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Prime genome editing in rice and wheat
Abstract
Prime editors, which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusions programmed with prime editing guide RNAs (pegRNAs), can edit bases in mammalian cells without donor DNA or double-strand breaks. We adapted prime editors for use in plants through codon, promoter, and editing-condition optimization. The resulting suite of plant prime editors enable point mutations, insertions and deletions in rice and wheat protoplasts. Regenerated prime-edited rice plants were obtained at frequencies of up to 21.8%.
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“Prime editing allows for all types of desired base substitutions, small insertions up to 44 bp and deletions up to 88 bp at selected target sites with the use of CRSIPR/Cas9 nickase-reverse transcriptase fusions (Anzalone et al., 2019;Lin et al., 2020).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Lin et al., 2020
In the citing paper
“Plant prime-editing systems have been used in rice and wheat, but not in barley (Lin et al., 2020;Xu et al., 2020).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Lin et al., 2020
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Cites
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Self-citationProgrammable base editing of A•T to G•C in genomic DNA without DNA cleavage
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Self-citationGenomic variation in 3,010 diverse accessions of Asian cultivated rice
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Self-citationA CRISPR/Cas9 toolkit for multiplex genome editing in plants
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Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion
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Cited by
Sorted by citations
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors
Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237
Self-citationGenome engineering for crop improvement and future agriculture
Gao, C. (2021) · Cell · doi:10.1016/j.cell.2021.01.005 · Cited by 1,070
“…RT template in the pegRNA, using other RTs, processing the pegRNAs with a ribozyme, raising the culture temperature to favor reverse transcription (Lin et al., 2020), using enhanced promoters for pegRNA expression (Jiang et al., 2020), and enriching for transformed cells (Xu et al., 2020a, 2020b).”
InfluentialSelf-citationApplications of CRISPR–Cas in agriculture and plant biotechnology
Zhu, H., Li, C., & Gao, C. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00288-9 · Cited by 870
Self-citationEnhanced prime editing systems by manipulating cellular determinants of editing outcomes
Chen, P. J., Hussmann, J. A., Yan, J., Knipping, F., Ravisankar, P., Chen, P.-F., Chen, C.-D., Nelson, J. W., Newby, G. A., Şahin, M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.018 · Cited by 841
“, 2021), rice and wheat (Lin et al., 2020), zebrafish (Petri et al.”
BackgroundSelf-citationPrime editing for precise and highly versatile genome manipulation
Chen, P. J., & Liu, D. R. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00541-1 · Cited by 644
Self-citationPast, present, and future of CRISPR genome editing technologies
Pacesa, M., Pelea, O., & Jinek, M. (2024) · Cell · doi:10.1016/j.cell.2024.01.042 · Cited by 609
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants
Siegner, S. M., Karasu, M. E., Schröder, M., Kontarakis, Z., & Corn, J. E. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04034-6 · Cited by 436
Precise plant genome editing using base editors and prime editors
Molla, K. A., Sretenovic, S., Bansal, K. C., & Qi, Y. (2021) · Nature Plants · doi:10.1038/s41477-021-00991-1 · Cited by 387
CRISPR/Cas: A powerful tool for gene function study and crop improvement
Zhang, D., Zhang, Z., Unver, T., & Zhang, B. (2021) · Journal of Advanced Research · doi:10.1016/j.jare.2020.10.003 · Cited by 373
“Currently, prime editing has been successfully to replace genes in several important plant species, including rice [55–58], wheat [55], tomato [59], and maize [60].”
BackgroundHigh-efficiency prime editing with optimized, paired pegRNAs in plants
Lin, Q., Jin, S., Zong, Y., Yu, H., Zhu, Z., Liu, G., Kou, L., Wang, Y., Qiu, J.-L., Li, J., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00868-w · Cited by 325
Self-citationPhage-assisted evolution and protein engineering yield compact, efficient prime editors
Doman, J. L., Pandey, S., Neugebauer, M. E., An, M., Davis, J. R., Randolph, P. B., McElroy, A. N., Gao, X. D., Raguram, A., Richter, M. F., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.039 · Cited by 327
“Nevertheless, the location of the PE6Cas9mutations suggest potential explanations for their site-specific benefits to PE.”
