The DOI matches its Crossref record; 136 of the 140 references it cites were found in a registry or an index.
CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing
Open accessAbstract
Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its high efficiency, ease of use, and accuracy. It can be used to add desirable and remove undesirable alleles simultaneously in a single event. Here, we discuss various applications of CRISPR/Cas9 in a range of important crops, compare it with other GE tools, and review its mechanism, limitations, and future possibilities. Various newly emerging CRISPR/Cas systems, including base editing (BE), xCas9, and Cas12a (Cpf1), are also considered.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116 · cited 1×
“corresponds to an NGG consensus sequence which contains two G:C base pairs [104]”
BackgroundMultiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · cited 2×
“introduces in vitro dsDNA breaks at a specific site containing a sequence complementary to crRNA [45]”
BackgroundThe new frontier of genome engineering with CRISPR-Cas9
Doudna, J. A., & Charpentier, E. (2014) · Science · doi:10.1126/science.1258096 · Cited by 7,062 · cited 5×
“There are several BE systems that have been used for editing living organisms, including BE3 [32], BE4 [33], Targeted-AID [22], and dCpf1-BE [34].”
BackgroundMethodInfluentialCpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,761 · cited 1×
“The Francisella novicida U112 (FnCpf1) is analogous to CRISPR/Cas9 but exhibits some unique characteristics [17].”
BackgroundDNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741 · cited 1×
“The secondary structure of the RNA is a fundamental parameter for tuning the activity of various CRISPR systems, and gRNA structures can affect the cleavage of on- and off-target sites [41].”
BackgroundProgrammable base editing of A•T to G•C in genomic DNA without DNA cleavage
Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017) · Nature · doi:10.1038/nature24644 · Cited by 4,184
Nucleic acid detection with CRISPR-Cas13a/C2c2
Gootenberg, J. S., Abudayyeh, O. O., Lee, J. W., Essletzbichler, P., Dy, A. J., Joung, J., Verdine, V. K., Donghia, N. M., Daringer, N. M., Freije, C. A., et al. (2017) · Science · doi:10.1126/science.aam9321 · Cited by 3,887 · cited 1×
“Cas13 was used to direct ADAR2 deaminase for the modification of RNA (changing adenosine to inosine) in human cells for the recovery of functional proteins to halt disease progression [7].”
MethodZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013) · Trends in Biotechnology · doi:10.1016/j.tibtech.2013.04.004 · Cited by 3,820
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825
In vivo genome editing using Staphylococcus aureus Cas9
Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687
An updated evolutionary classification of CRISPR–Cas systems
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., et al. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3569 · Cited by 2,480 · cited 1×
“CRISPR/Cas systems are classified as types I to VI [97].”
BackgroundCrystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306
RNA targeting with CRISPR–Cas13
Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J., Belanto, J. J., Verdine, V., Cox, D. B. T., Kellner, M. J., Regev, A., et al. (2017) · Nature · doi:10.1038/nature24049 · Cited by 2,093 · cited 1×
“The Cas13 system has high RNA target specificity and efficiency [6].”
BackgroundWang, Y., Cheng, X., Shan, Q., Zhang, Y., Liu, J., Gao, C., & Qiu, J.-L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2969 · Cited by 2,072 · cited 1×
“resistance pathway to powdery mildew [114]”
Hilton, I. B., D’Ippolito, A. M., Vockley, C. M., Thakore, P. I., Crawford, G. E., Reddy, T. E., & Gersbach, C. A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3199 · Cited by 1,931 · cited 1×
“This allows the exploitation of CRISPR/Cas for various site-specific modifications, including epigenetic changes [79], regulation of gene expression [3], and BE without induction of DSB, such as facilitated by fusion with deaminases in rice, wheat, and maize [36] or imaging of genomic loci in live leaf cells of N.”
BackgroundBase editing: precision chemistry on the genome and transcriptome of living cells
Rees, H. A., & Liu, D. R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0059-1 · Cited by 1,675 · cited 1×
“7), which recognizes a broader range of protospacer adjacent motifs (PAMs) [10].”
BackgroundEngineered CRISPR-Cas9 nucleases with altered PAM specificities
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., Zheng, Z., Gonzales, A. P. W., Li, Z., Peterson, R. T., Yeh, J.-R. J., et al. (2015) · Nature · doi:10.1038/nature14592 · Cited by 1,624
Evolved Cas9 variants with broad PAM compatibility and high DNA specificity
Hu, J. H., Miller, S. M., Geurts, M. H., Tang, W., Chen, L., Sun, N., Zeina, C. M., Gao, X., Rees, H. A., Lin, Z., et al. (2018) · Nature · doi:10.1038/nature26155 · Cited by 1,552 · cited 4×
“Phage-assisted continuous evolution was used to develop an SpCas9 variant, xCas9(3.7), which recognizes a broader range of protospacer adjacent motifs (PAMs) [10]. xCas9 possesses a higher DNA specificity and editing efficiency, lower off-target activity, and broader PAM compatibility (including NG, GAA, and GAT) than…”
BackgroundInfluentialLi, J., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G. M., & Sheen, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2654 · Cited by 1,533
RNA virus interference via CRISPR/Cas13a system in plants
Aman, R., Ali, Z., Butt, H., Mahas, A., Aljedaani, F., Khan, M. Z., Ding, S., & Mahfouz, M. (2018) · Genome Biology · doi:10.1186/s13059-017-1381-1 · Cited by 1,497
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273
Self-citationProgrammed DNA destruction by miniature CRISPR-Cas14 enzymes
Harrington, L. B., Burstein, D., Chen, J. S., Páez-Espino, D., Ma, E., Witte, I. P., Cofsky, J. C., Kyrpides, N. C., Banfield, J. F., & Doudna, J. A. (2018) · Science · doi:10.1126/science.aav4294 · Cited by 1,243 · cited 2×
“Unlike other known class II systems, Cas14a does not require a flanking sequence (PAM) near the target site [28].”
