Enhancing efficiency and precision in CRISPR genome editing for plants using computational tools
ENHANCING EFFICIENCY AND PRECISION IN CRISPR GENOME EDITING FOR COMPUTATIONAL TOOLS
325 / 4
Authors
-
MEGHA S SOGALAD
ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad-500 030, Telangana
-
USHAKIRAN B
ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad-500 030, Telangana
-
V DINESH KUMAR
ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad-500 030, Telangana
Keywords:
Computational platforms, Efficiency, Features, Limitations, Off-target effects Precision, sgRNA designingAbstract
Integrating computational tools into CRISPR-Cas9 genome editing has significantly enhanced the precision and efficiency of plant genetic modifications. This review explores bioinformatics resources' development, functionality, and application in designing, optimizing, and analyzing CRISPR-based experiments. From initial discoveries of CRISPR arrays to their evolution as powerful gene-editing technologies, computational advancements have played a pivotal role in predicting guideRNA(gRNA) efficiency, minimizing off-target effects, and streamlining editing processes. This article highlights key web-based platforms, such as CHOPCHOP, CRISPOR, CRISPR-P, Benchling, and Deskgen, comparing their features for gRNA design and off-target prediction. Tools like TIDE and TIDER for downstream analysis for evaluating editing outcomes are also discussed. By leveraging bioinformatics, researchers can overcome the complexities of plant genomes, enhance experimental accuracy, and accelerate crop improvement initiatives. This review underscores the transformative impact of computational tools in improving the efficiency of CRISPR-Cas mediated genome editing technologies for sustainable agriculture.
Downloads
References
Abudayyeh O O, Gootenberg J S, Konermann S, Joung J, Slaymaker I M, Cox D B and Zhang F 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science, 353(6299): 5573. DOI: https://doi.org/10.1126/science.aaf5573
Alkhnbashi O S, Tobias Meier, Alexander Mitrofanov, Rolf Backofen and V Björn 2020. CRISPR-Cas bioinformatics. Methods, 172:3-11. doi: 10.1016/j.ymeth.2019.07.013. DOI: https://doi.org/10.1016/j.ymeth.2019.07.013
Bhaya D, Davison M and Barrangou R 2011. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics, 45: 273-297.doi: 10.1146/annurev-genet-110410-132430. PMID: 22060043. DOI: https://doi.org/10.1146/annurev-genet-110410-132430
Bassett A and Liu JL 2014. CRISPR/Cas9 mediated genome engineering in Drosophila. Methods, 69(2): 128-36. DOI: https://doi.org/10.1016/j.ymeth.2014.02.019
Brinkman EK, Chen T, Amendola M and V and Steensel B 2014. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Research, 42(22): 168. DOI: https://doi.org/10.1093/nar/gku936
Chen K, Wang Y, Zhang R, Zhang H and Gao C 2019. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. Annual Review of Plant Biology, 70: 667-697. DOI: https://doi.org/10.1146/annurev-arplant-050718-100049
Concordet J P and Haeussler M 2018. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments. Nucleic Acids Research, 46(1): 242-245. DOI: https://doi.org/10.1093/nar/gky354
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA and Zhang F 2013. Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121): 819-23. doi: 10.1126/science.1231143 DOI: https://doi.org/10.1126/science.1231143
Chen Feng, Chen Lu, Yan Zhao, Xu Jingyuan, Feng Luoluo, He Na, Guo Mingli, Zhao Jiaxiong, Chen Zhijun, Chen Huiqi, Yao Gengzhen and Liu Chunping 2023. Recent advances of CRISPR-based genome editing for enhancing staple crops. Frontiers in Plant Science, 15. DOI: https://doi.org/10.3389/fpls.2024.1478398
