Abstract
Genome editing is an indispensable technique utilized in life science and medicine. Development of genome editing tools with high efficiency and reliability has been a major challenge. Development of the CRISPR-Cas system for application in genome editing sparked a revolution due to its ease of use compared with previously developed genome editing tools. CRISPR nucleases are very versatile and fundamental genome editing tools, which recognize target sites in a guide RNA-dependent manner. CRISPR nucleases basically aim to generate DNA double-strand breaks (DSBs) at desired sites, but it was reported that CRISPR-mediated DNA DSBs frequently cause unforeseen large chromosomal deletions or genomic rearrangements and also induce the p53-mediated DNA damage response. Remarkably, through the development of new derivatives including base editor (BE) or prime editor (PE), the CRISPR-Cas system has the capability of overcoming such issues. Development of new genome editing tools based on the CRISPR-Cas system that are capable of enhancing the editing efficiency as well as compensating for deficiencies is ongoing. In this chapter, we report on the history of genome editing tools with an emphasis on the development of the CRISPR-Cas system and its status in the field of genome editing. In addition, we review the limitations of currently utilized genome editing tools that are based on the CRISPR-Cas system and consider the potential of the CRISPR-Cas system.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abudayyeh OO et al (2019) A cytosine deaminase for programmable single-base RNA editing. Science 365:382–386
Ahmad A et al (2008) ERCC1-XPF endonuclease facilitates DNA double-strand break repair. Mol Cell Biol 28:5082–5092. https://doi.org/10.1128/MCB.00293-08
Aird EJ, Lovendahl KN, St Martin A, Harris RS, Gordon WR (2018) Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template. Commun Biol 1:54. https://doi.org/10.1038/s42003-018-0054-2
Anzalone AV et al (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149–157. https://doi.org/10.1038/s41586-019-1711-4
Anzalone AV et al (2021) Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat Biotechnol. https://doi.org/10.1038/s41587-021-01133-w
Avery OT, MacLeod CM, McCarty M (1944) Studies of the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a deoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137–158
Barrangou R et al (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712
Berg JM (1988) Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. Proc Natl Acad Sci U S A 85:99–102
Bhargava R, Onyango DO, Stark JM (2016) Regulation of single-Strand annealing and its role in genome maintenance. Trends Genet 32:566–575. https://doi.org/10.1016/j.tig.2016.06.007
Boch J et al (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–1512
Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology (Reading) 151:2551–2561. https://doi.org/10.1099/mic.0.28048-0
Carlson-Stevermer J et al (2017) Assembly of CRISPR ribonucleoproteins with biotinylated oligonucleotides via an RNA aptamer for precise gene editing. Nat Commun 8:1711. https://doi.org/10.1038/s41467-017-01875-9
Ceccaldi R, Rondinelli B, D’Andrea AD (2016) Repair pathway choices and consequences at the double-strand break. Trends Cell Biol 26:52–64. https://doi.org/10.1016/j.tcb.2015.07.009
Chen SP, Wang HH (2019) An engineered Cas-transposon system for programmable and site-directed DNA transpositions. CRISPR J 2:376–394. https://doi.org/10.1089/crispr.2019.0030
Chen PJ et al (2021) Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184:5635–5652 e5629. https://doi.org/10.1016/j.cell.2021.09.018
Choi J et al (2021) Precise genomic deletions using paired prime editing. Nat Biotechnol. https://doi.org/10.1038/s41587-021-01025-z
Christian M et al (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761. https://doi.org/10.1534/genetics.110.120717
Cox DBT et al (2017) RNA editing with CRISPR-Cas13. Science 358:1019–1027
Craig NL (1996) Transposable elements. Current topics in microbiology and immunology, vol 204. Springer, Berlin/Heidelberg, pp 27–48
d’Adda di Fagagna F, Weller GR, Doherty AJ, Jackson SP (2003) The Gam protein of bacteriophage Mu is an orthologue of eukaryotic Ku. EMBO Rep 4:47–52. https://doi.org/10.1038/embor709
Davis L, Maizels N (2014) Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair. Proc Natl Acad Sci U S A 111:E924–E932. https://doi.org/10.1073/pnas.1400236111
Dummer AM et al (2016) Binding of the Fkh1 Forkhead associated domain to a Phosphopeptide within the Mph1 DNA helicase regulates mating-type switching in budding yeast. PLoS Genet 12:e1006094. https://doi.org/10.1371/journal.pgen.1006094