BackgroundCRISPR interference (CRISPRi) for sequence-specific control of gene expression
Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., & Qi, L. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.132 · Cited by 1,241 · cited 1×
“Therefore, CRISPRi has been considered as an effective and precise genome-targeting platform for transcription control without changing the target DNA sequence [84].”
BackgroundStructures of Cas9 endonucleases reveal RNA-mediated conformational activation
Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230 · cited 1×
“pyogenes and comprises three components: the CRISPR RNA (crRNA), trans-activating crRNA (tracrRNA), and a Cas9 protein [99].”
BackgroundDNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins
Woo, J. W., Kim, J., Kwon, S. I., Corvalán, C., Cho, S. W., Kim, H., Kim, S.-G., Kim, S.-T., Choe, S., & Kim, J.-S. (2015) · Nature Biotechnology · doi:10.1038/nbt.3389 · Cited by 1,219 · cited 2×
“) [68], Medicago truncatula [69],Marchantia polymorpha [70], tobacco (Nicotiana tabacum L.”
BackgroundEngineered CRISPR-Cas9 nuclease with expanded targeting space
Nishimasu, H., Shi, X., Ishiguro, S., Gao, L., Hirano, S., Okazaki, S., Noda, T., Abudayyeh, O. O., Gootenberg, J. S., Mori, H., et al. (2018) · Science · doi:10.1126/science.aas9129 · Cited by 1,100
Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes
Liang, Z., Chen, K., Li, T., Zhang, Y., Wang, Y., Zhao, Q., Liu, J., Zhang, H., Liu, C., Ran, Y., et al. (2017) · Nature Communications · doi:10.1038/ncomms14261 · Cited by 987
Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion
Zong, Y., Wang, Y., Li, C., Zhang, R., Chen, K., Ran, Y., Qiu, J., Wang, D., & Gao, C. (2017) · Nature Biotechnology · doi:10.1038/nbt.3811 · Cited by 896 · cited 2×
“This allows the exploitation of CRISPR/Cas for various site-specific modifications, including epigenetic changes [79], regulation of gene expression [3], and BE without induction of DSB, such as facilitated by fusion with deaminases in rice, wheat, and maize [36] or imaging of genomic loci in live leaf cells of N.”
BackgroundBeyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.2 · Cited by 832 · cited 1×
“The histone demethylase Lys-specific histone demethylase 1 (LSD1) fused to Neisseria meningitidis dCas9 has been used for experimentally controlling gene repression [92].”
BackgroundDevelopment of broad virus resistance in non‐transgenic cucumber using CRISPR/Cas9 technology
Chandrasekaran, J., Brumin, M., Wolf, D., Leibman, D., Klap, C., Pearlsman, M., Sherman, A., Arazi, T., & Gal‐On, A. (2016) · Molecular Plant Pathology · doi:10.1111/mpp.12375 · Cited by 823 · cited 2×
“the crucial role in the Potyviridae life cycle [66]”
BackgroundKomor, A. C., Zhao, K. T., Packer, M. S., Gaudelli, N. M., Waterbury, A. L., Koblan, L. W., Kim, Y. B., Badran, A. H., & Liu, D. R. (2017) · Science Advances · doi:10.1126/sciadv.aao4774 · Cited by 783
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA
Yamano, T., Nishimasu, H., Zetsche, B., Hirano, H., Slaymaker, I. M., Li, Y., Fedorova, I., Nakane, T., Makarova, K. S., Koonin, E. V., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.003 · Cited by 776 · cited 1×
“Cpf1 consists of a RuvC-like endonuclease domain along with a Nuc domain to cleave the DNA [20].”
BackgroundDNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins
Malnoy, M., Viola, R., Jung, M., Koo, O. J., Kim, S., Kim, J., Velasco, R., & Kanchiswamy, C. N. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01904 · Cited by 766 · cited 1×
“) [73], apple (Malus pumila) [74], tropical staple cassava (Manihot esculenta) [75], watermelon (Citrullus lanatus) [76], and others (Table 2).”
Kim, Y. B., Komor, A. C., Levy, J. M., Packer, M. S., Zhao, K. T., & Liu, D. R. (2017) · Nature Biotechnology · doi:10.1038/nbt.3803 · Cited by 758
Peng, A., Chen, S., Lei, T., Xu, L., He, Y., Liu, W., Yao, L., & Zou, X. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12733 · Cited by 732
In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni
Kim, E., Koo, T., Park, S. W., Kim, D., Kim, K., Cho, H.-Y., Song, D. W., Lee, K. J., Jung, M. H., Kim, S., et al. (2017) · Nature Communications · doi:10.1038/ncomms14500 · Cited by 715
Kleinstiver, B. P., Sousa, A. A., Walton, R. T., Tak, Y. E., Hsu, J. Y., Clement, K., Welch, M. M., Horng, J. E., Malagon-Lopez, J., Scarfò, I., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0011-0 · Cited by 698 · cited 1×
“A high-fidelity version of enAsCas12a (enAsCas12a-HF1) has also been engineered to reduce off-target effects [23].”
BackgroundA CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants
Tang, X. D., Lowder, L. G., Zhang, T., Malzahn, A. A., Zheng, X., Voytas, D. F., Zhong, Z., Chen, Y., Ren, Q., Li, Q., et al. (2017) · Nature Plants · doi:10.1038/nplants.2017.18 · Cited by 619 · cited 2×
“This allows the exploitation of CRISPR/Cas for various site-specific modifications, including epigenetic changes [79], regulation of gene expression [3], and BE without induction of DSB, such as facilitated by fusion with deaminases in rice, wheat, and maize [36] or imaging of genomic loci in live leaf cells of N.”
BackgroundDNA Replicons for Plant Genome Engineering
Baltes, N. J., Gil‐Humanes, J., Čermák, T., Atkins, P., & Voytas, D. F. (2014) · The Plant Cell · doi:10.1105/tpc.113.119792 · Cited by 552 · cited 1×
“) [71], Nicotiana attenuata [68], Petunia hybrida [72], grape (Vitis vinifera L.”
