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Roy KR, Smith JD, Li S, Vonesch SC, Nguyen M, Burnett WT, Orsley KM, Lee CS, Haber JE, St Onge RP, Steinmetz LM. Dissecting quantitative trait nucleotides by saturation genome editing. bioRxiv 2024:2024.02.02.577784. [PMID: 38352467 PMCID: PMC10862795 DOI: 10.1101/2024.02.02.577784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Genome editing technologies have the potential to transform our understanding of how genetic variation gives rise to complex traits through the systematic engineering and phenotypic characterization of genetic variants. However, there has yet to be a system with sufficient efficiency, fidelity, and throughput to comprehensively identify causal variants at the genome scale. Here we explored the ability of templated CRISPR editing systems to install natural variants genome-wide in budding yeast. We optimized several approaches to enhance homology-directed repair (HDR) with donor DNA templates, including donor recruitment to target sites, single-stranded donor production by bacterial retrons, and in vivo plasmid assembly. We uncovered unique advantages of each system that we integrated into a single superior system named MAGESTIC 3.0. We used MAGESTIC 3.0 to dissect causal variants residing in 112 quantitative trait loci across 32 environmental conditions, revealing an enrichment for missense variants and loci with multiple causal variants. MAGESTIC 3.0 will facilitate the functional analysis of the genome at single-nucleotide resolution and provides a roadmap for improving template-based genome editing systems in other organisms.
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Affiliation(s)
- Kevin R Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Sibylle C Vonesch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Laboratory for Genome Editing and Systems Genetics, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- KU Leuven Center for Microbial and Plant Genetics, Department M2S, Leuven, Belgium
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Wallace T Burnett
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Kevin M Orsley
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheng-Sheng Lee
- Brandeis University, Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Waltham, MA
| | - James E Haber
- Brandeis University, Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Waltham, MA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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Narukawa-Nara M, Sasaki K, Ishii A, Baba K, Amano K, Kuroki M, Saitoh KI, Kamakura T. Identification and characterization of a novel gene encoding the NBS1 protein in Pyricularia oryzae. Biosci Biotechnol Biochem 2015; 79:1183-90. [PMID: 25774746 DOI: 10.1080/09168451.2015.1015951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The ascomycete Pyricularia oryzae (teleomorph: Magnaporthe oryzae) causes one of the most serious diseases known as rice blast. The Nijmegen breakage syndrome protein (NBS1) is essential for DNA repair; thus, we studied the P. oryzae NBS1 homolog (PoNBS1). A PoNBS1 null mutant exhibited high sensitivity to DNA damage-inducing agents. The mutant also exhibited the retarded hyphal growth, and induced abnormal conidial germination and shape, but showed normal appressorium formation. The phenotypes of the null mutant were complemented by introducing the cDNA of PoNBS1 driven by a TrpC promoter of Aspergillus nidulans. In addition, the null mutant similarly complemented with the PoNBS1 cDNA lacking the FHA domain that had a normal phenotype except for hyphal growth. These results suggest that PoNBS1 is involved in DNA repair and normal development in P. oryzae. Moreover, the FHA domain of PoNBS1 participates in normal hyphal growth.
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Affiliation(s)
- Megumi Narukawa-Nara
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Japan
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