Randomizing the human genome by engineering recombination between repeat elements

• 成果类型: Article
• 署名作者: Koeppel, Jonas; Ferreira, Raphael; Vanderstichele, Thomas; Riedmayr, Lisa Maria; Peets, Elin Madli; Girling, Gareth; Weller, Juliane; Murat, Pierre; Liberante, Fabio Giuseppe; Ellis, Tom; Church, George McDonald; Parts, Leopold
• 署名单位: Wellcome Trust Sanger Institute; Harvard University; Harvard Medical School; Harvard University; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; Imperial College London; Harvard University; Harvard Medical School
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8115
• DOI: 10.1126/science.ado3979
• 发表日期: 2025-01-31
• 关键词: structural variation; annotation; EVOLUTION

摘要

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.