BackgroundLawrenson, T., Shorinola, O., Stacey, N., Li, C., Østergaard, L., Patron, N., Uauy, C., & Harwood, W. (2015) · Genome Biology · doi:10.1186/s13059-015-0826-7 · Cited by 551
Andersson, M., Turesson, H., Nicolia, A., Fält, A., Samuelsson, M., & Hofvander, P. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-2062-3 · Cited by 540
Sun, Y., Zhang, X., Wu, C., He, Y., Ma, Y., Hou, H., Guo, X., Du, W., Zhao, Y., & Xia, L. (2016) · Molecular Plant · doi:10.1016/j.molp.2016.01.001 · Cited by 535
Cas9-Guide RNA Directed Genome Editing in Soybean
Li, Z., Liu, Z.-B., Xing, A., Moon, B. P., Koellhoffer, J. P., Huang, L., Ward, R. T., Clifton, E., Falco, S. C., & Cigan, A. M. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.00783 · Cited by 528 · cited 1×
“CRISPR/Cas9 technology has been used to modify a wide range of plant species, includingArabidopsis [53], rice [54], wheat (Triticum aestivum) [55], maize [56], soybean (Glycine max) [57], sorghum [58], cotton (Gossypium hirsutum L.”
BackgroundHi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems
Liu, Q., Wang, C., Jiao, X., Zhang, H., Song, L., Li, Y., Gao, C., & Wang, K. (2018) · Science China Life Sciences · doi:10.1007/s11427-018-9402-9 · Cited by 503
Veres, A., Gosis, B. S., Ding, Q., Collins, R., Ragavendran, A., Brand, H., Erdin, S., Cowan, C. A., Talkowski, M. E., & Musunuru, K. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.04.020 · Cited by 474 · cited 1×
“WGS is a most effective technique for the identification of various kinds of mutations, such as small indels, SNPs, and structural variations, including major deletions, inversions, duplications, and rearrangements [51], and has already been exploited for detecting off-target mutations caused by Cas9 in various crops.”
BackgroundThe CRISPR-Cas immune system: Biology, mechanisms and applications
Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015) · Biochimie · doi:10.1016/j.biochi.2015.03.025 · Cited by 471 · cited 1×
“Type II CRISPR/Cas systems utilize Cas1, Cas2, Cas9, and a fourth protein (Csn2 or Cas4), whereas the type III CRISPR/Cas systems comprise the Cas10 with an indistinct role [98].”
BackgroundA male-expressed rice embryogenic trigger redirected for asexual propagation through seeds
Khanday, I., Skinner, D. J., Yang, B., Mercier, R., & Sundaresan, V. (2018) · Nature · doi:10.1038/s41586-018-0785-8 · Cited by 470 · cited 1×
“[83] showed that expression of BABY BOOM1 (BBM1) in sperm cells of rice and its ectopic expression in the egg cell is adequate for parthenogenesis.”
BackgroundEngineered Cpf1 variants with altered PAM specificities
Gao, L., Cox, D. B. T., Yan, W. X., Manteiga, J. C., Schneider, M. W., Yamano, T., Nishimasu, H., Nureki, O., Crosetto, N., & Zhang, F. (2017) · Nature Biotechnology · doi:10.1038/nbt.3900 · Cited by 460 · cited 1×
“Thewide range of Cpf1 targetable genes has been extended by engineering Cpf1 variants [26].”
BackgroundA cytosine deaminase for programmable single-base RNA editing
Abudayyeh, O. O., Gootenberg, J. S., Franklin, B., Koob, J. G., Kellner, M. J., Ladha, A., Joung, J., Kirchgatterer, P. C., Cox, D. B. T., & Zhang, F. (2019) · Science · doi:10.1126/science.aax7063 · Cited by 460
Progress and prospects in plant genome editing
Yin, K., Gao, C., & Qiu, J. (2017) · Nature Plants · doi:10.1038/nplants.2017.107 · Cited by 445
Crystal Structure of Staphylococcus aureus Cas9
Nishimasu, H., Cong, L., Yan, W. X., Ran, F. A., Zetsche, B., Li, Y., Kurabayashi, A., Ishitani, R., Zhang, F., & Nureki, O. (2015) · Cell · doi:10.1016/j.cell.2015.08.007 · Cited by 443
Gene replacements and insertions in rice by intron targeting using CRISPR–Cas9
Li, J., Meng, X., Zong, Y., Chen, K., Zhang, H., Li, J., Li, J., & Gao, C. (2016) · Nature Plants · doi:10.1038/nplants.2016.139 · Cited by 442
Macovei, A., Sevilla, N. R., Cantos, C. F., Jonson, G. B., Slamet‐Loedin, I. H., Čermák, T., Voytas, D. F., Choi, I., & Chadha‐Mohanty, P. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12927 · Cited by 442 · cited 1×
“CRISPR/Cas9 technology has been used to modify a wide range of plant species, includingArabidopsis [53], rice [54], wheat (Triticum aestivum) [55], maize [56], soybean (Glycine max) [57], sorghum [58], cotton (Gossypium hirsutum L.”
BackgroundEfficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A
Zong, Y., Song, Q., Li, C., Jin, S., Zhang, D., Wang, Y., Qiu, J., & Gao, C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4261 · Cited by 440 · cited 1×
“BE3 plays a critical role in the conversion of targeted cytidine to thymidine in DNA [37], and both the efficiency and specificity of its PAM have been increased [38].”
BackgroundAn APOBEC3A-Cas9 base editor with minimized bystander and off-target activities
Gehrke, J. M., Cervantes, O., Clement, K., Wu, Y., Zeng, J., Bauer, D. E., Pinello, L., & Joung, J. K. (2018) · Nature Biotechnology · doi:10.1038/nbt.4199 · Cited by 439 · cited 1×
“As with other evolved or engineered Cas9 variants, xCas9 requires high precision matching between gRNA and the target sequence, which must include a G at the 5ʹ end of gRNA and the corresponding first position of the protospacer [12].”