InfluentialSelf-citationNanotechnology to advance CRISPR–Cas genetic engineering of plants
Demirer, G. S., Silva, T. N., Jackson, C. T., Thomas, J. B., Ehrhardt, D. W., Rhee, S. Y., Mortimer, J. C., & Landry, M. P. (2021) · Nature Nanotechnology · doi:10.1038/s41565-021-00854-y · Cited by 305
Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize
Jiang, Y., Chai, Y., Lu, M., Han, X., Lin, Q., Zhang, Y., Zhang, Q., Zhou, Y., Wang, X., Gao, C., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02170-5 · Cited by 281
“Excluding the data based on enriching strategies or that are unsuitable for comparison, a total of 164 prime-edited rice lines transformed with 39 prime editors targeting 11 endogenous rice genes were generated in these previous reports [2, 3, 5, 6, 8].”
MethodSelf-citationPredicting the efficiency of prime editing guide RNAs in human cells
Kim, H. K., Yu, G., Park, J., Min, S., Lee, S., Yoon, S., & Kim, S. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0677-y · Cited by 282
Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice
Liu, P., Liang, S.-Q., Zheng, C., Mintzer, E., Zhao, Y. G., Ponnienselvan, K., Mir, A., Sontheimer, E. J., Gao, G., Flotte, T. R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22295-w · Cited by 273
Designing future crops: challenges and strategies for sustainable agriculture
Tian, Z., Wang, J., Li, J., & Han, B. (2020) · The Plant Journal · doi:10.1111/tpj.15107 · Cited by 275
“…modulator (e.g. dCas9-SunTag and dCas9-TV system) have greatly expanded the scope and capabilities of genome editing in crops (Lowder et al., 2015; Piatek et al., 2015; Vazquez-Vilar et al., 2016; Li et al., 2017; Anzalone et al., 2019; Papikian et al., 2019; Lin et al., 2020; Lu et al., 2020).”
BackgroundPrecise genomic deletions using paired prime editing
Choi, J., Chen, W., Suiter, C. C., Lee, C., Chardon, F. M., Yang, W., Leith, A., Daza, R. M., Martin, B., & Shendure, J. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01025-z · Cited by 260
An engineered prime editor with enhanced editing efficiency in plants
Zong, Y., Liu, Y., Xue, C., Li, B., Li, X., Wang, Y., Li, J., Liu, G., Huang, X., Cao, X., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01254-w · Cited by 257
“The low editing efficiency of original prime editors severely limits the utility of prime editing 2,6,9 .”
Self-citationPrime editing for functional repair in patient-derived disease models
Schene, I. F., Joore, I. P., Oka, R., Mokrý, M., van Vugt, A. H. M., van Boxtel, R., van der Doef, H. P. J., van der Laan, L. J. W., Verstegen, M. M. A., van Hasselt, P. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19136-7 · Cited by 250
Targeted genome-modification tools and their advanced applications in crop breeding
Li, B., Sun, C., Li, J., & Gao, C. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00720-2 · Cited by 269
Self-citationApplication of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants
Kumar, M., Prusty, M. R., Pandey, M. K., Singh, P. K., Bohra, A., Guo, B. Z., & Varshney, R. K. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1157678 · Cited by 251
“To date, prime editing has been applied to corn, rice, wheat, and tomato (Jiang et al., 2020; Lin et al., 2020; Lu et al., 2021a).”
BackgroundTargeted, efficient sequence insertion and replacement in rice
Lu, Y., Tian, Y., Shen, R., Yao, Q., Wang, M., Chen, M., Dong, J., Zhang, T., Li, F., Lei, M., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0581-5 · Cited by 225
Efficient generation of mouse models with the prime editing system
Liu, Y., Li, X., He, S., Huang, S., Li, C., Chen, Y., Liu, Z., Huang, X., & Wang, X. (2020) · Cell Discovery · doi:10.1038/s41421-020-0165-z · Cited by 213
“Furthermore, the editing ef fi ciency in mutant mice is equivalent to that in prime-edited plants 10 .”
BackgroundEngineering herbicide resistance via prime editing in rice
Butt, H., Rao, G. S., Sedeek, K., Aman, R., Kamel, R., & Mahfouz, M. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13399 · Cited by 220
“While this work was prepared for publication, similar findings were reported in pants (Li et al., 2020; Lin et al., 2020; Tang et al., 2020).”
