Synthetic Human Chromosomes Explained

By Hugo Francisco de SouzaReviewed by Benedette Cuffari, M.Sc.

Introduction
Technologies enabling synthetic chromosomes
Applications in research and medicine
Ethical and safety considerations
Future outlook
References
Further reading

From synthetic chromosomes and recoded genomes to next-generation gene therapies and engineered cells, discover how genome-scale engineering is redefining the possibilities of biology while reshaping the future of medicine and biotechnology.

Image Credit: wavebreakmedia / Shutterstock.com

Introduction

Synthetic genomics is a specialized branch of synthetic biology characterized by the de novo design, chemical synthesis, assembly, and functional activation of complete genomes or chromosomes to create living viruses or cells. In addition to synthetic microbial genomes, modern genome engineering increasingly focuses on chromosome-scale manipulation, including synthetic yeast chromosomes, human artificial chromosomes (HACs), genome recoding, chromosome fusion, and designer genomes with altered biological properties.^1,2,4 Recent advances in genome engineering technologies have enabled the rational design or modification of chromosomal architecture to elicit specific desirable phenotypes, such as viral resistance or customized metabolic pathways.

Technologies enabling synthetic chromosomes

Genome-scale construction begins with short oligonucleotides 60-80 base pairs (bp) in length, synthesized by phosphoramidite chemistry.² These oligos are subsequently assembled into megabase-scale sequences using techniques like Gibson Assembly, an isothermal reaction using exonucleases, as well as DNA polymerases and ligases.¹ For constructs larger than 100 kilobases (kb), Saccharomyces cerevisiae, which possesses a remarkably high-efficiency homologous recombination machinery, is frequently used as an assembly chassis.^2,4

Chromosome-scale engineering has also been enabled by transformation-associated recombination (TAR) cloning in yeast, which allows large DNA fragments and even entire genomes to be assembled, maintained, and modified as yeast artificial chromosomes prior to transfer into recipient systems.^1,7 For HACs, current strategies are commonly described as bottom-up construction from centromeric and other chromosomal elements or top-down engineering of existing human chromosomes into smaller artificial chromosomes.¹

Conventional synthetic chemistry inherently limits the size of the terminal construct, prompting researchers to investigate novel enzymatic DNA synthesis approaches, particularly those leveraging terminal deoxynucleotidyl transferase (TdT), to overcome these limitations.^1,5 In vivo genome-editing tools like multiplex automated genome engineering (MAGE), clustered regularly interspaced short palindromic repeats (CRISPR), and conjugative assembly genome engineering (CAGE) have also been utilized to support large-scale recoding.²

These editing technologies facilitate the simultaneous introduction of many directed nucleotide changes, which were essential for recoding bacterial genomes and freeing selected codons for possible reassignment to non-standard amino acids.² For example, E. coli Syn61 was designed by replacing 18,214 instances of two sense codons and one stop codon across a 4.0-Mb genome, creating a 61-codon organism with altered translational capacity and potential viral resistance advantages.^1,6

Beyond genome recoding, synthetic genomics has demonstrated extensive chromosome restructuring. Experimental studies in yeast have shown that multiple native chromosomes can be fused into a single functional chromosome while maintaining viability, highlighting the remarkable plasticity of eukaryotic genome organization.^4,10

Image Credit: Anusorn Nakdee / Shutterstock.com

Applications in research and medicine

In disease modeling and gene function studies, synthetic genomic platforms enable the reconstruction of pathogens from digital data, enabling researchers to study these agents before natural isolates are available.⁷ Using a yeast-based synthetic genomics platform, researchers reconstructed SARS-CoV-2 from synthetic DNA fragments and recovered an infectious virus approximately one week after receiving the synthesized DNA, demonstrating the speed with which emerging pathogens can be experimentally characterized.⁷

Synthetic genomics has emerged as a novel approach to address persistent challenges in medical gene therapy and regenerative medicine. Human artificial chromosomes (HACs) represent one of the most promising chromosome-engineering technologies because they can function as independent episomal chromosomes, avoid insertional mutagenesis associated with genome integration, and accommodate very large genomic regions together with their native regulatory elements.¹ These properties make HACs especially relevant for disorders caused by large genes or complex loci that exceed the capacity of conventional viral vectors.¹

Similarly, in regenerative medicine, synthetic genomics has enabled xenotransplantation by humanizing animal genomes. In 2022, a 57-year-old male patient received a pig heart containing 10 genetic modifications, including 3 gene knockouts to prevent hyperacute rejection and 6 human gene additions to regulate the immune response.¹

Genome-scale engineering has also enabled the construction of minimal cells and the extensive redesign of microbial genomes. The synthetic minimal bacterium JCVI-syn3.0 contains only 473 genes and serves as a platform for investigating the core genetic requirements for cellular life.³

For industrial applications, synthetic genomics provides the logical basis driving the development of self-amplifying ribonucleic acid (RNA) (SAM) vaccines and microbial sources for sustainable production.¹ Engineered yeast strains are widely used in biotechnological chassis for producing pharmacologically important compounds like artemisinin.²

