New Breakthrough in Human Genome Synthesis Sheds light on Genetic Disorder Treatment

Recently, a research team led by Chinese Academy of Sciences Academician, Yingjin Yuan — affiliated with the State Key Laboratory of Synthetic Biology at Tianjin University, and the School of Synthetic Biology and Biological Manufacturing at Tianjin University — has achieved, for the first time, the precise synthesis and assembly of megabase (Mb)-scale human DNA, along with its cross-species delivery. The study was published in Nature Methods on July 10 under the title "De novo Assembly and Delivery of Synthetic Megabase-Scale Human DNA into Mouse Early Embryos." This breakthrough advances human genome synthesis and transfer technologies, offering important implications for synthetic human genomes.

Since the completion of the Human Genome Project in the early 21st century, scientists have sought to develop the capability of genome writing. Genome synthesis enables researchers to establish causal relationships between DNA sequences and their biological functions, representing a paradigm shift from passively "reading" genetic information through sequencing to actively coding life. In 2015, Professor Yingjin Yuan's team successfully synthesized chromosomes V and X in Saccharomyces cerevisiae, while developing high-efficiency techniques for bug mapping and precision repair. Following the publication of these groundbreaking results in Science (2017), the team has been dedicated to overcoming key technological barriers in human genome synthesis.

De novo design and synthesis of higher eukaryotic genomes face two fundamental technical bottlenecks: 1) the feasible synthesis and assembly of Mb-scale DNA with designer sequences corresponding to potentially any human genome locus, including conserved highly repetitive sequences, and 2) the efficient delivery of such large, intact DNA molecules across species. These technical constraints have substantially hindered the application and development of synthetic genomics in higher organisms. To address these challenges, Prof. Yuan's team developed SynNICE, a method that involves: the de novo assembly of synthetic Mb-scale human genomic DNA in yeast, followed by NICE (Nucleus Isolation for Chromosomes Extraction) to obtain yeast nuclei with intact chromosomes while preserving chromatin architecture.

As proof of concept, the 1.14 Mb human AZFa (hAZFa) region, whose microdeletion leads to a severe form of male infertility without any available clinical solution. This region comprises 69.38% repetitive sequences and was chemically synthesized and assembled in yeast. Using NICE, the intact hAZFa region maintained its chromosomal structure in isolated yeast nuclei without the need for crosslinking. DNA integrity was preserved, even after storage for at least six months at –80°C. The spontaneous incorporation of mouse histones was observed in yeast nuclear DNA, which occurred both with and without parthenogenetic activation. Novel, de novo DNA methylation of synthetic, naïve Mb-scale human DNA was enriched for repeat elements and intergenic regions, independent of H3K9me3 reinforcement.

This study represents a breakthrough in de novo assembly, cross-species transfer, and functional reconstitution of megabase-scale human genomic DNA. The SynNICE method demonstrates two major significances: Firstly, it reveals how cellular environments remodel and regulate synthetic genomes lacking mammalian epigenetic modifications. Secondly, it holds promise for transformative applications in biomedicine and the treatment of human genetic disorders.

By Liu Yue

Editor: Eva Yin