The Sc2.0 project has inspired related technologies and projects, many directly generated by Sc2.0 activities.

• Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution – SCRaMbLE – using Sc2.0 to generate and explore combinatorial genome diversity
• The Dark Matter Project using synthetic biology to understand regulatory genomics and non-protein-coding DNA
• Science Across Virtual Institutes – SAVI – an NSF initiative for international collaborations
• Genome Project Write – GP-write – extending the concepts of Sc2.0 to mammalian genome writing
• The BAG Network teaching the next generation of synthetic biologists how to build a genome

SCRaMbLE

The SCRaMbLE system engineered into Sc2.0 strains has been a rich source of information about the yeast genome structure, function, and evolutionary constraints. Here is an entry to the SCRaMbLE literature, highlighting the awesome power of yeast genetics.

SCRaMbLE description

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD. Nature. 2011 Sep 14;477(7365):471-6. doi: 10.1038/nature10403. PMID: 21918511; PMCID: PMC3774833. Full text

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS. Genome Res. 2016 Jan;26(1):36-49. doi: 10.1101/gr.193433.115. Epub 2015 Nov 13. PMID: 26566658; PMCID: PMC4691749. Full text

Nature Communications Collection

A collection of SCRaMbLE publications is available from Nature Communications:

Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE

Construction of a synthetic Saccharomyces cerevisiae pan-genome neo-chromosome

Chromosome drives via CRISPR-Cas9 in yeast

Improved betulinic acid biosynthesis using synthetic yeast chromosome recombination and semi-automated rapid LC-MS screening

Ring synthetic chromosome V SCRaMbLE

Precise control of SCRaMbLE in synthetic haploid and diploid yeast

Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome

Heterozygous diploid and interspecies SCRaMbLEing

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods

In vitro DNA SCRaMbLE

Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES

L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast

The collection also includes commentaries and perspectives:

Building better yeast

Designing with living systems in the synthetic yeast project

SCRaMbLEing to understand and exploit structural variation in genomes

Additional Publications

Probing eukaryotic genome functions with synthetic chromosomes. Luo Z, Hoffmann SA, Jiang S, Cai Y, Dai J. Exp Cell Res. 2020 May 1;390(1):111936. doi: 10.1016/j.yexcr.2020.111936. Epub 2020 Mar 9. PMID: 32165165 Review. Full text

Compacting a synthetic yeast chromosome arm. Luo Z, Yu K, Xie S, Monti M, Schindler D, Fang Y, Zhao S, Liang Z, Jiang S, Luan M, Xiao C, Cai Y, Dai J. Genome Biol. 2021 Jan 4;22(1):5. doi: 10.1186/s13059-020-02232-8. PMID: 33397424 Full text

SCRaMbLE: A Study of Its Robustness and Challenges through Enhancement of Hygromycin B Resistance in a Semi-Synthetic Yeast. Ong JY, Swidah R, Monti M, Schindler D, Dai J, Cai Y. Bioengineering (Basel). 2021 Mar 23;8(3):42. doi: 10.3390/bioengineering8030042. PMID: 33806931 Full text

Chromosomal Rearrangements of Synthetic Yeast by SCRaMbLE. Luo Z, Jiang S, Dai J. Methods Mol Biol. 2021;2196:153-165. doi: 10.1007/978-1-0716-0868-5_12. PMID: 32889719 Full text

3D organization of synthetic and scrambled chromosomes. Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R. Science. 2017 Mar 10;355(6329):eaaf4597. doi: 10.1126/science.aaf4597. Full text

The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Dymond J, Boeke J. Bioeng Bugs. 2012 May-Jun;3(3):168-71. doi: 10.4161/bbug.19543. Epub 2012 May 1. PMID: 22572789 Full text

SCRaMbLE-in: A Fast and Efficient Method to Diversify and Improve the Yields of Heterologous Pathways in Synthetic Yeast. Swidah R, Auxillos J, Liu W, Jones S, Chan TF, Dai J, Cai Y. Methods Mol Biol. 2020;2205:305-327. doi: 10.1007/978-1-0716-0908-8_17. PMID: 32809206 Full text

Systematical Engineering of Synthetic Yeast for Enhanced Production of Lycopene. Zhang Y, Chiu TY, Zhang JT, Wang SJ, Wang SW, Liu LY, Ping Z, Wang Y, Chen A, Zhang WW, Chen T, Wang Y, Shen Y. Bioengineering (Basel). 2021 Jan 19;8(1):14. doi: 10.3390/bioengineering8010014. PMID: 33477926 Full text