Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Brief Communication
  • Published:

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


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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

Accession codes

Primary accessions

Sequence Read Archive


  1. Wang, H.H. et al. Nature 460, 894–898 (2009).

    Article  CAS  Google Scholar 

  2. Warner, J.R., Reeder, P.J., Karimpour-Fard, A., Woodruff, L.B. & Gill, R.T. Nat. Biotechnol. 28, 856–862 (2010).

    Article  CAS  Google Scholar 

  3. Garst, A.D. et al. Nat. Biotechnol. 35, 48–55 (2017).

    Article  CAS  Google Scholar 

  4. Barbieri, E.M., Muir, P., Akhuetie-Oni, B.O., Yellman, C.M. & Isaacs, F.J. Cell 171, 1453–1467.e13 (2017).

    Article  CAS  Google Scholar 

  5. Bao, Z. et al. ACS Synth. Biol. 4, 585–594 (2015).

    Article  CAS  Google Scholar 

  6. Cong, L. et al. Science 339, 819–823 (2013).

    Article  CAS  Google Scholar 

  7. Wang, T., Wei, J.J., Sabatini, D.M. & Lander, E.S. Science 343, 80–84 (2014).

    Article  CAS  Google Scholar 

  8. Xiao, H. & Zhao, H. Biotechnol. Biofuels 7, 78 (2014).

    Article  Google Scholar 

  9. Sandoval, N.R. et al. Proc. Natl. Acad. Sci. USA 109, 10540–10545 (2012).

    Article  CAS  Google Scholar 

  10. Streich, F.C. Jr. & Lima, C.D. Nature 536, 304–308 (2016).

    Article  CAS  Google Scholar 

  11. Yunus, A.A. & Lima, C.D. Mol. Cell 35, 669–682 (2009).

    Article  CAS  Google Scholar 

  12. Kim, H. & Kim, J.S. Nat. Rev. Genet. 15, 321–334 (2014).

    Article  CAS  Google Scholar 

  13. Naito, Y., Hino, K., Bono, H. & Ui-Tei, K. Bioinformatics 31, 1120–1123 (2015).

    Article  CAS  Google Scholar 

  14. Gietz, R.D. & Schiestl, R.H. Nat. Protoc. 2, 31–34 (2007).

    Article  CAS  Google Scholar 

  15. Hegemann, J.H. & Heick, S.B. Methods Mol. Biol. 765, 189–206 (2011).

    Article  CAS  Google Scholar 

Download references


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.

Author information

Authors and Affiliations



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.

Ethics declarations

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)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bao, Z., HamediRad, M., Xue, P. et al. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. Nat Biotechnol 36, 505–508 (2018).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research