The LORE1 insertion mutant resource

TY - JOUR

T1 - The LORE1 insertion mutant resource

AU - Malolepszy, Anna

AU - Mun, Terry

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

N1 - This article is protected by copyright. All rights reserved.

PY - 2016/10/1

Y1 - 2016/10/1

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.

AB - 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.

KW - DNA methylation

KW - Long terminal repeat retrotransposon

KW - Lotus japonicus

KW - mutagenesis

KW - palindrome

UR - http://www.scopus.com/inward/record.url?scp=84988314523&partnerID=8YFLogxK

U2 - 10.1111/tpj.13243

DO - 10.1111/tpj.13243

M3 - Journal article

C2 - 27322352

SN - 0960-7412

VL - 88

SP - 306

EP - 317

JO - The Plant Journal

JF - The Plant Journal

IS - 2

ER -