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Nat Commun. 2018 May 18;9(1):1995. doi: 10.1038/s41467-018-04256-y.

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks.

Author information

1
Genome Engineering Program, Strategic Innovative Research-Domain, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan.
2
Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Tokyo, 153-8902, Japan. odar@bio.c.u-tokyo.ac.jp.
3
Universal Biology Institute, The University of Tokyo, Hongo 7-3-1, Tokyo, 113-0033, Japan. odar@bio.c.u-tokyo.ac.jp.
4
Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Tokyo, 153-8902, Japan.
5
Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan.
6
Future Project Division, Toyota Motor Corporation, 1 Toyota-cho, Toyota, 471-8572, Japan.
7
Cellular & Molecular Biology Laboratory, RIKEN Advanced Science Institute, Wako-shi, Saitama, 351-0198, Japan.
8
Genome Engineering Program, Strategic Innovative Research-Domain, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan. e1190@mosk.tytlabs.co.jp.
9
Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Tokyo, 153-8902, Japan. kohta@bio.c.u-tokyo.ac.jp.
10
Universal Biology Institute, The University of Tokyo, Hongo 7-3-1, Tokyo, 113-0033, Japan. kohta@bio.c.u-tokyo.ac.jp.

Abstract

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies.

PMID:
29777105
PMCID:
PMC5959919
DOI:
10.1038/s41467-018-04256-y
[Indexed for MEDLINE]
Free PMC Article

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