ResultCRISPR-based genome editing through the lens of DNA repair
Nambiar, T. S., Baudrier, L., Billon, P., & Ciccia, A. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.026 · Cited by 227
Development of Plant Prime-Editing Systems for Precise Genome Editing
Xu, R., Li, J., Liu, X., Shan, T., Qin, R., & Wei, P. (2020) · Plant Communications · doi:10.1016/j.xplc.2020.100043 · Cited by 209
“During the preparation and submission of this paper, four independent groups have reported successful plant prime editing at exogenous or endogenous targets by transiently or stably expressing PEs in rice and other plant species (Li et al., 2020b; Lin et al., 2020; Tang et al., 2020; Xu et al., 2020b).”
BackgroundCRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells
Petri, K., Zhang, W., Ma, J., Schmidts, A., Lee, H., Horng, J. E., Kim, D. Y., Kurt, I. C., Clement, K., Hsu, J. Y., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-00901-y · Cited by 208
“PE has been used to edit the genomes of mammalian cells and organoids in culture, plants, Drosophila, and somatic cells in mice with the PE components delivered as DNAs or RNAs 1,3–7 .”
Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing
Tao, J., Bauer, D. E., & Chiarle, R. (2023) · Nature Communications · doi:10.1038/s41467-023-35886-6 · Cited by 232
CRISPR‐Cas Biochemistry and CRISPR‐Based Molecular Diagnostics
Weng, Z., You, Z., Yang, J., Mohammad, N., Lin, M., Wei, Q., Gao, X., & Zhang, Y. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202214987 · Cited by 213
Next-Generation Breeding Strategies for Climate-Ready Crops
Razzaq, A., Kaur, P., Akhter, N., Wani, S. H., & Saleem, F. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.620420 · Cited by 226
Precise integration of large DNA sequences in plant genomes using PrimeRoot editors
Sun, C., Yuan, L., Li, B., Gao, Q., Li, Y., Cao, W., Yang, C., Li, H., Wang, Z., Li, Y., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01769-w · Cited by 212
“Plasmids expressing epegRNAs to produce short insertions were cloned as previously described 46,55 .”
Self-citationPrime editing: advances and therapeutic applications
Zhao, Z., Shang, P., Mohanraju, P., & Geijsen, N. (2023) · Trends in biotechnology · doi:10.1016/j.tibtech.2023.03.004 · Cited by 205
PrimeDesign software for rapid and simplified design of prime editing guide RNAs
Hsu, J. Y., Grünewald, J., Szalay, R. N., Shih, J., Anzalone, A. V., Lam, K. C., Shen, M. W., Petri, K., Liu, D. R., Joung, J. K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21337-7 · Cited by 194
“(5) Dissocation of prime editor (6) Flap competition (7) Flap excision and ligation (8) Target strand nick by a ngRNA (PE3) (9) Preferential repair of the NTS sequence (top strand) WT sequence”
Self-citationAdvantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement
Ahmar, S., Mahmood, T., Fiaz, S., Mora, F., Shafique, M. S., Chattha, M. S., & Jung, K.-H. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.663849 · Cited by 186
“, CRISPR/Cas9, CRISPR–CRISPR from Prevotella and Francisella 1 (Cpf1), base editing, and prime editing, were shown to be powerful tools for the successful modification of genome sequence in a precise and straightforward manner (Puchta et al., 1993; Wright et al., 2005; Christian et al., 2010; Butler et al., 2016; Tang…”
MethodJang, H., Jo, D. H., Cho, C. S., Shin, J. H., Seo, J. H., Yu, G., Gopalappa, R., Kim, D., Cho, S., Kim, J. H., et al. (2021) · Nature Biomedical Engineering · doi:10.1038/s41551-021-00788-9 · Cited by 186
Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair
da Silva, J. F., Oliveira, G. P., Arasa-Verge, E. A., Kagiou, C., Moretton, A., Timelthaler, G., Jiricny, J., & Loizou, J. I. (2022) · Nature Communications · doi:10.1038/s41467-022-28442-1 · Cited by 189
“Due to its versatility, PE has been used in a wide variety of models, such as zebrafish (Petri et al., 2021), rice and wheat (Lin et al., 2020), mouse (Liu et al., 2020) and human stem cells (Sürün et al., 2020).”
