Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration

Jee Loon Foo, Shohei Kitano, Adelia Vicanatalita Susanto, Zhu Jin, Yicong Lin, Zhouqing Luo, Linsen Huang, Zhenzhen Liang, Leslie A. Mitchell, Kun Yang, Adison Wong, Yizhi Cai, Jitong Cai, Giovanni Stracquadanio, Joel S. Bader, Jef D. Boeke, Junbiao Dai, Matthew Wook Chang

Research output: Contribution to journalArticlepeer-review


Chromosome-level design-build-test-learn cycles (chrDBTLs) allow systematic combinatorial reconfiguration of chromosomes with ease. Here, we established chrDBTL with a redesigned synthetic Saccharomyces cerevisiae chromosome XV, synXV. We designed and built synXV to harbor strategically inserted features, modified elements, and synonymously recoded genes throughout the chromosome. Based on the recoded chromosome, we developed a method to enable chrDBTL: CRISPR-Cas9-mediated mitotic recombination with endoreduplication (CRIMiRE). CRIMiRE allowed the creation of customized wild-type/synthetic combinations, accelerating genotype-phenotype mapping and synthetic chromosome redesign. We also leveraged synXV as a “build-to-learn” model organism for translation studies by ribosome profiling. We conducted a locus-to-locus comparison of ribosome occupancy between synXV and the wild-type chromosome, providing insight into the effects of codon changes and redesigned features on translation dynamics in vivo. Overall, we established synXV as a versatile reconfigurable system that advances chrDBTL for understanding biological mechanisms and engineering strains.

Original languageEnglish (US)
Article number100435
JournalCell Genomics
Issue number11
StatePublished - Nov 8 2023


  • CRISPR-Cas9
  • Saccharomyces cerevisiae
  • chromosome reconfiguration
  • design-build-test-learn
  • mitotic recombination
  • synthetic biology
  • synthetic chromosome
  • synthetic genomics
  • synthetic yeast

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Genetics


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