skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

We developed a CRISPR–Cas9- and homology-directed-repairassisted 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.

Authors:
ORCiD logo; ORCiD logo; ORCiD logo; ; ; ; ; ORCiD logo
Publication Date:
Research Org.:
University of Illinois at Urbana-Champaign
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1486877
DOE Contract Number:  
SC0018260
Resource Type:
Journal Article
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 36; Journal Issue: 6; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English

Citation Formats

Bao, Zehua, HamediRad, Mohammad, Xue, Pu, Xiao, Han, Tasan, Ipek, Chao, Ran, Liang, Jing, and Zhao, Huimin. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. United States: N. p., 2018. Web. doi:10.1038/nbt.4132.
Bao, Zehua, HamediRad, Mohammad, Xue, Pu, Xiao, Han, Tasan, Ipek, Chao, Ran, Liang, Jing, & Zhao, Huimin. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. United States. doi:10.1038/nbt.4132.
Bao, Zehua, HamediRad, Mohammad, Xue, Pu, Xiao, Han, Tasan, Ipek, Chao, Ran, Liang, Jing, and Zhao, Huimin. Mon . "Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision". United States. doi:10.1038/nbt.4132.
@article{osti_1486877,
title = {Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision},
author = {Bao, Zehua and HamediRad, Mohammad and Xue, Pu and Xiao, Han and Tasan, Ipek and Chao, Ran and Liang, Jing and Zhao, Huimin},
abstractNote = {We developed a CRISPR–Cas9- and homology-directed-repairassisted 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.},
doi = {10.1038/nbt.4132},
journal = {Nature Biotechnology},
issn = {1087-0156},
number = 6,
volume = 36,
place = {United States},
year = {2018},
month = {5}
}

Works referenced in this record:

Capturing a substrate in an activated RING E3/E2–SUMO complex
journal, August 2016

  • Streich Jr, Frederick C.; Lima, Christopher D.
  • Nature, Vol. 536, Issue 7616
  • DOI: 10.1038/nature19071

Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes
journal, November 2017


CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
journal, December 2014


Multiplex Genome Engineering Using CRISPR/Cas Systems
journal, January 2013


Structure of the Siz/PIAS SUMO E3 Ligase Siz1 and Determinants Required for SUMO Modification of PCNA
journal, September 2009


Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
journal, July 2010

  • Warner, Joseph R.; Reeder, Philippa J.; Karimpour-Fard, Anis
  • Nature Biotechnology, Vol. 28, Issue 8, p. 856-862
  • DOI: 10.1038/nbt.1653

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae
journal, September 2014

  • Bao, Zehua; Xiao, Han; Liang, Jing
  • ACS Synthetic Biology, Vol. 4, Issue 5
  • DOI: 10.1021/sb500255k

A guide to genome engineering with programmable nucleases
journal, April 2014

  • Kim, Hyongbum; Kim, Jin-Soo
  • Nature Reviews Genetics, Vol. 15, Issue 5, p. 321-334
  • DOI: 10.1038/nrg3686

Strategy for directing combinatorial genome engineering in Escherichia coli
journal, June 2012

  • Sandoval, N. R.; Kim, J. Y. H.; Glebes, T. Y.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 26, p. 10540-10545
  • DOI: 10.1073/pnas.1206299109

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016

  • Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur
  • Nature Biotechnology, Vol. 35, Issue 1, p. 48-55
  • DOI: 10.1038/nbt.3718

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

  • Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A.
  • Nature, Vol. 460, Issue 7257, p. 894-898
  • DOI: 10.1038/nature08187

High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method
journal, January 2007


Genetic Screens in Human Cells Using the CRISPR-Cas9 System
journal, December 2013


    Works referencing / citing this record:

    Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast
    journal, August 2018

    • Després, Philippe C.; Dubé, Alexandre K.; Nielly-Thibault, Lou
    • G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
    • DOI: 10.1534/g3.118.200461

    Biosystems design by directed evolution
    journal, July 2019


    Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae
    journal, July 2019

    • Zhang, Peng; Chen, Qian; Fu, Guiming
    • World Journal of Microbiology and Biotechnology, Vol. 35, Issue 7
    • DOI: 10.1007/s11274-019-2684-z

    Biosystems design by directed evolution
    journal, July 2019


    Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae
    journal, July 2019

    • Zhang, Peng; Chen, Qian; Fu, Guiming
    • World Journal of Microbiology and Biotechnology, Vol. 35, Issue 7
    • DOI: 10.1007/s11274-019-2684-z

    Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast
    journal, August 2018

    • Després, Philippe C.; Dubé, Alexandre K.; Nielly-Thibault, Lou
    • G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
    • DOI: 10.1534/g3.118.200461