Doench J G, Hartenian E, Graham D B, Tothova Z, Hegde M, Smith I and Root D E 2014. Rational design of highly active sgRNAsfor CRISPR-Cas9-mediated gene inactivation. Nature Biotechnology, 32(12): 1262-1267. DOI: https://doi.org/10.1038/nbt.3026
Doench J G, Fusi N, Sullender M, Hegde M, Vaimberg E W, Donovan K F and Listgarten J 2016. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology, 34(2): 184-191. DOI: https://doi.org/10.1038/nbt.3437
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y and Pirzada ZA 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature, 471: 602-607.doi: 10.1038/nature09886. DOI: https://doi.org/10.1038/nature09886
Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK and Sander JD 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nature Biotechnology, 31(9): 822-6. doi: 10.1038/nbt.2623. DOI: https://doi.org/10.1038/nbt.2623
GaoCaixia 2021. Genome engineering for crop improvement and future agriculture. Cell, 184(6): 1621-1635. DOI: https://doi.org/10.1016/j.cell.2021.01.005
Gan W C and Ling A P K 2022. CRISPR/Cas9 in plant biotechnology: applications and challenges. Biotechnologia, 103(1): 81-93. https://doi.org/10.5114/bta.2022.113919. DOI: https://doi.org/10.5114/bta.2022.113919
Holme I B, Gregersen P L and Brinch-Pedersen H 2019. Induced Genetic Variation in Crop Plants by Random or Targeted Mutagenesis: Convergence and Differences. Frontiers in Plant Science, 10: 1468. DOI: https://doi.org/10.3389/fpls.2019.01468
Hsu P D, Lander E S and Zhang F 2013. Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6): 1262-1278. DOI: https://doi.org/10.1016/j.cell.2014.05.010
Heigwer F, Kerr G and Boutros M 2015. E-CRISP: Fast CRISPR target site identification. Nature Methods, 11(2): 122-123. DOI: https://doi.org/10.1038/nmeth.2812
Ishino Y, Shinagawa H, Makino K, Amemura M and Nakata A 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology, 169(12): 5429-5433. DOI: https://doi.org/10.1128/jb.169.12.5429-5433.1987
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA and Charpentier E 2012. Aprogrammable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096): 816-21. doi: 10.1126/science.1225829. DOI: https://doi.org/10.1126/science.1225829
Khush G S 2001. Green revolution: the way forward, Nature Reviews Genetics, 2: 815-822. DOI: https://doi.org/10.1038/35093585
Koonin E V, Makarova K S and Zhang F 2017. Diversity, classification and evolution of CRISPR-Cas systems. Current Opinion in Microbiology, 37: 67-78. DOI: https://doi.org/10.1016/j.mib.2017.05.008
Koonin E V and Makarova K S 2019. Origins and evolution of CRISPR-Cas systems. Philosophical Transactions of the Royal Society Biological Sciences, 374(1772): 20180087. DOI: https://doi.org/10.1098/rstb.2018.0087
Liang X, Potter J, Kumar S, Ravinder N and Chesnut J D 2016. Enhanced CRISPR/Cas9-mediated precise genome editing by improved design and delivery of gRNA, Cas9 nuclease, and donor DNA. Journal of Biotechnology, 241: 136-146. DOI: https://doi.org/10.1016/j.jbiotec.2016.11.011
Livak K J and Schmittgen T D 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25(4): 402-8. DOI: https://doi.org/10.1006/meth.2001.1262
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo J E, Norville J E and Church G M 2013. RNA-guided human genome engineering via Cas9. Science, 339(6121):823-6. doi: 10.1126/science.1232033. DOI: https://doi.org/10.1126/science.1232033
Makarova K S, Wolf Y I, Iranzo J, Shmakov S A, Alkhnbashi O S, Brouns S J and Koonin E V 2020. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. NatureReviews Microbiology, 18(2): 67-83.
