Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

Abstract

We developed a CRISPR–Cas9- and homology-directed-repair-assisted genome-scale engineering method named CHAnGE that can rapidly output tens of thousands of specific genetic variants in yeast. More than 98% of target sequences were efficiently edited with an average frequency of 82%. We validate the single-nucleotide resolution genome-editing capability of this technology by creating a genome-wide gene disruption collection and apply our method to improve tolerance to growth inhibitors.

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Figure 1: CHAnGE enables rapid generation of genome-wide yeast disruption mutants and directed evolution of complex phenotypes.
Figure 2: CHAnGE enables genome editing with a single-nucleotide resolution.

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Sequence Read Archive

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Acknowledgements

This work was supported by the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign and the US Department of Energy (DE-SC0018260). We thank A. Hernandez and C. Wright for assistance with next-generation sequencing, J. Zadeh for assistance with NGS data processing and analysis.

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Authors

Contributions

Z.B. and H.Z. conceived this project. Z.B., M.H., and H.X. designed the CHAnGE cassettes. R.C. and J.L. generated the ORF list and all possible guide sequences. M.H. sorted and selected the guide and homology arm sequences. Z.B., P.X., and I.T. performed the experiments. Z.B. analyzed the data. H.Z. supervised the research. Z.B. and H.Z. wrote the manuscript.

Corresponding author

Correspondence to Huimin Zhao.

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Competing interests

A patent application has been filed on this technology, on which H.Z. and Z.B. are authors.

Supplementary information

Supplementary Text and Figures

Supplementary Notes 1 and 2, Supplementary Figures 1–18, and Supplementary Tables 1, 2, 4, 5, 7. (PDF 3306 kb)

Life Sciences Reporting Summary (PDF 129 kb)

Supplementary Table 3

A summary of 24865 CHAnGE cassette sequences. (XLS 7358 kb)

Supplementary Table 6

A summary of 580 SIZ1 CHAnGE cassette sequences. (XLSX 87 kb)

Supplementary Code

Supplementary Code (PDF 35 kb)

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Bao, Z., HamediRad, M., Xue, P. et al. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. Nat Biotechnol 36, 505–508 (2018). https://doi.org/10.1038/nbt.4132

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