Randomizing the human genome by engineering recombination between repeat elements

作者：Jonas Koeppel, Raphaël Ferreira, Thomas Vanderstichele, Lisa Maria Riedmayr, Elin Madli Peets, Gareth Girling, Juliane Weller, Pierre Murat, Fabio G. Liberante, Tom Ellis, George M. Church, Leopold Parts · 发表于：Science · 年份：2025 · DOI：10.1126/science.ado3979 · 被引用次数：28 · 研究领域：CRISPR and Genetic Engineering、Chromosomal and Genetic Variations、RNA and protein synthesis mechanisms

We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell. We tracked these rearrangements over time to measure selection pressures, finding a preference for shorter variants that avoided essential genes. We characterized 29 clones with multiple rearrangements, finding an impact of deletions on expression of genes in the variant but not on nearby genes. This genome-scrambling strategy enables large deletions, sequence relocations, and the insertion of regulatory elements to explore genome dispensability and organization.