Submitted Successfully!
To reward your contribution, here is a gift for you: A free trial for our video production service.
Thank you for your contribution! You can also upload a video entry or images related to this topic.
Version Summary Created by Modification Content Size Created at Operation
1 + 3066 word(s) 3066 2022-03-02 04:26:23 |
2 corrected the format Meta information modification 3066 2022-03-08 01:41:03 | |
3 remove some unnecessary words -1 word(s) 3065 2022-03-08 01:43:42 |

Video Upload Options

We provide professional Video Production Services to translate complex research into visually appealing presentations. Would you like to try it?

Confirm

Are you sure to Delete?
Cite
If you have any further questions, please contact Encyclopedia Editorial Office.
Achary, V.M.; Mehta, S.; Chattopadhyay, A. Genome Editing Technologies. Encyclopedia. Available online: https://encyclopedia.pub/entry/20297 (accessed on 16 February 2025).
Achary VM, Mehta S, Chattopadhyay A. Genome Editing Technologies. Encyclopedia. Available at: https://encyclopedia.pub/entry/20297. Accessed February 16, 2025.
Achary, V. Mohan, Sahil Mehta, Anirudha Chattopadhyay. "Genome Editing Technologies" Encyclopedia, https://encyclopedia.pub/entry/20297 (accessed February 16, 2025).
Achary, V.M., Mehta, S., & Chattopadhyay, A. (2022, March 07). Genome Editing Technologies. In Encyclopedia. https://encyclopedia.pub/entry/20297
Achary, V. Mohan, et al. "Genome Editing Technologies." Encyclopedia. Web. 07 March, 2022.
Genome Editing Technologies
Edit

Genome editing is the technique of precise genome modifications that facilitate the targeted modifications within the genome through the deletions, insertions, or substitution of single base or specific sequences.

Genome editing CRISPR/Cas systems Food security Crop Improvement

1. Introduction

Over the last decade, the rapid pace of research on genome editing has revolutionized the field of applied biotechnology [1][2]. It enabled scientists to deploy these techniques in human health, crop improvement, etc. that has shown incredible potential to benefit human society. Interestingly, continuous crop improvement is compulsory to feed the mammoth 7.6 billion population, which will exceed the whopping mark of 9.7 billion by 2050 [3][4]. In the 20th century, crop improvement can be largely made through conventional breeding approaches, viz., mutagenesis and hybridization. Still, these approaches are now widely used in crop improvement. However, linkage drag of undesirable genes is a major drawback. Along with this, the labor-intensive, time-consuming, costly program makes it very complicated; thus, it becomes difficult to cope with the rapidly escalating demand for quality food to endure the world’s hunger and malnutrition challenges.
To resolve these issues of conventional breeding, modern approaches like marker-assisted breeding (MAS) and genome-wide association mapping (GWAS), aided with advanced genomic tools, were employed. Although they have great potential to speed up the breeding program, their efficiency and effectiveness were much less for the traits governed by the recessive genes/alleles, multiple genes (i.e., true polygenic traits), etc. Furthermore, the cost of genotyping is too high in the case of MAS and GWAS. To tackle these limitations, gene knock-in/gene knock-out strategies are adopted [5]. Of them, RNA Interference (RNAi) can be practiced to knock down the expression of a specific gene(s), but still has limited scope for wider application. Thus, the search for more powerful, precise, fast, and robust tools is always continuing for targeted crop genome improvement, which is of an urgent need to meet the global food demands.
Targeted genome modification is the best strategy to resolve all these problems permanently. This can be achieved through genetic engineering, which is a highly complicated and time-consuming venture. The genetic engineering tools lead to modifications in the genome via stable integration of foreign DNA elements but do not able to reach the end-users, mainly due to less social acceptance and higher bio-safety concerns [6]. Although it has a rich history in creating new crop genomes, it has been gradually outpaced by the emergence of genome editing tools. Genome editing mediates the targeted gene modification either through deletion or insertion. The genome editing tools make this targeted gene modification process simpler than the conventionally preferred methods, as well as genetic engineering. The genome editing (GE) tools, viz., clustered regularly interspaced short palindromic repeats (CRISPR) and transcription activator-like effector nucleases (TALEN), can be employed to make precise deletion and insertion of sequences that lead to the loss of gene function [7]. Nevertheless, these GE tools also have a gene regulatory property to upregulate or downregulate the gene expression. Thus, large-scale employment of genome editing technologies is evident in many crop plants, including rice (Oryza sativa L.; Family, Poaceae) [8][9].
Interestingly, genome editing technologies have been extensively exploited for rice genome modification to obtain numerous improved cultivars equipped with elite traits such as yield, quality, stress tolerance, etc. Yet, the biggest question still arises: ‘how much advancement in rice genome editing has been made in the last decade?’, especially concerning biotic stress tolerance. So far, many reviews are available that compile the pieces of evidence of rice genome editing for large-scale improvement [10][11][12][13]. However, the focus on the improvement of biotic stress tolerance is still limited. Thus, researchers are trying to collate all the information systematically in this article, so that various questions like the trait of interest to be edited, the strategy of genomic changes, steps to DNA modification, the scope of success, and the advent of different challenges, etc., could be addressed easily in the near future.

