SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Yue Shen, Giovanni Stracquadanio, Yun Wang, Kun Yang, Leslie A. Mitchell, Yaxin Xue, Yizhi Cai, Tai Chen, Jessica S. Dymond, Kang Kang, Jianhui Gong, Xiaofan Zeng, Yongfen Zhang, Yingrui Li, Qiang Feng, Xun Xu, Jun Wang, Jian Wang, Huanming Yang, Jef D. BoekeJoel S. Bader

    Research output: Contribution to journalArticle

    Abstract

    Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm synIXR (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 synIXR 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 loxPsym 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 3ΠUTR 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.

    Original languageEnglish (US)
    Pages (from-to)36-49
    Number of pages14
    JournalGenome Research
    Volume26
    Issue number1
    DOIs
    StatePublished - Jan 2016

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    ASJC Scopus subject areas

    • Genetics
    • Genetics(clinical)

    Cite this

    Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, L. A., Xue, Y., Cai, Y., Chen, T., Dymond, J. S., Kang, K., Gong, J., Zeng, X., Zhang, Y., Li, Y., Feng, Q., Xu, X., Wang, J., Wang, J., Yang, H., ... Bader, J. S. (2016). SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research, 26(1), 36-49. https://doi.org/10.1101/gr.193433.115