Duportet X et al (2014) A platform for rapid prototyping of synthetic gene networks in mammalian cells. Nucleic Acids Res 42:13440–13451. https://doi.org/10.1093/nar/gku1082
Fiers W et al (1976) Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260:500–507
Gaudelli NM et al (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551:464–471. https://doi.org/10.1038/nature24644
Grunewald J et al (2019) CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat Biotechnol 37:1041–1048. https://doi.org/10.1038/s41587-019-0236-6
Gu B, Posfai E, Rossant J (2018) Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos. Nat Biotechnol 36:632–637. https://doi.org/10.1038/nbt.4166
Hu JH et al (2018) Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556:57–63. https://doi.org/10.1038/nature26155
Huang TP et al (2019) Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat Biotechnol 37:626–631. https://doi.org/10.1038/s41587-019-0134-y
Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169:5429–5433
Itakura K et al (1977) Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. Science 198:1056–1063
Jansen R, Van Embden JDA, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565–1575
Jeong YK, Song B, Bae S (2020) Current status and challenges of DNA Base editing tools. Mol Ther 28:1938–1952. https://doi.org/10.1016/j.ymthe.2020.07.021
Jiang T, Zhang XO, Weng Z, Xue W (2021) Deletion and replacement of long genomic sequences using prime editing. Nat Biotechnol. https://doi.org/10.1038/s41587-021-01026-y
Jinek M et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821
Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93:1156–1160
Kim Y et al (2013) A library of TAL effector nucleases spanning the human genome. Nat Biotechnol 31:251–258. https://doi.org/10.1038/nbt.2517
Kim YB et al (2017) Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat Biotechnol 35:371–376. https://doi.org/10.1038/nbt.3803
Kleinstiver BP et al (2016) Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol 34:869–874. https://doi.org/10.1038/nbt.3620
Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH (2019) Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature 571:219–225. https://doi.org/10.1038/s41586-019-1323-z
Koblan LW et al (2018) Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol 36:843–846. https://doi.org/10.1038/nbt.4172
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–424. https://doi.org/10.1038/nature17946
Komor AC et al (2017) Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci Adv 3:eaao4774. https://doi.org/10.1126/sciadv.aao4774
Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 37:67–78. https://doi.org/10.1016/j.mib.2017.05.008
Lampe DJ, Churchill MEA, Robertson HM (1996) A purified mariner transposase is sufficient to mediate transposition in vitro. EMBO J 15:5470–5479
Li X et al (2022a) Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun 13:1669. https://doi.org/10.1038/s41467-022-29339-9
Li X et al (2022b) Enhancing prime editing efficiency by modified pegRNA with RNA G-quadruplexes. J Mol Cell Biol 14. https://doi.org/10.1093/jmcb/mjac022
Lin S, Staahl BT, Alla RK, Doudna JA (2014) Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. elife 3:e04766. https://doi.org/10.7554/eLife.04766
Lin Q et al (2021) High-efficiency prime editing with optimized, paired pegRNAs in plants. Nat Biotechnol. https://doi.org/10.1038/s41587-021-00868-w
Liu Z et al (2019) Efficient base editing with expanded targeting scope using an engineered Spy-mac Cas9 variant. Cell Discov 5:58. https://doi.org/10.1038/s41421-019-0128-4
Liu Y et al (2021) Enhancing prime editing by Csy4-mediated processing of pegRNA. Cell Res 31:1134–1136. https://doi.org/10.1038/s41422-021-00520-x
Ma M et al (2017) Efficient generation of mice carrying homozygous double-floxp alleles using the Cas9-Avidin/biotin-donor DNA system. Cell Res 27:578–581. https://doi.org/10.1038/cr.2017.29
Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1:7. https://doi.org/10.1186/1745-6150-1-7
Meselson M, Yuan R (1968) DNA restriction enzyme from E. coli. Nature 217:1110–1114
Mohanraju P et al (2016) Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353:aad5147. https://doi.org/10.1126/science.aad5147
Mojica FJM, DÃez-Villaseñor C, Soria E, Juez G (2000) Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 36:244–246
Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501. https://doi.org/10.1126/science.1178817