Li, C., Brant, E. J., Budak, H., & Zhang, B. (2021) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2100009 · Cited by 191
“Although it has been used successfully to edit plant genes, the editing efficiency is much lower in plants than in animals (Anzalone et al., 2019; Li HY et al., 2020; Lin et al., 2020; Tang et al., 2020; Xu et al., 2020).”
BackgroundMethodDual-AAV delivering split prime editor system for in vivo genome editing
Zhi, S., Chen, Y., Wu, G., Wen, J., Wu, J., Liu, Q., Li, Y., Kang, R., Hu, S., Wang, J., et al. (2022) · Molecular Therapy · doi:10.1016/j.ymthe.2021.07.011 · Cited by 174
Bandyopadhyay, A., Kancharla, N., Javalkote, V. S., Dasgupta, S., & Brutnell, T. P. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.584151 · Cited by 182
Fine-tuning sugar content in strawberry
Xing, S., Chen, K., Zhu, H., Zhang, R., Zhang, H., Li, B., & Gao, C. (2020) · Genome biology · doi:10.1186/s13059-020-02146-5 · Cited by 178
Self-citationProtoplast Regeneration and Its Use in New Plant Breeding Technologies
Reed, K. M., & Bargmann, B. O. R. (2021) · Frontiers in Genome Editing · doi:10.3389/fgeed.2021.734951 · Cited by 173
Designing and executing prime editing experiments in mammalian cells
Doman, J. L., Sousa, A. A., Randolph, P. B., Chen, P. J., & Liu, D. R. (2022) · Nature Protocols · doi:10.1038/s41596-022-00724-4 · Cited by 172
Self-citationPrecision genome engineering in rice using prime editing system
Hua, K., Jiang, Y., Tao, X., & Zhu, J. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13395 · Cited by 171
“All rights reserved systems in rice and wheat were reported (Li et al., 2020; Lin et al., 2020; Tang et al., 2020; Xu et al., 2020a; Xu et al., 2020b).”
BackgroundTALE and TALEN genome editing technologies
Becker, S., & Boch, J. (2021) · Gene and Genome Editing · doi:10.1016/j.ggedit.2021.100007 · Cited by 183
Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System
Xu, W., Zhang, C., Yang, Y., Zhao, S., Kang, G., He, X., Song, J., & Yang, J. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.03.012 · Cited by 165
Precise genome modification in tomato using an improved prime editing system
Lu, Y., Tian, Y., Shen, R., Yao, Q., Zhong, D., Zhang, X., & Zhu, J. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13497 · Cited by 164
“Several research groups have adopted this method for use in monocotyledonous plants, including rice andwheat (Butt et al., 2020; Hua et al., 2020; Li et al., 2020; Lin et al., 2020; Tang et al., 2020; Xu et al., 2020).”
MethodApplication of Gene Editing for Climate Change in Agriculture
Karavolias, N. G., Horner, W., Abugu, M. N., & Evanega, S. D. (2021) · Frontiers in Sustainable Food Systems · doi:10.3389/fsufs.2021.685801 · Cited by 167
CRISPR ribonucleoprotein-mediated genetic engineering in plants
Zhang, Y., Iaffaldano, B. J., & Qi, Y. (2021) · Plant Communications · doi:10.1016/j.xplc.2021.100168 · Cited by 169
“Cas proteins can be further engineered to recruit effector protein domains in order to achieve base editing (Kim, 2018), prime editing (Li et al., 2020b; Butt et al., 2020; Lin et al., 2020; Lu et al., 2020; Tang et al., 2020; Xu et al., 2020), epigenome editing (GallegoBartolomé et al.”
BackgroundA web tool for the design of prime-editing guide RNAs
Chow, R. D.-W., Chen, J., Shen, J., & Chen, S. (2020) · Nature Biomedical Engineering · doi:10.1038/s41551-020-00622-8 · Cited by 165
Deng, Y., Ning, Y., Yang, D., Zhai, K., Wang, G., & He, Z. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.09.018 · Cited by 156
Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis
Su, P., Kang, H., Peng, Q., Wicaksono, W. A., Berg, G., Liu, Z., Ma, J., Zhang, D., Cernava, T., & Liu, Y. (2024) · Nature Communications · doi:10.1038/s41467-023-44335-3 · Cited by 164
“The transformation was performed using a rice transformation method 69 .”
