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Weiss T, Kumar J, Chen C, Guo S, Schlegel O, Lutterman J, Ling K, Zhang F. Dual activities of an X-family DNA polymerase regulate CRISPR-induced insertional mutagenesis across species. Nat Commun 2024; 15:6293. [PMID: 39060288 PMCID: PMC11282277 DOI: 10.1038/s41467-024-50676-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The canonical non-homologous end joining (c-NHEJ) repair pathway, generally viewed as stochastic, has recently been shown to produce predictable outcomes in CRISPR-Cas9 mutagenesis. This predictability, mainly in 1-bp insertions and small deletions, has led to the development of in-silico prediction programs for various animal species. However, the predictability of CRISPR-induced mutation profiles across species remained elusive. Comparing CRISPR-Cas9 repair outcomes between human and plant species reveals significant differences in 1-bp insertion profiles. The high predictability observed in human cells links to the template-dependent activity of human Polλ. Yet plant Polλ exhibits dual activities, generating 1-bp insertions through both templated and non-templated manners. Polλ knockout in plants leads to deletion-only mutations, while its overexpression enhances 1-bp insertion rates. Two conserved motifs are identified to modulate plant Polλ's dual activities. These findings unveil the mechanism behind species-specific CRISPR-Cas9-induced insertion profiles and offer strategies for predictable, precise genome editing through c-NHEJ.
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Affiliation(s)
- Trevor Weiss
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shengsong Guo
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Oliver Schlegel
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Lutterman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, 55108, USA.
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN, 55108, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55108, USA.
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Han TT, Liu WC, Lu YT. General control non-repressible 20 (GCN20) functions in root growth by modulating DNA damage repair in Arabidopsis. BMC PLANT BIOLOGY 2018; 18:274. [PMID: 30419826 PMCID: PMC6233562 DOI: 10.1186/s12870-018-1444-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 09/27/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Most ABC transporters are engaged in transport of various compounds, but its subfamily F lacks transmembrane domain essential for chemical transportation. Thus the function of subfamily F remains further elusive. RESULTS Here, we identified General Control Non-Repressible 20 (GCN20), a member of subfamily F, as new factor for DNA damage repair in root growth. While gcn20-1 mutant had a short primary root with reduced meristem size and cell number, similar primary root lengths were assayed in both wild-type and GCN20::GCN20 gcn20-1 plants, indicating the involvement of GCN20 in root elongation. Further experiments with EdU incorporation and comet assay demonstrated that gcn20-1 displays increased cell cycle arrest at G2/M checkpoint and accumulates more damaged DNA. This is possible due to impaired ability of DNA repair in gcn20-1 since gcn20-1 seedlings are hypersensitive to DNA damage inducers MMC and MMS compared with the wild type plants. This note was further supported by the observation that gcn20-1 is more sensitive than the wild type when subjected to UV treatment in term of changes of both fresh weight and survival rate. CONCLUSIONS Our study indicates that GCN20 functions in primary root growth by modulating DNA damage repair in Arabidopsis. Our study will be useful to understand the functions of non-transporter ABC proteins in plant growth.
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Affiliation(s)
- Tong-Tong Han
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Wen-Cheng Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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Risk associated with off-target plant genome editing and methods for its limitation. Emerg Top Life Sci 2017; 1:231-240. [PMID: 33525760 PMCID: PMC7288994 DOI: 10.1042/etls20170037] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/13/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Assessment for potential adverse effects of plant genome editing logically focuses on the specific characteristics of the derived phenotype and its release environment. Genome-edited crops, depending on the editing objective, can be classified as either indistinguishable from crops developed through conventional plant breeding or as crops which are transgenic. Therefore, existing regulatory regimes and risk assessment procedures accommodate genome-edited crops. The ability for regulators and the public to accept a product focus in the evaluation of genome-edited crops will depend on research which clarifies the precision of the genome-editing process and evaluates unanticipated off-target edits from the process. Interpretation of genome-wide effects of genome editing should adhere to existing frameworks for comparative risk assessment where the nature and degree of effects are considered relative to a baseline of genome-wide mutations as found in crop varieties developed through conventional breeding methods. Research addressing current uncertainties regarding unintended changes from plant genome editing, and adopting procedures that clearly avoid the potential for gene drive initiation, will help to clarify anticipated public and regulatory questions regarding risk of crops derived through genome editing.
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Roy S. Maintenance of genome stability in plants: repairing DNA double strand breaks and chromatin structure stability. FRONTIERS IN PLANT SCIENCE 2014; 5:487. [PMID: 25295048 PMCID: PMC4172009 DOI: 10.3389/fpls.2014.00487] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/03/2014] [Indexed: 05/19/2023]
Abstract
Plant cells are subject to high levels of DNA damage resulting from plant's obligatory dependence on sunlight and the associated exposure to environmental stresses like solar UV radiation, high soil salinity, drought, chilling injury, and other air and soil pollutants including heavy metals and metabolic by-products from endogenous processes. The irreversible DNA damages, generated by the environmental and genotoxic stresses affect plant growth and development, reproduction, and crop productivity. Thus, for maintaining genome stability, plants have developed an extensive array of mechanisms for the detection and repair of DNA damages. This review will focus recent advances in our understanding of mechanisms regulating plant genome stability in the context of repairing of double stand breaks and chromatin structure maintenance.
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Affiliation(s)
- Sujit Roy
- *Correspondence: Sujit Roy, Protein Chemistry Laboratory, Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India e-mail:
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