Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes
Deciphering the context-specific relationship between sequence and function is a major challenge in genomics. Existing tools for inducing locus-specific hypermutation and evolution in the native genome context are limited. Here we present a programmable platform for long-range, locus-specific hypermutation called helicase-assisted continuous editing (HACE). HACE leverages CRISPR-Cas9 to target a processive helicase-deaminase fusion that incurs mutations across large (>1000-base pair) genomic intervals. We applied HACE to identify mutations in mitogen-activated protein kinase kinase 1 (MEK1) that confer kinase inhibitor resistance, to dissect the impact of individual variants in splicing factor 3B subunit 1 (SF3B1)-dependent missplicing, and to evaluate noncoding variants in a stimulation-dependent immune enhancer of CD69. HACE provides a powerful tool for investigating coding and noncoding variants, uncovering combinatorial sequence-to-function relationships, and evolving new biological functions.
Authors
- Haiqi Chen (ORCID: https://orcid.org/0000-0001-7179-3229)
- Yifan Zhang (ORCID: https://orcid.org/0000-0003-0484-9418)
- A. Torres (ORCID: https://orcid.org/0009-0008-9497-7395)
- Xi Chen (ORCID: https://orcid.org/0000-0001-8127-6014)
- Benno C. Orr (ORCID: https://orcid.org/0000-0001-7231-4488)
- Mounica Vallurupalli (ORCID: https://orcid.org/0000-0002-1995-5283)
- Yu-Kai Chao (ORCID: https://orcid.org/0000-0001-9440-6746)
- Emre Tkacik (ORCID: https://orcid.org/0000-0001-8274-1248)
- B Bernstein (ORCID: https://orcid.org/0000-0002-5726-6278)
- Gary Sun (ORCID: https://orcid.org/0009-0008-6910-0161)
- George Wythes (ORCID: https://orcid.org/0009-0007-2104-8870)
- Ka Thao (ORCID: https://orcid.org/0009-0004-5315-6233)
- Fei Chen (ORCID: https://orcid.org/0000-0003-2308-3649)
- Zeyu Chen (ORCID: https://orcid.org/0000-0001-6393-1986)
- Jing Sun (ORCID: https://orcid.org/0000-0001-9103-0747)
- Mehdi Borji (ORCID: https://orcid.org/0009-0002-7023-434X)
Institutions
- Broad Institute (US)
- Harvard University (US)
- Foundation Center (US)
- Southwestern Medical Center (US)
- Quantitative BioSciences (US)
- Novo Nordisk (United States) (US)
- Dana-Farber Cancer Institute (US)
- Harvard Stem Cell Institute (US)
- The University of Texas Southwestern Medical Center (US)
Publication Details
- Journal
- Science
- Published
- 2024-10-10
- DOI
- https://doi.org/10.1126/science.adn5876
- Citations
- 30
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 7.01