MethodGenome Editing in Bacteria: CRISPR-Cas and Beyond
Arroyo-Olarte, R. D., Rodríguez, R. B., & Morales‐Ríos, E. (2021) · Microorganisms · doi:10.3390/microorganisms9040844 · Cited by 161
“Prime-editing has been successfully applied in mice [87] and plants [88], but its feasibility for bacterial genome editing still needs to be explored.”
BackgroundLi, X., Zhou, L., Gao, B., Li, G., Wang, X., Wang, Y., Wei, J., Han, W., Wang, Z., Li, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29339-9 · Cited by 142
Self-citationConstruct design for CRISPR/Cas-based genome editing in plants
Hassan, M. M., Zhang, Y., Yuan, G., De, K., Chen, J., Muchero, W., Tuskan, G. A., Qi, Y., & Yang, X. (2021) · Trends in Plant Science · doi:10.1016/j.tplants.2021.06.015 · Cited by 139
An Outlook on Global Regulatory Landscape for Genome-Edited Crops
Ahmad, A., Munawar, N., Khan, Z., Qumsani, A. T., Khan, S. H., Jamil, A., Ashraf, S., Ghouri, M. Z., Aslam, S., Mubarik, M. S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222111753 · Cited by 140
Li, X., Guo, T., Wang, J., Bekele, W. A., Sukumaran, S., Vanous, A. E., McNellie, J. P., Tibbs‐Cortes, L. E., Lopes, M. S., Lamkey, K. R., et al. (2021) · Molecular Plant · doi:10.1016/j.molp.2021.03.010 · Cited by 140
Targeted mutagenesis in mouse cells and embryos using an enhanced prime editor
Park, S.-J., Jeong, T. Y., Shin, S. K., Yoon, D. E., Lim, S.-Y., Kim, S. P., Choi, J., Lee, H., Hong, J.-I., Ahn, J., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02389-w · Cited by 133
Efficient and versatile multiplex prime editing in hexaploid wheat
Ni, P., Zhao, Y., Zhou, X., Liu, Z., Huang, Z., Ni, Z., Sun, Q., & Zong, Y. (2023) · Genome biology · doi:10.1186/s13059-023-02990-1 · Cited by 142
“Some studies have reported driving pegRNA expression with enhanced promoters [21, 22], using dual pegRNAs [23], designing the pegRNA sequence based on melting-temperature preferences [23], and optimizing pegRNA by adding RNA motifs at the 3′ terminus of pegRNA to enhance its stability in rice and maize [24–27].”
BackgroundMethodInfluentialSelf-citationGenome-wide specificity of prime editors in plants
Jin, S., Lin, Q., Luo, Y., Zhu, Z., Liu, G., Li, Y., Chen, K., Qiu, J., & Gao, C. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00891-x · Cited by 131
Self-citationCRISPR–Cas applications in agriculture and plant research
Tuncel, A., Pan, C., Clem, J. S., Liu, D., & Qi, Y. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00834-3 · Cited by 145
“However, it was recently used to knock up the expression of photosynthesis gene OsPBS1 to levels that could otherwise be achieved by transgenic overexpression 194 .”