BackgroundBase editing with a Cpf1–cytidine deaminase fusion
Li, X., Wang, Y., Liu, Y., Yang, B., Wang, X., Wei, J., Lu, Z., Zhang, Y., Wu, J., Huang, X., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4102 · Cited by 426
Pan, C., Ye, L., Li, Q., Liu, X., He, Y., Wang, J., Chen, L., & Lu, G. (2016) · Scientific Reports · doi:10.1038/srep24765 · Cited by 391 · cited 1×
“basic helix-loophelix multigene family [133]”
CRISPR/Cas9‐mediated efficient targeted mutagenesis in grape in the first generation
Wang, X., Tu, M., Wang, D., Liu, J., Li, Y., Li, Z., Wang, Y., & Wang, X. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12832 · Cited by 385 · cited 1×
“) [73], apple (Malus pumila) [74], tropical staple cassava (Manihot esculenta) [75], watermelon (Citrullus lanatus) [76], and others (Table 2).”
Structure and Engineering of Francisella novicida Cas9
Hirano, H., Gootenberg, J. S., Horii, T., Abudayyeh, O. O., Kimura, M., Hsu, P. D., Nakane, T., Ishitani, R., Hatada, I., Zhang, F., et al. (2016) · Cell · doi:10.1016/j.cell.2016.01.039 · Cited by 369 · cited 1×
“structural information for creating a variant which can identify more relaxed 5ʹ-YG-3ʹ PAM [105]”
BackgroundBillon, P., Bryant, E. E., Joseph, S. A., Nambiar, T. S., Hayward, S. B., Rothstein, R., & Ciccia, A. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.08.008 · Cited by 363 · cited 1×
“The BE systems can use predicted gRNAs for converting codons CAG, TGG, CAA, and CAG into stop codons via C to T conversions [39].”
MethodClonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes
Wang, C., Liu, Q., Shen, Y. X., Hua, Y., Wang, J., Lin, J., Wu, M., Sun, T., Cheng, Z., Mercier, R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0003-0 · Cited by 357 · cited 2×
“It can be achieved in two ways, by either constructing multiple gRNA expression cassettes in separate vectors or assembling various sgRNAs in a single vector [82].”
BackgroundAn Agrobacterium‐delivered CRISPR /Cas9 system for high‐frequency targeted mutagenesis in maize
Char, S. N., Neelakandan, A. K., Nahampun, H. N., Frame, B. R., Main, M., Spalding, M. H., Becraft, P. W., Meyers, B. C., Walbot, V., Wang, K., et al. (2016) · Plant Biotechnology Journal · doi:10.1111/pbi.12611 · Cited by 352 · cited 1×
“The NHEJ frequently leads to random DNA indels at the cleavage position, whereas HDR executes the precise sequence insertion or gene replacement by adding a donor DNA template with sequence homology at the predicted DSB site [100].”
BackgroundIncreasing the specificity of CRISPR systems with engineered RNA secondary structures
Kocak, D. D., Josephs, E. A., Bhandarkar, V., Adkar, S. S., Kwon, J. B., & Gersbach, C. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0095-1 · Cited by 351 · cited 1×
“A study by Kocak and coworkers [40] showed that the engineering of a hairpin secondary structure onto the spacer region of sgRNAs (hp-sgRNAs) can increase the specificity by several orders of magnitude when combined with numerous CRISPR effectors.”
BackgroundDesign of a bacterial speck resistant tomato by CRISPR /Cas9‐mediated editing of Sl JAZ 2
Ortigosa, A., Ibanez, S. G., Leonhardt, N., & Solano, R. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.13006 · Cited by 344 · cited 1×
“) [63], potato (Solanum tuberosum) [64], sweet orange (Citrus sinensis L.”
Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development
Gao, Y., Zhang, Y., Zhang, D., Dai, X., Estelle, M. A., & Zhao, Y. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1500365112 · Cited by 339 · cited 1×
“plays a role in strigolactone transport [129]”
Towards CRISPR /Cas crops – bringing together genomics and genome editing
Scheben, A., Wolter, F., Batley, J., Puchta, H., & Edwards, D. (2017) · New Phytologist · doi:10.1111/nph.14702 · Cited by 329 · cited 1×
“As described above, the CRISPR/Cas system can induce sequence-specific mutagenesis to interrupt genes to evaluate their functions and be used for trait improvement in crops [77].”
BackgroundZischewski, J., Fischer, R., & Bortesi, L. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2016.12.003 · Cited by 323 · cited 2×
“Further sequencing and gel electrophoresis might be used to analyze amplicons [48].”
BackgroundMethodJia, H., Orbović, V., Jones, J. B., & Wang, N. (2015) · Plant Biotechnology Journal · doi:10.1111/pbi.12495 · Cited by 315
CRISPR/Cas9‐mediated targeted mutagenesis of GmFT2a delays flowering time in soya bean
Cai, Y., Chen, L., Liu, X., Guo, C., Sun, S., Wu, C., Jiang, B., Han, T., & Hou, W. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12758 · Cited by 309
Applying CRISPR/Cas for genome engineering in plants: the best is yet to come
Puchta, H. (2016) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2016.11.011 · Cited by 305 · cited 2×
“The tracrRNA binds to the crRNA and Cas9 protein that is recruited to the complex [2].”
