Yizhi Cai

TargetMITO: A rule-based model for generating highly functional synthetic mitochondrial targeting sequence in yeast

The paper develops a rule-based model to generate synthetic mitochondrial targeting sequences in yeast and demonstrates their functionality in directing proteins to mitochondria.

Synthetic yeast genome SCRaMbLEing uncovers a new role for ribosomal proteins in genetic code expansion

The paper improves orthogonal translation in yeast by enhancing a pyrrolysyl-tRNA synthetase system and identifies ribosomal protein deletions that increase non-canonical amino acid incorporation.

Engineering stringent genetic biocontainment of yeast with a protein stability switch

The paper develops a genetic biocontainment system for yeast using a protein stability switch, identifying essential genes that can be conditionally stabilized with estradiol to achieve stringent containment.

High plasticity of ribosomal DNA organization in budding yeast

This study constructs synthetic rDNA arrays in budding yeast and shows that reducing copy numbers or dispersing arrays does not harm cell growth or transcriptomes.

Screening and characterization of aging regulators using synthesized yeast chromosome XIII

The paper constructs a synthetic yeast chromosome and identifies aging regulators through replicative lifespan studies and genome-scale analysis.

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

The paper constructs a synthetic disomic yeast using SCRaMbLE and a newly synthesized chromosome to study aneuploidy phenotypes, finding that both copy number and specific chromosomal regions affect fitness.

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

The paper uses CRISPR D-BUGS and chromosome swapping to identify and resolve genetic interactions in synthetic chromosomes, revealing unexpected links between transcription, inositol metabolism, and tRNA abundance.

Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae

This study demonstrates that genomic rearrangements in yeast can be efficiently induced using SCRaMbLE, leading to diverse genetic changes and phenotypic effects.

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

This paper designs and synthesizes a functional neochromosome in yeast that replaces a native chromosome arm, demonstrating genome plasticity and synthetic chromosome viability.

Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements

The paper debugs a synthetic yeast chromosome and uses laboratory evolution to identify genomic rearrangements that suppress growth defects caused by synthetic modifications.

Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand

The paper constructs a synthetic yeast chromosome XI and demonstrates how non-coding DNA modifications affect cell fitness, enabling on-demand extrachromosomal circular DNA formation.