InfluentialSelf-citationAhmad, M. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1133036 · Cited by 135
“However, it took nine years from the discovery of ZFNs to the first ZFN-based plant genome editing due to the challenge of developing ZFNs with high sequence affinity and high off-target efficiency (Zetsche et al., 2015; Kim et al., 2016; Komor et al., 2016; Anzalone et al., 2019; Zhang et al., 2019; Lin et al., 2020;…”
BackgroundHeat stress in wheat: a global challenge to feed billions in the current era of the changing climate
Farhad, M., Kumar, U., Tomar, V., Bhati, P. K., Navaneetha Krishnan, J., Mustarin, K. E., Bárek, V., Brestič, M., & Hossain, A. (2023) · Frontiers in Sustainable Food Systems · doi:10.3389/fsufs.2023.1203721 · Cited by 152
Multiplex genome-editing technologies for revolutionizing plant biology and crop improvement
Abdelrahman, M., Wei, Z., Rohila, J. S., & Zhao, K. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.721203 · Cited by 125
Genome editing for plant research and crop improvement
Zhan, X., Lu, Y., Zhu, J., & Botella, J. R. (2020) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13063 · Cited by 121
Xu, R., Liu, X., Li, J., Qin, R., & Wei, P. (2021) · Nature Plants · doi:10.1038/s41477-021-00942-w · Cited by 123
Tuning plant phenotypes by precise, graded downregulation of gene expression
Xue, C., Qiu, F., Wang, Y., Li, B., Zhao, K. T., Chen, K., & Gao, C. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01707-w · Cited by 122
“By next-generation sequencing, we found that OsBRI1-T4 pegRNA, used together with the plant prime editor (PPE2) 27 , was the most effective in introducing uORF OsBRI1 (−99, 28 aa) (Extended Data Fig.”
MethodSelf-citationCRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences
Karlson, C. K. S., Noor, S. N. M., Nolte, N., & Tan, B. C. (2021) · Plants · doi:10.3390/plants10102055 · Cited by 139
“[83] recently adapted prime editors to induce point mutations, insertions and deletions in rice.”
BackgroundPrime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato
Perroud, P., Guyon‐Debast, A., Veillet, F., Kermarrec, M.-P., Chauvin, L., Chauvin, J.-É., Gallois, J., & Nogué, F. (2021) · Plant Science · doi:10.1016/j.plantsci.2021.111162 · Cited by 130
Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops
Villalobos-López, M. Á., Arroyo-Becerra, A., Quintero-Jiménez, A., & Iturriaga, G. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231912053 · Cited by 129
Biotechnological Exploration of Transformed Root Culture for Value-Added Products
Shi, M., Liao, P., Nile, S. H., et al. (2020) · Trends in biotechnology · doi:10.1016/j.tibtech.2020.06.012 · Cited by 118
PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
Hwang, G., Jeong, Y. K., Habib, O., Hong, S.-A., Lim, K., Kim, J., & Bae, S. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab319 · Cited by 122
Enhancement of prime editing via xrRNA motif-joined pegRNA
Zhang, G., Liu, Y., Huang, S., Qu, S., Cheng, D., Yao, Y., Ji, Q., Wang, X., Huang, X., & Liu, J. (2022) · Nature Communications · doi:10.1038/s41467-022-29507-x · Cited by 117
“plasmids for PE2 and WT pegRNAs or different xr-pegRNAs targeting indicated (6) genomic loci for base conversions.”
BackgroundA haplotype-led approach to increase the precision of wheat breeding
Brinton, J., Ramirez-Gonzalez, R. H., Simmonds, J., Wingen, L. U., Orford, S., Griffiths, S., 10 Wheat Genome Project, Haberer, G., Spannagl, M., Walkowiak, S., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-01413-2 · Cited by 113
Gasparini, K., Moreira, J. D. R., Peres, L. E. P., & Zsögön, A. (2021) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2021.102006 · Cited by 115
Bhat, M. A., Mir, R. A., Kumar, V., Shah, A. A., Zargar, S. M., Rahman, S., & Jan, A. T. (2021) · Physiologia Plantarum · doi:10.1111/ppl.13359 · Cited by 120
Zheng, C., Liang, S., Liu, B., Liu, P., Kwan, S.-Y., Wolfe, S. A., & Xue, W. (2022) · Molecular Therapy · doi:10.1016/j.ymthe.2022.01.005 · Cited by 119
Advances in Crop Breeding Through Precision Genome Editing
Nerkar, G., Devarumath, S., Purankar, M. V., Kumar, A., Valarmathi, R., Devarumath, R. M., & Appunu, C. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.880195 · Cited by 124
SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition
Xu, Z., Kuang, Y., Ren, B., Yan, D., Yan, F., Spetz, C., Sun, W., Wang, G., Zhou, X., & Zhou, H. (2021) · Genome biology · doi:10.1186/s13059-020-02231-9 · Cited by 117
Increasing the efficiency and precision of prime editing with guide RNA pairs
Zhuang, Y., Liu, J., Wu, H., Zhu, Q., Yan, Y., Meng, H., Chen, P. R., & Yi, C. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00889-1 · Cited by 112
CRISPR/Cas9 gene editing in legume crops: Opportunities and challenges
Bhowmik, P., Konkin, D. J. F., Polowick, P. L., Hodgins, C. L., Subedi, M., Xiang, D., Yu, B., Patterson, N. A., Rajagopalan, N., Babic, V., et al. (2021) · Legume Science · doi:10.1002/leg3.96 · Cited by 113
“This method enables a wide range of editing applications including insertions, deletions, and point mutations without double-stranded DNA breaks or donor DNA templates (Anzalone et al., 2019; Lin et al., 2020).”