BackgroundMutation detection using Surveyor™ nuclease
Qiu, P., Shandilya, H., D'Alessio, J. M., O’Connor, K. C., Durocher, J. A., & Gerard, G. F. (2004) · BioTechniques · doi:10.2144/04364pf01 · Cited by 299
Wang, P., Zhang, J., Sun, L., Ma, Y., Xu, J., Liang, S., Deng, J., Tan, J., Zhang, Q., Tu, L., et al. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12755 · Cited by 296 · cited 1×
“reporter due to its different benefits over other report proteins [117]”
BackgroundTargeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain
Gallego‐Bartolomé, J., Gardiner, J., Liu, W., Papikian, A., Ghoshal, B., Kuo, H. Y., Zhao, J. M.-C., Segal, D. J., & Jacobsen, S. E. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1716945115 · Cited by 294 · cited 7×
“CRISPR/Cas9 technology has been used to modify a wide range of plant species, includingArabidopsis [53], rice [54], wheat (Triticum aestivum) [55], maize [56], soybean (Glycine max) [57], sorghum [58], cotton (Gossypium hirsutum L.) [52,59], rapeseed (Brassica napus L.) [60], barley (Hordeum vulgare L.) [61], Nicotian…”
BackgroundInfluentialKaur, N., Alok, A., Shivani, Kaur, N., Pandey, P., Awasthi, P., & Tiwari, S. (2017) · Functional & Integrative Genomics · doi:10.1007/s10142-017-0577-5 · Cited by 286
Braatz, J., Harloff, H., Mascher, M., Stein, N., Himmelbach, A., & Jung, C. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.00426 · Cited by 283
CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion
Ali, Z., Ali, S., Tashkandi, M., Zaidi, S. S., & Mahfouz, M. M. (2016) · Scientific Reports · doi:10.1038/srep26912 · Cited by 282 · cited 1×
“CRISPR/Cas14a is a potential system for engineering resistance against plant ssDNA viruses belonging to the Geminiviridae and Nanoviridae families [29].”
BackgroundEfficient CRISPR/Cas9-based gene knockout in watermelon
Tian, S., Jiang, L., Gao, Q., Zhang, J., Zong, M., Zhang, H., Ren, Y., Guo, S., Gong, G., Liu, F., et al. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-2089-5 · Cited by 278 · cited 2×
“Guided by the sgRNA, the sgRNA and Cas9 search for the target across the genome and create blunt-ended DSBs at about 3 bp upstream of the PAM site (Figure 1A) [76].”
BackgroundA potent Cas9-derived gene activator for plant and mammalian cells
Li, Z., Zhang, D., Xiong, X., Yan, B., Xie, W., Sheen, J., & Li, J. (2017) · Nature Plants · doi:10.1038/s41477-017-0046-0 · Cited by 278 · cited 1×
“This assembly promoted up to 55-fold activation of the target gene compared with the conventional dCas9-VP64 system [89].”
BackgroundCRISPR/Cas9-Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L.
Sugano, S. S., Shirakawa, M., Takagi, J., Matsuda, Y., Shimada, T., Hara‐Nishimura, I., & Kohchi, T. (2014) · Plant and Cell Physiology · doi:10.1093/pcp/pcu014 · Cited by 269 · cited 1×
“) [68], Medicago truncatula [69],Marchantia polymorpha [70], tobacco (Nicotiana tabacum L.”
BackgroundRapid breeding of parthenocarpic tomato plants using CRISPR/Cas9
Ueta, R., Abe, C., Watanabe, T., Sugano, S. S., Ishihara, R., Ezura, H., Osakabe, Y., & Osakabe, K. (2017) · Scientific Reports · doi:10.1038/s41598-017-00501-4 · Cited by 256
The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells
Lee, C. M., Cradick, T. J., & Bao, G. (2016) · Molecular Therapy · doi:10.1038/mt.2016.8 · Cited by 250 · cited 1×
“NmCas9 can use an sgRNA to direct its activity [107]”
Efficient CRISPR/Cas9 Genome Editing of Phytoene desaturase in Cassava
Odipio, J., Alicai, T., Ingelbrecht, I., Nusinow, D. A., Bart, R. S., & Taylor, N. J. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.01780 · Cited by 247 · cited 2×
“the carotenoid biosynthesis pathway [75]”
Zhou, H. L., He, M., Li, J., Chen, L., Huang, Z., Zheng, S., Zhu, L., Ni, E., Jiang, D., Zhao, B., et al. (2016) · Scientific Reports · doi:10.1038/srep37395 · Cited by 244
Direct observation of DNA target searching and cleavage by CRISPR-Cas12a
Jeon, Y., Choi, Y. H., Jang, Y., Yu, J., Goo, J., Lee, G., Jeong, Y. K., Lee, S. H., Kim, I.-S., Kim, J.-S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05245-x · Cited by 239 · cited 3×
“However, it lacks the His-Asn-His (HNH) domain and it may include a single active site in the RuvC domain [21].”
BackgroundMethodInfluentialSubburaj, S., Chung, S. J., Lee, C., Ryu, S.-M., Kim, D. H., Kim, J.-S., Bae, S., & Lee, G.-J. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-1937-7 · Cited by 237
Application of CRISPR/Cas9 in plant biology
Liu, X., Wu, S., Xu, J., Sui, C., & Wei, J. (2017) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2017.01.002 · Cited by 235 · cited 1×
“The HNH domain cuts a complementary strand of crRNA, whereas the RuvC-like domain cuts an opposite strand of dsDNA [101].”
BackgroundActivities and specificities of CRISPR /Cas9 and Cas12a nucleases for targeted mutagenesis in maize
Lee, K., Zhang, Y., Kleinstiver, B. P., Guo, J. A., Aryee, M. J., Miller, J., Malzahn, A. A., Zarecor, S., Lawrence‐Dill, C. J., Joung, J. K., et al. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12982 · Cited by 235 · cited 1×
“CRISPR/Cas9 technology has been used to modify a wide range of plant species, includingArabidopsis [53], rice [54], wheat (Triticum aestivum) [55], maize [56], soybean (Glycine max) [57], sorghum [58], cotton (Gossypium hirsutum L.”
BackgroundMethods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes
Hess, G. T., Tycko, J., Yao, D., & Bassik, M. C. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.029 · Cited by 234 · cited 14×
“NHEJ-mediated repair can be used to generate point mutations via gene replacement when the target sequences of CRISPR/Cas9 are located in introns.”