Makarova K S, Aravind L, Grishin N V, Rogozin I B and Koonin E V 2002. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Research, 30(2): 482-496. DOI: https://doi.org/10.1093/nar/30.2.482
Manghwar H, Lindsey K, Zhang X and Jin S 2019. CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing. Trends in Plant Science, 24(12): 1102-1125. DOI: https://doi.org/10.1016/j.tplants.2019.09.006
Makarova K S, Haft D H, Barrangou R, Brouns S J, Charpentier E, Horvath P and Koonin E V 2011. Evolution and classification of the CRISPR-Cas systems. Nature Reviews Microbiology, 9(6): 467-477. DOI: https://doi.org/10.1038/nrmicro2577
Montague T G 2014. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool. Nucleic Acids Research, 42(1): 401-407. DOI: https://doi.org/10.1093/nar/gku410
Makarova K S, Wolf Y I, Iranzo J, Shmakov S A, Alkhnbashi O S, Brouns S J and Koonin E V 2020. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2):67-83. DOI: https://doi.org/10.1038/s41579-019-0299-x
Mojica F J, Diez-Villasenor C, Soria E and Juez G 2000. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Molecular Microbiology, 36(1): 244-246. DOI: https://doi.org/10.1046/j.1365-2958.2000.01838.x
Mojica F J M, Diez-Villasenor C, Garcia-Martinez J and Soria E 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, Journal of Molecular Evolution, 60(2): 174-182. DOI: https://doi.org/10.1007/s00239-004-0046-3
Mahmood T and Yang P C 2012. Western blot: technique, theory, and trouble shooting. North American Journal of Medical and Sciences, 4(9): 429-34. DOI: https://doi.org/10.4103/1947-2714.100998
Mendoza B J and Trinh C T 2018. Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms. Bioinformatics, 34(1): 16-23. DOI: https://doi.org/10.1093/bioinformatics/btx564
Naito Y, Hino K, Bono H and Ui-Tei K 2014. CRISPRdirect: software for designingCRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics, 31(7): 1120-3. DOI: https://doi.org/10.1093/bioinformatics/btu743
Park J 2015. Cas-Designer: CRISPR guide RNA design for knockouts. Bioinformatics, 31(24): 4014-4016. DOI: https://doi.org/10.1093/bioinformatics/btv537
Pattanayak V, Lin S, Guilinger J P, Ma E, Doudna J A and Liu D R 2013. High-throughput profiling of off-target DNAcleavage reveals RNA-programmed Cas9 nuclease specificity. Nature Biotechnology, 31(9): 839-843. doi: 10.1038/nbt.2673. DOI: https://doi.org/10.1038/nbt.2673
Prykhozhij S V, Rajan V, Gaston D and Berman J N 2015. CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One, 10(3): e0119372. DOI: https://doi.org/10.1371/journal.pone.0119372
Raman R 2017. The impact of genetically modified (GM) crops in modern agriculture: A review. GM Crops and Food, 8: 195-208. DOI: https://doi.org/10.1080/21645698.2017.1413522
Shukla V, Doyon Y and Miller J 2009. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature, 459: 437-441. https://doi.org/10.1038/nature07992. DOI: https://doi.org/10.1038/nature07992
Springmann M, Clark M, Mason-D'Croz D, Wiebe K, Bodirsky B L, Lassaletta L, de Vries W, Vermeulen S J, Herrero M and Carlson K M 2018. Options for keeping the food system within environmental limits, Nature, 562: 519-525. DOI: https://doi.org/10.1038/s41586-018-0594-0
Shan Q, Zhang Y, Chen K, Zhang K and Gao C 2015. Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology. Plant Biotechnology Journal, 13: 791-800. https://doi.org/10.1111/pbi.12312. DOI: https://doi.org/10.1111/pbi.12312
Scheben A, Wolter F, Batley J, Puchta H and Edwards D 2017. Towards CRISPR/Cas crops- bringing together genomics and genome editing. New Phytologist, 216(3): 682-698. DOI: https://doi.org/10.1111/nph.14702
Shmakov S, Abudayyeh O O, Makarova K S, Wolf Y I, Gootenberg J S, Semenova E and Koonin E V 2015. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Molecular Cell, 60(3): 385-397.