BackgroundMethodPresent and future prospects for wheat improvement through genome editing and advanced technologies
Li, S., Zhang, C., Li, J., Yan, L., Wang, N., & Xia, L. (2021) · Plant Communications · doi:10.1016/j.xplc.2021.100211 · Cited by 118
“efficiencies at some target sites in rice are still lower, indicating that PE activity may not parallel Cas9 nuclease cleavage activity in plants, at least for the tested targets (Xu et al., 2020c; Li et al., 2020e; Lin et al., 2020).”
BackgroundGenome Editing Technologies for Rice Improvement: Progress, Prospects, and Safety Concerns
Zafar, K., Sedeek, K. E. M., Rao, G. S., Khan, M. Z., Amin, I. U., Kamel, R., Mukhtar, Z., Zafar, M., Mansoor, S., & Mahfouz, M. M. (2020) · Frontiers in Genome Editing · doi:10.3389/fgeed.2020.00005 · Cited by 113
“The RT uses the pegRNA as a template to copy the desired edits into the genome (Anzalone et al., 2019; Lin et al., 2020).”
BackgroundMethodEngineered prime editors with PAM flexibility
Kweon, J., Yoon, J.-K., Jang, A.-H., Shin, H. R., See, J.-E., Jang, G., Kim, J., & Kim, Y. (2021) · Molecular Therapy · doi:10.1016/j.ymthe.2021.02.022 · Cited by 111
Calvin–Benson cycle regulation is getting complex
Gurrieri, L., Fermani, S., Zaffagnini, M., Sparla, F., & Trost, P. (2021) · Trends in Plant Science · doi:10.1016/j.tplants.2021.03.008 · Cited by 109
Targeted DNA insertion in plants
Dong, O. X., & Ronald, P. C. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004834117 · Cited by 107
Schenke, D., & Cai, D. (2020) · iScience · doi:10.1016/j.isci.2020.101478 · Cited by 116
“Also, this system has already been successfully applied in plants, such as rice and wheat (Lin et al., 2020), and will become a more versatile tool in resistance breeding than ‘‘simple’’ KO applications (Figure 2E).”
BackgroundGenome Editing for Resistance to Insect Pests: An Emerging Tool for Crop Improvement
Tyagi, S., Karthik, K., Saakre, M., Rathinam, M., Raman, V., Pattanayak, D., & Sreevathsa, R. (2020) · ACS Omega · doi:10.1021/acsomega.0c01435 · Cited by 104
A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing
Tong, Y., Jørgensen, T. S., Whitford, C. M., Weber, T., & Lee, S. Y. (2021) · Nature Communications · doi:10.1038/s41467-021-25541-3 · Cited by 104
Jiang, Y., Chai, Y., Qiao, D., Wang, J., Xin, C., Sun, W. Y., Cao, Z., Zhang, Y., Zhou, Y., Wang, X., et al. (2022) · Molecular Plant · doi:10.1016/j.molp.2022.09.006 · Cited by 103
A design optimized prime editor with expanded scope and capability in plants
Xu, W., Yang, Y., Yang, B., Krueger, C. J., Xiao, Q., Zhao, S., Zhang, L., Kang, G., Wang, F., Yi, H., et al. (2021) · Nature Plants · doi:10.1038/s41477-021-01043-4 · Cited by 101
Advances in Delivery Mechanisms of CRISPR Gene-Editing Reagents in Plants
Laforest, L. C., & Nadakuduti, S. S. (2022) · Frontiers in Genome Editing · doi:10.3389/fgeed.2022.830178 · Cited by 101
Gao, P., Lyu, Q., Ghanam, A. R., Lazzarotto, C. R., Newby, G. A., Zhang, W., Choi, M., Slivano, O. J., Holden, K., Walker, J. A., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02304-3 · Cited by 96
Self-citationGupta, A., Liu, B., Chen, Q., & Yang, B. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14049 · Cited by 105
“The initial PE was less efficient and produced undesired insertion/deletion by-products, and editing efficiency varies widely across different species, cell types, loci and edit sequences (Lin et al ., 2020).”