BackgroundMethodInfluentialRobust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems
Lowder, L. G., Zhou, J., Zhang, Y., Malzahn, A., Zhong, Z., Hsieh, T.-F., Voytas, D. F., Zhang, Y., & Qi, Y. (2018) · Molecular Plant · doi:10.1016/j.molp.2017.11.010 · Cited by 232 · cited 1×
“These tools can activate more than four genes at the same time and can be used to evaluate positive feedback transcriptional loops and the control of tissue-specific gene activation [87]; however, it does introduce more off-target effects [88].”
BackgroundEditing of an Alpha-Kafirin Gene Family Increases, Digestibility and Protein Quality in Sorghum
Li, A., Jia, S., Yobi, A., Ge, Z., Sato, S. J., Zhang, C., Angelovici, R., Clemente, T. E., & Holding, D. R. (2018) · PLANT PHYSIOLOGY · doi:10.1104/pp.18.00200 · Cited by 220
Michno, J., Wang, X., Liu, J., Curtin, S. J., Kono, T. J. Y., & Stupar, R. M. (2015) · GM crops & food · doi:10.1080/21645698.2015.1106063 · Cited by 213 · cited 1×
“) [68], Medicago truncatula [69],Marchantia polymorpha [70], tobacco (Nicotiana tabacum L.”
BackgroundLi, J., Manghwar, H., Sun, L., Wang, P., Wang, G., Sheng, H., Zhang, J., Liu, H., Qin, L., Rui, H., et al. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.13020 · Cited by 211
CRISPR Cpf1 proteins: structure, function and implications for genome editing
Safari, F., Zare, K., Negahdaripour, M., Barekati‐Mowahed, M., & Ghasemi, Y. (2019) · Cell & Bioscience · doi:10.1186/s13578-019-0298-7 · Cited by 208
Jansing, J., Sack, M., Augustine, S. M., Fischer, R., & Bortesi, L. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12981 · Cited by 204
Epigenetic Modifications and Plant Hormone Action
Yamamuro, C., Zhu, J., & Yang, Z. (2015) · Molecular Plant · doi:10.1016/j.molp.2015.10.008 · Cited by 203 · cited 1×
“Epigenetic and post-translational protein modifications, for example, DNA and histone acetylation/ methylation, ubiquitination, SUMOylation, and phosphorylation, can alter chromatin structure and regulate gene expression patterns [90].”
BackgroundKnockdown of MLO genes reduces susceptibility to powdery mildew in grapevine
Pessina, S., Lenzi, L., Perazzolli, M., Campa, M., Costa, L. D., Urso, S., Valè, G., Salamini, F., Velasco, R., & Malnoy, M. (2016) · Horticulture Research · doi:10.1038/hortres.2016.16 · Cited by 200
Yang, H., Wu, J.-J., Tang, T., Liu, K.-D., & Dai, C. (2017) · Scientific Reports · doi:10.1038/s41598-017-07871-9 · Cited by 199 · cited 1×
“are serving as negative regulators of organ size [122]”
BackgroundTargeted mutagenesis in the medicinal plant Salvia miltiorrhiza
Li, B., Cui, G., Shen, G., Zhan, Z.-L., Huang, L., Chen, J., & Qi, X. (2017) · Scientific Reports · doi:10.1038/srep43320 · Cited by 191
Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3′-overhang
Moon, S. B., Lee, J. M., Kang, J. G., Lee, N.-E., Ha, D.-I., Kim, D. Y., Kim, S. H., Yoo, K., Kim, J., Kim, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06129-w · Cited by 187
Genome editing in plants by engineered CRISPR–Cas9 recognizing NG PAM
Endo, M., Mikami, M., Endo, A., Kaya, H., Itoh, T., Nishimasu, H., Nureki, O., & Toki, S. (2018) · Nature Plants · doi:10.1038/s41477-018-0321-8 · Cited by 186 · cited 1×
“SpCas9-NG has been used for gene disruption and cytosine BE in rice [15].”
MethodOkada, A., Arndell, T., Borisjuk, N. V., Sharma, N., Watson‐Haigh, N. S., Tucker, E. J., Baumann, U., Langridge, P., & Whitford, R. (2019) · Plant Biotechnology Journal · doi:10.1111/pbi.13106 · Cited by 181 · cited 1×
“CRISPR/Cas9 technology has been used to modify a wide range of plant species, includingArabidopsis [53], rice [54], wheat (Triticum aestivum) [55], maize [56], soybean (Glycine max) [57], sorghum [58], cotton (Gossypium hirsutum L.”
BackgroundApplications of CRISPR/Cas System to Bacterial Metabolic Engineering
Cho, S., Shin, J., & Cho, B. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19041089 · Cited by 180 · cited 1×
“In bacterial cells, CRISPRi is a more useful genetic engineering tool for gene knockdown compared with RNAi, because it avoids cell death through disruption of the genome [85].”
BackgroundQin, L., Li, J., Wang, Q., Xu, Z., Sun, L., Alariqi, M., Manghwar, H., Wang, G., Li, B., Ding, X. L., et al. (2019) · Plant Biotechnology Journal · doi:10.1111/pbi.13168 · Cited by 179
C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism
Liu, L., Chen, P., Wang, M., Li, X., Wang, J., Yin, M., & Wang, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.11.040 · Cited by 177 · cited 1×
“with a bi-lobed architecture that consists of an REC and NUC lobe [111] Table 1.”
BackgroundOrdon, J., Gantner, J., Kemna, J., Lennart, S., Reschke, M., Streubel, J., Boch, J., & Stuttmann, J. (2016) · The Plant Journal · doi:10.1111/tpj.13319 · Cited by 176 · cited 1×
“regulators of plant innate immunity [131]”
CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field
Schaeffer, S. M., & Nakata, P. A. (2015) · Plant Science · doi:10.1016/j.plantsci.2015.09.011 · Cited by 166 · cited 1×
“CRISPR/Cas has successfully been used for gene replacement in plants [94].”
MethodA high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.)
