU - Fukai, Eigo

AU - Hirakawa, Hideki

AU - Tabata, Satoshi

AU - Nadzieja, Marcin

AU - Markmann, Katharina

AU - Su, Junyi

AU - Umehara, Yosuke

AU - Soyano, Takashi

AU - Miyahara, Akira

AU - Sato, Shusei

AU - Hayashi, Makoto

AU - Stougaard, Jens

AU - Andersen, Stig Uggerhøj

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N2 - 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.

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KW - mutagenesis

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The LORE1 insertion mutant resource

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Keywords

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