Ethical and safety considerations

Despite the promising future of synthetic genomics, ethical concerns regarding the repurposing of these technologies for harm and the potential for unintended consequences emphasize the importance of robust safeguards before their large-scale deployment. The accidental or irresponsible release of synthetic organisms into the environment could result in ecological and medical disruptions, potentially leading to wild-type strains inheriting synthetic resistance genes.¹ To mitigate this risk, researchers use semantic and trophic biocontainment strategies like redesigning essential enzymes to depend on synthetic, non-standard amino acids for survival.^1,2

The de novo synthesis of pathogens is a primary public health risk, with reviews estimating that about 20% of the current global synthesis capacity operates outside voluntary screening frameworks.¹ Modern biosecurity efforts increasingly focus on screening synthetic DNA orders for sequences associated with pathogens or hazardous biological functions. Recent studies have shown that AI-assisted protein design tools can generate modified sequences that evade traditional homology-based screening methods, underscoring the need for function-aware screening approaches and stronger international oversight.⁹ Ethical evaluation also extends beyond biosecurity to questions of justice, access, environmental stewardship, and public trust in the governance of synthetic biology.⁸

Future outlook

The Synthetic Yeast Genome Project (Sc2.0) continues to build designer eukaryotes through systematic chromosome redesign, including the removal of destabilizing sequences and the insertion of engineered features, such as recombination sites for inducible genome rearrangement. The project represents one of the most ambitious chromosome-engineering efforts ever undertaken and has demonstrated that extensive redesign of eukaryotic chromosomes can be achieved while preserving cellular viability.^2,4 Separately, the fusion of all 16 yeast chromosomes into a single massive chromosome demonstrated the structural plasticity of eukaryotes.¹⁰

Simultaneously, researchers are increasingly exploring the concept of artificial biological intelligence (ABI), in which large language models trained on natural DNA sequences predict the functional outcomes of novel genetic designs.¹ The integration of AI platforms in synthetic genomics is hypothesized to shift the field from trial-and-error toward a predictive engineering discipline.^1,2

Nevertheless, significant challenges persist, necessitating strategies that ensure meiotic stability and faithful inheritance of synthetic chromosomes across generations to create stable humanized animal models. For synthetic human chromosomes specifically, major hurdles include reliable chromosome assembly, long-term epigenetic stability, centromere function, accurate segregation during cell division, and efficient delivery of megabase-scale DNA into target cells.^1,4 Furthermore, the efficiency of delivering megabase-sized constructs into recipient cells remains low.^1,4

References

1. Venter, J. C., Glass, J. I., Hutchison, C. A., III, & Vashee, S. (2022). Synthetic chromosomes, genomes, viruses, and cells. Cell 185(15); 2708-2724. DOI: 10.1016/j.cell.2022.06.046. https://www.sciencedirect.com/science/article/pii/S009286742200798X
2. Annaluru, N., Ramalingam, S., & Chandrasegaran, S. (2015). Rewriting the blueprint of life by synthetic genomics and genome engineering. Genome Biology 16(1). DOI: 10.1186/s13059-015-0689-y. https://link.springer.com/article/10.1186/s13059-015-0689-y
3. Hutchison, C. A., Chuang, R., Noskov, V. N., et al. (2016). Design and synthesis of a minimal bacterial genome. Science 351(6280). DOI: 10.1126/science.aad6253. https://cba.mit.edu/docs/papers/16.04.minimal.pdf
4. Coradini, A. L. V., Hull, C. B., & Ehrenreich, I. M. (2020). Building genomes to understand biology. Nature Communications 11(1). DOI: 10.1038/s41467-020-19753-2. https://www.nature.com/articles/s41467-020-19753-2
5. Barthel, S., Palluk, S., Hillson, N. J., et al. (2020). Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3′ Terminal Structures for Enzymatic De Novo DNA Synthesis. Genes 11(1); 102. DOI: 10.3390/genes11010102. https://www.mdpi.com/2073-4425/11/1/102
6. Fredens, J., Wang, K., de la Torre, D., et al. (2019). Total synthesis of Escherichia coli with a recoded genome. Nature 569(7757); 514-518. DOI: 10.1038/s41586-019-1192-5. https://www.nature.com/articles/s41586-019-1192-5
7. Thi Nhu Thao, T., Labroussaa, F., Ebert, N., et al. (2020). Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature 582(7813); 561-565. DOI: 10.1038/s41586-020-2294-9. https://www.nature.com/articles/s41586-020-2294-9
8. Paleri, V. A., & Hens, K. (2026). Imagining an ethics for synthetic biology. Frontiers in Genetics 17. DOI: 10.3389/fgene.2026.1746379. https://pmc.ncbi.nlm.nih.gov/articles/PMC12945332/
9. Wittmann, B. J., Alexanian, T., Bartling, C., et al. (2025). Strengthening nucleic acid biosecurity screening against generative protein design tools. Science 390(6768); 82–87. DOI: 10.1126/science.adu8578. https://www.science.org/doi/10.1126/science.adu8578
10. Shao, Y., Lu, N., Wu, Z., et al. (2018). Creating a functional single-chromosome yeast. Nature 560(7718); 331-335. DOI: 10.1038/s41586-018-0382-x. https://life.sjtu.edu.cn/teacher/assets/userfiles/files/Net/20201224164232488/Files/20201225/6374451329402685708599773.pdf

Further Reading

• All Gene Therapy Content
• What is Gene Therapy?
• Gene Therapy History
• Gene Therapy Issues
• Gene Therapy Types

Last Updated: Jun 30, 2026