Li, C., Ünver, T., & Zhang, B. (2017) · Scientific Reports · doi:10.1038/srep43902 · Cited by 158 · cited 1×
“involved in the development of cotton fiber [118]”
BackgroundCRISPR-Cpf1: A New Tool for Plant Genome Editing
Zaidi, S. S.-E.-A., Mahfouz, M. M., & Mansoor, S. (2017) · Trends in Plant Science · doi:10.1016/j.tplants.2017.05.001 · Cited by 155 · cited 1×
“However, Cpf1mediated GE is cheaper than SpCas9 because it requires only short synthetic single-guide RNA (sgRNA) sequences [19].”
BackgroundExploiting the CRISPR/Cas9 System for Targeted Genome Mutagenesis in Petunia
Zhang, B., Yang, X., Yang, C., Li, M., & Guo, Y. (2016) · Scientific Reports · doi:10.1038/srep20315 · Cited by 153 · cited 1×
“the biosynthesis of carotenoid and chlorophyll [132]”
A Streamlined CRISPR Pipeline to Reliably Generate Zebrafish Frameshifting Alleles
Talbot, J. C., & Amacher, S. L. (2014) · Zebrafish · doi:10.1089/zeb.2014.1047 · Cited by 152
Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system
Chen, X., Lu, X., Shu, N., Wang, S., Wang, J., Wang, D., Guo, L., & Ye, W. (2017) · Scientific Reports · doi:10.1038/srep44304 · Cited by 152 · cited 1×
“method Mutations were detected in cotton protoplast – [116]”
MethodRen, B., Liu, L., Li, S., Kuang, Y., Wang, J., Zhang, D., Zhou, X., Lin, H., & Zhou, H. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.03.010 · Cited by 148 · cited 2×
“Recently, Ren and coworkers [14] evaluated the nuclease activity of Cas9-NG towards various NGN PAMs by Box 1.”
BackgroundGenome Engineering in Rice Using Cas9 Variants that Recognize NG PAM Sequences
Hua, K., Tao, X., Han, P., Wang, R., & Zhu, J. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.03.009 · Cited by 143
Che, P., Anand, A., Wu, E., Sander, J. D., Simon, M. K., Zhu, W., Sigmund, A. L., Zastrow‐Hayes, G., Miller, M., Liu, D., et al. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12879 · Cited by 138
Mercx, S., Smargiasso, N., Chaumont, F., Pauw, E. D., Boutry, M., & Navarre, C. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00403 · Cited by 137
Overcoming Self-Incompatibility in Diploid Potato Using CRISPR-Cas9
Enciso-Rodríguez, F. E., Manrique-Carpintero, N. C., Nadakuduti, S. S., Buell, C. R., Zarka, D. G., & Douches, D. S. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00376 · Cited by 137
Live‐cell CRISPR imaging in plants reveals dynamic telomere movements
Dreißig, S., Schiml, S., Schindele, P., Weiß, O., Rutten, T. L. M., Schubert, V., Gladilin, E., Mette, M. F., Puchta, H., & Houben, A. (2017) · The Plant Journal · doi:10.1111/tpj.13601 · Cited by 134
Wang, L., Wang, L., Tan, Q. W., Fan, Q., Zhu, H., Hong, Z., Zhang, Z., & Duanmu, D. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01333 · Cited by 128
The Current State and Future of CRISPR-Cas9 gRNA Design Tools
Wilson, L. O. W., O’Brien, A. R., & Bauer, D. C. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.00749 · Cited by 124
The CRISPR /Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists
Wolter, F., & Puchta, H. (2018) · The Plant Journal · doi:10.1111/tpj.13899 · Cited by 113 · cited 2×
“Due to the presence of higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains, it is associated with RNase activity [5].”
BackgroundHeavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing
Mir, A., Alterman, J. F., Hassler, M. R., Debacker, A. J., Hudgens, E. D., Echeverria, D., Brodsky, M. H., Khvorova, A., Watts, J. K., & Sontheimer, E. J. (2018) · Nature Communications · doi:10.1038/s41467-018-05073-z · Cited by 112
Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation
Braun, C. J., Bruno, P. M., Horlbeck, M. A., Gilbert, L. A., Weissman, J. S., & Hemann, M. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600582113 · Cited by 104
xC as9 expands the scope of genome editing with reduced efficiency in rice
Wang, J., Meng, X., Hu, X., Sun, T., Li, J., Wang, K., & Yu, H. J. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.13053 · Cited by 88 · cited 4×
“Phage-assisted continuous evolution was used to develop an SpCas9 variant, xCas9(3.7), which recognizes a broader range of protospacer adjacent motifs (PAMs) [10]. xCas9 possesses a higher DNA specificity and editing efficiency, lower off-target activity, and broader PAM compatibility (including NG, GAA, and GAT) than…”
BackgroundInfluentialcis–trans Engineering: Advances and Perspectives on Customized Transcriptional Regulation in Plants
Shrestha, A., Khan, A., & Dey, N. (2018) · Molecular Plant · doi:10.1016/j.molp.2018.05.008 · Cited by 86 · cited 2×
“dCas9 fused to epigenetic regulatory factors involved in histone acetylation, or methylation of DNA, can be used to modulate chromatin activity and gene expression patterns involved in plant development and environmental adaptation [86].”
BackgroundMolecular architectures and mechanisms of Class 2 CRISPR-associated nucleases
Garcia‐Doval, C., & Jínek, M. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.015 · Cited by 85
Simultaneous site-directed mutagenesis of duplicated loci in soybean using a single guide RNA
Kanazashi, Y., Hirose, A., Takahashi, I., Mikami, M., Endo, M., Hirose, S., Toki, S., Kaga, A., Naito, K., Ishimoto, ., et al. (2018) · Plant Cell Reports · doi:10.1007/s00299-018-2251-3 · Cited by 83
Li, C., Hao, M., Wang, W., Wang, H., Chen, F., Chu, W., Zhang, B., Mei, D., Cheng, H., & Hu, Q. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00442 · Cited by 74
Targeting Plant ssDNA Viruses with Engineered Miniature CRISPR-Cas14a
Khan, M. Z., Haider, S., Mansoor, S., & Amin, I. U. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.03.015 · Cited by 73 · cited 3×
“It has been shown by in vitro validation of the PAM requirement that Cas14a can cleave target sites irrespective of the different sequences adjacent to the targets of these different guides [27].”
