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SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Shen, Yue and Stracquadanio, Giovanni and Wang, Yun and Yang, Kun and Mitchell, Leslie A and Xue, Yaxin and Cai, Yizhi and Chen, Tai and Dymond, Jessica S and Kang, Kang and Gong, Jianhui and Zeng, Xiaofan and Zhang, Yongfen and Li, Yingrui and Feng, Qiang and Xu, Xun and Wang, Jun and Wang, Jian and Yang, Huanming and Boeke, Jef D and Bader, Joel S (2016) 'SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.' Genome Research, 26 (1). pp. 36-49. ISSN 1088-9051

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Abstract

<jats:p>Synthetic chromosome rearrangement and modification by <jats:italic>loxP</jats:italic>-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm <jats:italic>synIXR</jats:italic> (43 recombinase sites) and then used a computational pipeline to infer or unscramble the sequence of recombinations that created the observed genomes. Deep sequencing of 64 <jats:italic>synIXR</jats:italic> SCRaMbLE strains revealed 156 deletions, 89 inversions, 94 duplications, and 55 additional complex rearrangements; several duplications are consistent with a double rolling circle mechanism. Every SCRaMbLE strain was unique, validating the capability of SCRaMbLE to explore a diverse space of genomes. Rearrangements occurred exclusively at designed <jats:italic>loxPsym</jats:italic> sites, with no significant evidence for ectopic rearrangements or mutations involving synthetic regions, the 99% nonsynthetic nuclear genome, or the mitochondrial genome. Deletion frequencies identified genes required for viability or fast growth. Replacement of 3′ UTR by non-UTR sequence had surprisingly little effect on fitness. SCRaMbLE generates genome diversity in designated regions, reveals fitness constraints, and should scale to simultaneous evolution of multiple synthetic chromosomes.</jats:p>

Item Type: Article
Uncontrolled Keywords: Chromosomes; Saccharomyces cerevisiae; DNA, Fungal; Directed Molecular Evolution; Sequence Analysis, DNA; Gene Rearrangement; Sequence Deletion; Genome, Fungal; Chromosome Inversion; Chromosome Duplication; High-Throughput Nucleotide Sequencing
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Science and Health
Faculty of Science and Health > Computer Science and Electronic Engineering, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 13 Jan 2017 14:05
Last Modified: 18 Aug 2022 11:32
URI: http://repository.essex.ac.uk/id/eprint/18690

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