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Creating functional chromosome fusions in yeast with CRISPR–Cas9


CRISPR–Cas9-facilitated functional chromosome fusion allows the generation of a series of yeast strains with progressively reduced chromosome numbers that are valuable resources for the study of fundamental concepts in chromosome biology, including replication, recombination and segregation. We created a new yeast strain with a single chromosome by using the protocol for chromosome fusion described herein. To ensure the accuracy of chromosome fusions in yeast, the long redundant repetitive sequences near linear chromosomal ends are deleted, and the fusion orders are correspondingly determined. Possible influence on gene expression is minimized to retain gene functionality. This protocol provides experimentally derived guidelines for the generation of functional chromosome fusions in yeast, especially for the deletion of repetitive sequences, the determination of the fusion order and cleavage sites, and primary evaluation of the functionality of chromosome fusions. Beginning with design, one round of typical chromosome fusion and functional verifications can be accomplished within 18 d.

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Fig. 1: Overview of the generation of a functional single-chromosome yeast strain.
Fig. 2: Repetitive sequences near the chromosome ends.
Fig. 3: Diagram of different options for deletion of telomere-associated RSs and determination of the order of chromosome fusion.
Fig. 4: Different trial experiments for the fusion of chromosomes XV and XI.
Fig. 5: Growth curves of yeast strains with pairwise chromosome fusions.
Fig. 6: Timeline and overview of one round of chromosome fusion.
Fig. 7: Schematic representation of the design and construction of the gRNA expression plasmid.
Fig. 8: Design and construction of donor DNA cassettes for chromosome fusion.
Fig. 9: Confirmation of chromosome fusion.
Fig. 10: Schematic diagram of the removal of the selection marker and gRNA expression plasmid.

Data availability

The plasmids used in this protocol, including pCas9 (accession number 1.2624), pHIS426 (accession number 1.2623) and pXX11 (accession number 1.2613), can be obtained from the Registry and Database of Bioparts for Synthetic Biology ( upon reasonable request. All relevant data are reported in the article.


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This research was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB19000000, Z.Q.; 153D31KYSB20160074, Z.Q.), the National Natural Science Foundation of China (31830105, Z.Q.; 31770099 and 31200059, X.X.), Shanghai Research Project (18JC1420200, Z.Q.) and China Postdoctoral Science Foundation (2018M640427 and 2019T120362, Y.S.)

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Authors and Affiliations



Z.Q. and X.X. designed and analyzed all the experiments. Y.S. constructed the chromosome fusion yeast strains and performed PCR verification. N.L. conducted the PFGE confirmation experiment and growth assays. X.X. and Y.S. wrote the primary manuscript with a substantial contribution from Z.Q.

Corresponding authors

Correspondence to Xiaoli Xue or Zhongjun Qin.

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The authors declare no competing interests.

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Peer review information: Nature Protocols thanks Meru Sadhu and other anonymous reviewer(s) for their contribution to the peer review of this work.

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Key references using this protocol

Shao, Y. et al. Nature 560, 331–335 (2018):

Shao, Y., Lu, N., Qin, Z. & Xue, X. ACS Synth. Biol. 7, 2706–2708 (2018):

Shao, Y. et al. Cell Res. 29, 87–89 (2019):

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Shao, Y., Lu, N., Xue, X. et al. Creating functional chromosome fusions in yeast with CRISPR–Cas9. Nat Protoc 14, 2521–2545 (2019).

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