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Olaya I, Burgess SM, Rog O. Formation and resolution of meiotic chromosome entanglements and interlocks. J Cell Sci 2024; 137:jcs262004. [PMID: 38985540 DOI: 10.1242/jcs.262004] [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] [Indexed: 07/12/2024] Open
Abstract
Interactions between parental chromosomes during the formation of gametes can lead to entanglements, entrapments and interlocks between unrelated chromosomes. If unresolved, these topological constraints can lead to misregulation of exchanges between chromosomes and to chromosome mis-segregation. Interestingly, these configurations are largely resolved by the time parental chromosomes are aligned during pachytene. In this Review, we highlight the inevitability of topologically complex configurations and discuss possible mechanisms to resolve them. We focus on the dynamic nature of a conserved chromosomal interface - the synaptonemal complex - and the chromosome movements that accompany meiosis as potential mechanisms to resolve topological constraints. We highlight the advantages of the nematode Caenorhabditis elegans for understanding biophysical features of the chromosome axis and synaptonemal complex that could contribute to mechanisms underlying interlock resolution. In addition, we highlight advantages of using the zebrafish, Danio rerio, as a model to understand how entanglements and interlocks are avoided and resolved.
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Affiliation(s)
- Iván Olaya
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Sean M Burgess
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences , University of Utah, Salt Lake City, UT 84112, USA
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Liu X, Gu D, Zhang Y, Jiang Y, Xiao Z, Xu R, Qin R, Li J, Wei P. Conditional knockdown of OsMLH1 to improve plant prime editing systems without disturbing fertility in rice. Genome Biol 2024; 25:131. [PMID: 38773623 PMCID: PMC11110357 DOI: 10.1186/s13059-024-03282-y] [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: 02/18/2024] [Accepted: 05/16/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND High-efficiency prime editing (PE) is desirable for precise genome manipulation. The activity of mammalian PE systems can be largely improved by inhibiting DNA mismatch repair by coexpressing a dominant-negative variant of MLH1. However, this strategy has not been widely used for PE optimization in plants, possibly because of its less conspicuous effects and inconsistent performance at different sites. RESULTS We show that direct RNAi knockdown of OsMLH1 in an ePE5c system increases the efficiency of our most recently updated PE tool by 1.30- to 2.11-fold in stably transformed rice cells, resulting in as many as 85.42% homozygous mutants in the T0 generation. The high specificity of ePE5c is revealed by whole-genome sequencing. To overcome the partial sterility induced by OsMLH1 knockdown of ePE5c, a conditional excision system is introduced to remove the RNAi module by Cre-mediated site-specific recombination. Using a simple approach of enriching excision events, we generate 100% RNAi module-free plants in the T0 generation. The increase in efficiency due to OsMLH1 knockdown is maintained in the excised plants, whose fertility is not impaired. CONCLUSIONS This study provides a safe and reliable plant PE optimization strategy for improving editing efficiency without disturbing plant development via transient MMR inhibition with an excisable RNAi module of MLH1.
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Affiliation(s)
- Xiaoshuang Liu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Dongfang Gu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Yiru Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Yingli Jiang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Zhi Xiao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| | - Rongfang Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Ruiying Qin
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Juan Li
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China.
| | - Pengcheng Wei
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
- Research Centre for Biological Breeding Technology, Advance Academy, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
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Qiao D, Wang J, Lu MH, Xin C, Chai Y, Jiang Y, Sun W, Cao Z, Guo S, Wang XC, Chen QJ. Optimized prime editing efficiently generates heritable mutations in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:900-906. [PMID: 36478403 DOI: 10.1111/jipb.13428] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Low efficiency is the main obstacle to using prime editing in maize (Zea mays). Recently, prime-editing efficiency was greatly improved in mammalian cells and rice (Oryza sativa) plants by engineering prime-editing guide RNAs (pegRNAs), optimizing the prime editor (PE) protein, and manipulating cellular determinants of prime editing. In this study, we tested PEs optimized via these three strategies in maize. We demonstrated that the ePE5max system, composed of PEmax, epegRNAs (pegRNA-evopreQ. 1), nicking single guide RNAs (sgRNAs), and MLH1dn, efficiently generated heritable mutations that conferred resistance to herbicides that inhibit 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), acetolactate synthase (ALS), or acetyl CoA carboxylase (ACCase) activity. Collectively, we demonstrate that the ePE5max system has sufficient efficiency to generate heritable (homozygous or heterozygous) mutations in maize target genes and that the main obstacle to using PEs in maize has thus been removed.
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Affiliation(s)
- Dexin Qiao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Junya Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Min-Hui Lu
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Cuiping Xin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yiping Chai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuanyuan Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhenghong Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Siyi Guo
- Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004, China
| | - Xue-Chen Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qi-Jun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
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Liu K, Chen E, Gu Z, Dai B, Wang A, Zhu Z, Feng Q, Zhou C, Zhu J, Shangguan Y, Wang Y, Li Z, Hou Q, Lv D, Wang C, Huang T, Wang Z, Huang X, Han B. A retrotransposon insertion in MUTL-HOMOLOG 1 affects wild rice seed set and cultivated rice crossover rate. PLANT PHYSIOLOGY 2022; 190:1747-1762. [PMID: 35976143 PMCID: PMC9614510 DOI: 10.1093/plphys/kiac378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 06/06/2023]
Abstract
Wild rice (Oryza rufipogon) has a lower panicle seed setting rate (PSSR) and gamete fertility than domesticated rice (Oryza sativa), but the genetic mechanisms of this phenomenon remain unknown. Here, we cloned a null allele of OsMLH1, an ortholog of MutL-homolog 1 to yeast and mammals, from wild rice O. rufipogon W1943 and revealed a 5.4-kb retrotransposon insertion in OsMLH1 is responsible for the low PSSR in wild rice. In contrast to the wild-type, a near isogenic line NIL-mlh1 exhibits defective crossover (CO) formation during meiosis, resulting in reduced pollen viability, partial embryo lethality, and low PSSR. Except for the mutant of mismatch repair gene postmeiotic segregation 1 (Ospms1), all other MutL mutants from O. sativa indica subspecies displayed male and female semi-sterility similar to NIL-mlh1, but less severe than those from O. sativa japonica subspecies. MLH1 and MLH3 did not contribute in an additive fashion to fertility. Two types of MutL heterodimers, MLH1-PMS1 and MLH1-MLH3, were identified in rice, but only the latter functions in promoting meiotic CO formation. Compared to japonica varieties, indica cultivars had greater numbers of CO events per meiosis. Our results suggest that low fertility in wild rice may be caused by different gene defects, and indica and japonica subspecies have substantially different CO rates responsible for the discrepancy between the fertility of mlh1 and mlh3 mutants.
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Affiliation(s)
- Kun Liu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Erwang Chen
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zhoulin Gu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Bingxin Dai
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Ahong Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zhou Zhu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qi Feng
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Congcong Zhou
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Jingjie Zhu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yingying Shangguan
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongchun Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zhen Li
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qingqing Hou
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danfeng Lv
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Changsheng Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Tao Huang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zixuan Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
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