2. Advancements in Genome Editing Technologies

Genome editing is the technique of precise genome modifications that facilitate the targeted mutations within the genome [14] through the deletions, insertions, or substitution of single base or specific sequences [15][16]. The precursor of genome editing of plants dates back to the 1970s with the development of genetic engineering, in which the genome manipulation was carried out through the random introduction of specific gene sequences via homologous recombination (HR), and leads to the inactivation or ‘knock out’ of the targeted gene function. Further, the discovery of meganucleases during the 1980s improved the process of targeted genome engineering. All these discoveries led to the evolution of genome editing technologies which have been growing at a rapid pace over the past 10 years and have been established as an extraordinary genome engineering tool [17][18]. Genome editing can be performed both in vitro and in vivo [19] via in situ delivery of editing machinery, and the highly targeted genome alterations take place through the double-stranded DNA breaks (DSBs) by sequence-specific nucleases, followed by repairing either through non-homologous end-joining (NHEJ) or homologous recombination (HR)/homology-directed repair (HDR), depending on cellular types [20][21].
In the NHEJ mechanism, the broken ends are re-attached with the deletion or insertion of nucleotide sequences of varying lengths, which leads to the disruption of gene function [22], whereas, in the case of HDR, a homologous stretch of nucleotide sequences is introduced into the donor template that leads to more accurate repair with specific alterations of genomic sequences [23]. As the repairing in HDR is mediated with the help of a donor template, it is slower and less frequent than NHEJ [24], thus, the choice of HDR-mediated repair in plants is very difficult [25][26]. To create a gene knockout mutant via insertion/deletion or gene replacement, various sequence-specific nucleases, viz., zinc-finger nuclease (ZFN), TALENs, and CRISPR-associated proteins (Cas9, Cas12), can be employed. These nucleases are discovered through the groundbreaking work in bacteria, yeast, and mammalian systems, but are also applicable in a wide variety of crop plants for their trait improvement [27]. The details about these nucleases are highlighted in the below subsections.

2.1. Zinc Finger Nucleases (ZFNs)

ZFNs are an engineered protein consisting of a zinc finger domain at the N-terminal with an endonuclease domain at the C-terminal end [28][29]. The zinc finger domain is necessary for the specific recognition of the targeted DNA sequence, and the endonuclease domain of the FokI restriction enzyme (RE), isolated from the Flavobacterium okeanokoites, ensures the cleavage of the specific DNA sequences [30]. For its functionality, heterodimerization of FokI RE is indispensable; hence, two ZFNs must dimerize for binding both strands of DNA and to align FokI domains. ZFN contains a tandem array of three to six zinc fingers (Cys2His2), each recognizing approximately 3 bp of DNA [31]. The sequence-specific binding of the zinc-finger domain directs the nuclease to cleave a specific genomic site. This mechanism was exploited for designing ZFN mediated gene-editing tools that are extensively used for customized engineering of the genome in many organisms [32].
The breakthrough of ZFNs as programmable nuclease was initiated in mice to create gene knockout via DSBs of target sequences that rapidly disseminated in various laboratories [29]. Further, it was expanded in agriculture for crop improvement, but with restricted implications for genomic editing attempts in limited crops such as Arabidopsis, tobacco, and maize [33]. Further, the off-target binding of the ZF motifs, other than the target sequence, makes them inefficient as an editing tool [34]. Moreover, the designing of a ZFN molecule via protein engineering is very challenging and highly time-consuming; thus, it will not be cost-effective to create a particular mutation.
Table 1. Tabular comparison of major genome editing technologies available for plants improvement.