Nakade S et al (2014) Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9. Nat Commun 5:5560. https://doi.org/10.1038/ncomms6560
Nelson JW et al (2022) Engineered pegRNAs improve prime editing efficiency. Nat Biotechnol 40:402–410. https://doi.org/10.1038/s41587-021-01039-7
Nguyen DN et al (2020) Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency. Nat Biotechnol 38:44–49. https://doi.org/10.1038/s41587-019-0325-6
Nishida K et al (2016) Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353. https://doi.org/10.1126/science.aaf8729
Patterson JB, Samuel CE (1995) Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase. Mol Cell Biol 15:5376–5388
Pavletich NP, Pabo CO (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252:809–817
Peters JE (2014) Tn7. Microbiol Spectr 2:1–20. https://doi.org/10.1128/microbiolspec.MDNA3-0010-2014
Quadros RM et al (2017) Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins. Genome Biol 18:92. https://doi.org/10.1186/s13059-017-1220-4
Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE (2016) Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 34:339–344. https://doi.org/10.1038/nbt.3481
Roy KR et al (2018) Multiplexed precision genome editing with trackable genomic barcodes in yeast. Nat Biotechnol 36:512–520. https://doi.org/10.1038/nbt.4137
Sakuma T et al (2015) Homologous recombination-independent large gene cassette Knock-in in CHO cells using TALEN and MMEJ-directed donor plasmids. Int J Mol Sci 16:23849–23866. https://doi.org/10.3390/ijms161023849
Savic N et al (2018) Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. elife 7. https://doi.org/10.7554/eLife.33761
Shmakov S et al (2015) Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60:385–397. https://doi.org/10.1016/j.molcel.2015.10.008
Shy BR et al (2022) High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails. Nat Biotechnol. https://doi.org/10.1038/s41587-022-01418-8
Song B, Bae S (2022) Voyage to minimal base editors. Nat Chem Biol 18:920–921. https://doi.org/10.1038/s41589-022-01037-z
Strecker J et al (2019) RNA-guided DNA insertion with CRISPR-associated transposases. Science 364:48–53
Suzuki K et al (2016) In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540:144–149. https://doi.org/10.1038/nature20565
Suzuki K et al (2019) Precise in vivo genome editing via single homology arm donor mediated intron-targeting gene integration for genetic disease correction. Cell Res 29:804–819. https://doi.org/10.1038/s41422-019-0213-0
Wang H, Xu X (2017) Microhomology-mediated end joining: new players join the team. Cell Biosci 7:6. https://doi.org/10.1186/s13578-017-0136-8
Wang M et al (2006) PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res 34:6170–6182. https://doi.org/10.1093/nar/gkl840
Yang H et al (2020) Methods favoring homology-directed repair choice in response to CRISPR/Cas9 induced-double strand breaks. Int J Mol Sci 21. https://doi.org/10.3390/ijms21186461
Yao X et al (2017) Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res 27:801–814. https://doi.org/10.1038/cr.2017.76
Yao X et al (2018) Tild-CRISPR allows for efficient and precise gene Knockin in mouse and human cells. Dev Cell 45:526–536 e525. https://doi.org/10.1016/j.devcel.2018.04.021
Yeh CD, Richardson CD, Corn JE (2019) Advances in genome editing through control of DNA repair pathways. Nat Cell Biol 21:1468–1478. https://doi.org/10.1038/s41556-019-0425-z
Zetsche B et al (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771. https://doi.org/10.1016/j.cell.2015.09.038
Zhang G et al (2022) Enhancement of prime editing via xrRNA motif-joined pegRNA. Nat Commun 13:1856. https://doi.org/10.1038/s41467-022-29507-x
Zong Y et al (2022) An engineered prime editor with enhanced editing efficiency in plants. Nat Biotechnol 40:1394–1402. https://doi.org/10.1038/s41587-022-01254-w
Acknowledgments
This research was supported by grants from the National Research Foundation of Korea (NRF) no. 2021R1A2C3012908 to S.B. and no. 2021R1I1A1A01056885 to B.S.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Section Editor information
Rights and permissions
Copyright information
© 2023 Springer Nature Singapore Pte Ltd.
About this entry
Cite this entry
Song, B., Bae, S. (2023). Genome Editing Using CRISPR. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-19-9776-1_85
Download citation
DOI: https://doi.org/10.1007/978-981-19-9776-1_85
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-19-9775-4
Online ISBN: 978-981-19-9776-1
eBook Packages: Chemistry and Materials ScienceReference Module Physical and Materials ScienceReference Module Chemistry, Materials and Physics