Protoplasts: From Isolation to CRISPR/Cas Genome Editing Application
Yue, J.-J., Yuan, J.-L., Wu, F., Yuan, Y., Cheng, Q., Hsu, C., & Lin, C. (2021) · Frontiers in Genome Editing · doi:10.3389/fgeed.2021.717017 · Cited by 104
CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges
Mushtaq, M., Dar, A. A., Skalický, M., Tyagi, A., Bhagat, N., Basu, U., Bhat, B. A., Zaid, A., Ali, S., Dar, T. U. H., et al. (2021) · Genes · doi:10.3390/genes12060797 · Cited by 100
Nadakuduti, S. S., & Enciso-Rodríguez, F. E. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2020.637159 · Cited by 99
“Prime editing has been implemented in cereal crops (Butt et al., 2020; Lin et al., 2020; Tang et al., 2020; Xu et al., 2020) and is yet to be used in diverse plant species.”
BackgroundPrecise genome engineering in Drosophila using prime editing
Bosch, J. A., Birchak, G., & Perrimon, N. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021996118 · Cited by 93
A Review on Advanced CRISPR-Based Genome-Editing Tools: Base Editing and Prime Editing
Sichani, A. S., Ranjbar, M., Baneshi, M., Zadeh, F. T., & Fallahi, J. (2022) · Molecular Biotechnology · doi:10.1007/s12033-022-00639-1 · Cited by 105
“It is noteworthy to mention that due to the versatility of PE, it has been used in a wide variety of model organisms, such as rice and wheat [58, 59], zebrafish [71], flies [72], mouse embryos [73], post-natal mice [34, 35], human stem cells [74], and patient-derived organoids [75].”
BackgroundPrime editing using CRISPR-Cas12a and circular RNAs in human cells
Liang, R., He, Z., Zhao, K. T., Zhu, H., Hu, J., Liu, G., Gao, Q., Liu, M., Zhang, R., Qiu, J., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02095-x · Cited by 100
“Although many reverse transcriptases have been used in prime editors, M-MLV RT is still the most efficient enzyme and is widely adopted 12,26 .”
Self-citationPlant base editing and prime editing: The current status and future perspectives
Li, J., Zhang, C., He, Y., Li, S., Yan, L., Li, Y., Zhu, Z., & Xia, L. (2022) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13425 · Cited by 94
Self-citation
Metadata
- Authors
- Lin, Q., Zong, Y., Xue, C., Wang, S., Jin, S., Zhu, Z., Wang, Y., Anzalone, A. V., Raguram, A., Doman, J. L., Liu, D. R., & Gao, C.
- Affiliations
- Chinese Academy of Sciences (CN)
- Broad Institute (US)
- Corresponding author
- Gao, Caixia
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2020-03-16
- Volume
- 38
- Issue
- 5
- Pages
- 582-585
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W3012016445
- Semantic Scholar
- 8cfc62e789552485d639d0542c1caaaf730db03d
- Cited by
- 873
- References
- 23
- Citations by year
- 2026: 105 · 2025: 118 · 2024: 106 · 2023: 135 · 2022: 146 · 2021: 175 · 2020: 86
- FWCI
- 44.86
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (RM1HG009490)
- National Institute of General Medical Sciences (R35GM118062)
- National Institute of Allergy and Infectious Diseases (U01AI142756)
- National Institute of Biomedical Imaging and Bioengineering (R01EB022376)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Transgenic Plants and Applications
- Keywords
- prime editing, CRISPR/Cas9 nickase, reverse transcriptase, pegRNA, plant genome editing, rice, wheat, protoplast transformation, point mutations, indels, codon optimization, promoter optimization, plant regeneration
- MeSH terms
- Gene Editing, Deoxyribonuclease I, Oryza, Triticum, Genome, Plant, CRISPR-Cas Systems
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