BackgroundInfluentialAPOBEC: From mutator to editor
Yang, B., Li, X., Lei, L., & Chen, J. (2017) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2017.04.009 · Cited by 70 · cited 2×
“BE technology has been widely used in various organisms and cell lines [30,31].”
BackgroundMethodSchiml, S., Fauser, F., & Puchta, H. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603823113 · Cited by 68
The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing
Bayat, H., Modarressi, M. H., & Rahimpour, A. (2017) · Current Microbiology · doi:10.1007/s00284-017-1406-8 · Cited by 56
Heritability of targeted gene modifications induced by plant-optimized CRISPR systems
Mao, Y., Botella, J. R., & Zhu, J. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2380-1 · Cited by 55 · cited 1×
“The PAM is a 3-nt (NGG) sequence located immediately downstream of the single-guide RNA (sgRNA) target site, which plays an essential role in binding and for Cas9-mediated DNA cleavage [103].”
BackgroundPeng, C., Wang, H., Xu, X., Wang, X., Chen, X., Wei, W., Lai, Y., Liu, G., Godwin, I. D., Li, J., et al. (2018) · The Plant Journal · doi:10.1111/tpj.13961 · Cited by 53 · cited 1×
“It is an efficient, simple, and rapid method to detect induced mutations [43].”
MethodVerification of DNA motifs in Arabidopsis using CRISPR /Cas9‐mediated mutagenesis
Li, C., Chen, C., Chen, H., Wang, S., Chen, X., & Cui, Y. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12886 · Cited by 25 · cited 1×
“CRISPR/Cas9 technology has been used to modify a wide range of plant species, includingArabidopsis [53], rice [54], wheat (Triticum aestivum) [55], maize [56], soybean (Glycine max) [57], sorghum [58], cotton (Gossypium hirsutum L.”
BackgroundStructural Recognition between a Four-way DNA Junction and a Resolving Enzyme
Déclais, A., Liu, J., Freeman, A. D. J., & Lilley, D. M. J. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.037 · Cited by 22 · cited 1×
“T7E1 can, however, recognize and cleave various dsDNA molecules if their structure is curved and able to bend further [46].”
BackgroundResearch of methods to detect genomic mutations induced by CRISPR/Cas systems
Wang, K., Mei, D. Y., Liu, Q. N., Qiao, X. H., Ruan, W., Huang, T., & Cao, G. (2015) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2015.09.029 · Cited by 22
Cited by
Sorted by citations
CRISPR/Cas9 therapeutics: progress and prospects
Li, T., Yang, Y., Qi, H., Cui, W., Zhang, L., Fu, X., He, X., Liu, M., Li, P., & Yu, T. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01309-7 · Cited by 824
“INTRODUCTION Gene editing is a technology that precisely modifies the genome sequence to induce insertions, deletions, or base substitutions in the genome.(1,2) Many diseases are accompanied by changes in gene expression in vivo, particularly some genetic diseases caused by mutations in a single gene, and gene-editing…”
BackgroundPlant organellar genomes: much done, much more to do
Wang, J., Kan, S., Liao, X., Zhou, J., Tembrock, L. R., Daniell, H., Jin, S., & Wu, Z. (2024) · Trends in Plant Science · doi:10.1016/j.tplants.2023.12.014 · Cited by 288
Zhang, T., Chen, Y., Liu, Y., Lin, W., & Wang, J. (2021) · Nature Communications · doi:10.1038/s41467-021-22352-4 · Cited by 279
Chehelgerdi, M., Chehelgerdi, M., Khorramian-Ghahfarokhi, M., Shafieizadeh, M., Mahmoudi, E., Eskandari, F., Rashidi, M., Arshi, A., & Mokhtari-Farsani, A. (2024) · Molecular Cancer · doi:10.1186/s12943-023-01925-5 · Cited by 251
“Targeting these genes with drugs may disrupt critical cellular processes, leading to the selective killing or suppression of cancer cells while minimizing harm to normal cells [329, 331, 337, 338].”
BackgroundGenome editing with the CRISPR‐Cas system: an art, ethics and global regulatory perspective
Zhang, D., Hussain, A., Manghwar, H., Xie, K., Xie, S., Zhao, S., Larkin, R. M., Qing, P., Jin, S., & Ding, F. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13383 · Cited by 254
“Comparing with DSB-HDR-mediated genome editing, base editing systems comprise site-directed alteration of DNA base pairs along with manipulating a DNA repair mechanism to achieve a precise repairing of edited base (Hess et al., 2017; Manghwar et al., 2019).”
Method
Metadata
- Authors
- Manghwar, H., Lindsey, K., Zhang, X., & Jin, S.
- Affiliations
- Huazhong Agricultural University (CN)
- Durham University (GB)
- Corresponding author
- Zhang, Xianlong
- Jin, Shuangxia
- Venue
- Trends in Plant Science
- Publisher
- Elsevier BV
- Published
- 2019-12
- Volume
- 24
- Issue
- 12
- Pages
- 1102-1125
- ISSN
- 1360-1385 (ISSN-L)
- OpenAlex
- W2984281074
- Cited by
- 529
- References
- 140
- Citations by year
- 2026: 49 · 2025: 84 · 2024: 94 · 2023: 91 · 2022: 76 · 2021: 91 · 2020: 43
- FWCI
- 4.65
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Trends in Plant Science (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Durham Research Online (Durham University) (publishedVersion, other-oa)
- Durham Research Online (Durham University) (acceptedVersion, other-oa)
- Durham Research Online (Durham University) (submittedVersion, cc-by-nc-nd)
- Funders
- Ministry of Science and Technology of the People's Republic of China
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR/Cas9, genome editing, base editing, genome editing tools
- MeSH terms
- Gene Editing, Crops, Agricultural, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