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J and Mateo J L 2015. CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One, 10(4): 0124633. DOI: https://doi.org/10.1371/journal.pone.0124633
Shmakov S, Abudayyeh O O, Makarova K S, Wolf Y I, Gootenberg J S, Semenova E and Zhang F 2017. Discovery and functional characterization of diverse class 2CRISPR-Cas systems. Molecular Cell, 60(3): 385-397. DOI: https://doi.org/10.1016/j.molcel.2015.10.008
Saha D, Panda AK and Datta S 2024. Critical considerations and computational tools in plant genome editing. Heliyon, 11(1): e41135. DOI: https://doi.org/10.1016/j.heliyon.2024.e41135
Terns MP 2011. Terns RM. CRISPR-based adaptive immune systems. Current Opinion in Microbiology, 14(3): 321-7. doi: 10.1016/j.mib.2011.03.005. DOI: https://doi.org/10.1016/j.mib.2011.03.005
Tsai SQ and Joung JK 2016. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nature Review Genetic, 17(5): 300-12. DOI: https://doi.org/10.1038/nrg.2016.28
Wiedenheft B, Sternberg SH and Doudna JA 2012 RNA-Guided Genetic Silencing Systems in Bacteria and Archaea. Nature, 482: 331-338. DOI: https://doi.org/10.1038/nature10886
Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F and Sharp PA 2014. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nature Biotechnology, 32(7): 670-6. doi: 10.1038/nbt.2889. DOI: https://doi.org/10.1038/nbt.2889
Wang J, Wu Xiaohua, Wang Y, Wu Xinyi, Wang B, Lu Z and Li G 2023. Genome-wide characterization and expression analysis of the MLO gene family sheds light on powdery mildew resistance in Lagenaria siceraria. Heliyon, 9: 14624. https://doi.org/10.1016/j.heliyon.2023.e14624. DOI: https://doi.org/10.1016/j.heliyon.2023.e14624
Wang Y, Zafar N, Ali Q, Manghwar H, Wang G, Yu L,Ding X, Ding F, Hong N, Wang G and Jin S. 2022. CRISPR/Cas Genome editing technologies for plant improvement against biotic and abiotic stresses: advances, limitations, and future perspectives. Cells 11, 3928. https://doi.org/10.3390/cells 11233928. DOI: https://doi.org/10.3390/cells11233928
Xu H, Xiao T, Chen C H, Li W, Meyer C A, Wu Q and Brown M 2015. Sequence determinants of improved CRISPR sgRNA design. Genome Research, 25(8): 1147-1157. DOI: https://doi.org/10.1101/gr.191452.115
Xie K and Yang Y 2013. RNA-guided genome editing in plants using a CRISPR-Cas system. Molecular Plant, 6(6): 1975-1983. DOI: https://doi.org/10.1093/mp/sst119
Yang H 2014. CRISPR-P: an online tool for sgRNA design in plants. Molecular Plant, 7(5): 1012-1014.
Zetsche B, Gootenberg J S, Abudayyeh O O, Slaymaker I M, Makarova K S, Essletzbichler P and Zhang F 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell, 163(3): 759-771. DOI: https://doi.org/10.1016/j.cell.2015.09.038
Zhang D, Hussain A, Manghwar H, Xie K, Xie S, Zhao S, Larkin RM, Qing P, Jin S and Ding F 2020. Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective. Plant Biotechnology Journal, 18(8):1651-1669. DOI: https://doi.org/10.1111/pbi.13383
Zhang Y, Iaffaldano B and Qi Y 2021. CRISPR ribonucleoprotein-mediated genetic engineering in plants. Plant Communication, 2(2):100168. DOI: https://doi.org/10.1016/j.xplc.2021.100168