Attributes

ZFNs

TALENs

CRISPR/Cas9

Cleavage type

Protein-dependent

Protein-dependent

RNA-dependent

Size

Significantly smaller than Cas9

(+)

Comparatively larger than ZFNs

(++)

Significantly larger than both ZFNs and TALENS

(+++)

Components

Zinc finger domains, Non-specific FokI nuclease domain

TALE DNA-binding domains, Non-specific FokI nuclease domain

 

Cas9 protein, crRNAs

Catalytic domain(s)

FokI endonuclease domain

FokI endonuclease domain

HNH, RUVC

Structural components (Dimeric/Monomeric)

Dimeric

Dimeric

Monomeric

Target sequence length

18-36

24-59

20-22

gRNA production required

No

No

Yes

Cloning required

Yes

Yes

No

Protein engineering steps needed

Yes

Yes

No

Mode of action

Induce DSBs in target DNA

Induce DSBs in target DNA

Induce DSBs or single-strand DNA nicks in target DNA

Restriction target site

High G

5’T and 3’A

PAM sequence

Level of target recognition efficiency

High

High

Very high

Targeting

Poor

Good

Very good

Mutation rate level

High

Low

Very low

Off-target effects

Yes

Yes

Yes, but can be minimized by selection of unique crRNA sequence

Cleavage of methylated DNA possible

No

No

Yes, but it will be explored more

Multiplexing enabled

Highly difficult

Highly difficult

Yes

Labour intensiveness in experiment setup

Yes

Yes

No

Possible to generate large scale libraries

No

Yes, but it is highly challenging

Yes

Design feasibility

Difficult

Difficult

Easy

Technology cost

Very high

(£1000-£3000)

High

(£40-£350)

Comparatively low

(£30-£300)

2.2. TALENs

For many years, ZFN was explored as the only programmable site-specific nuclease, but it has been out-paced with the discovery of a DNA binding effector protein, called transcriptional activator-like effector (TALE), isolated from plant-pathogenic bacteria, Xanthomonas [35][36]. It primarily acts as the transcriptional regulator of the disease susceptibility (S) genes in rice. This protein is characterized by the C-terminal activation domain (AD) and nuclear localization signal (NLS) required for transcriptional regulation, the central tandem repeat sequence acting as a DNA binding domain (DBD), and the N-terminal translocation signal sequence [37]. A series of 33–35 amino-acid long repeat sequences in the DBD is present; of them, two hypervariable amino acids at the 12th and 13th position, also known as the repeat-variable di-residues (RVDs), are responsible for the specific recognition of nucleotide bases [38]. The sequence-specific binding property of DBD is exploited for the further development of new gene-editing technology, i.e., transcription activator-like effector nucleases (TALEN).
Similar to ZFN, TALENs are customized by fusing the DBD of the transcriptional activator-like effector (TALE) with the FokI restriction enzyme [39] (Table 1)​. However, unlike ZFN, the designing of TALEN is much easier, as the repeat sequence of the TALEs has specificity for targeting single sites in a genome. Further, the multimerization of the repeat sequence is not essential for the construction of a long array of DBD, as in ZFN; hence the engineering is quite easy and less time-consuming [40]. The identification of RVDs in repeat regions of TALEs helps in the recognition of their specificity for various binding targets, as each RVD has a single nucleotide target, thus allowing the flexibility for designing TALENs for a greater number of potential target sites than that of ZFNs. Therefore, the TALENs have been utilized for genome editing in a wide variety of plants. Additionally, the binding of TALEs with gene activators and receptors, apart from nuclease, leads to the formation of efficient artificial transcriptional regulators to achieve the desirable gene regulation. Despite the advantages of TALENs over ZFNs in terms of high target specificity and low off-target effect, the extensive repeat structure in the DBD of TALE protein becomes the major limiting factor for their use in target-specific editing of multiple genomes, and further, protein engineering is always tedious. To resolve these issues, genome editing using programmable RNA-guided DNA endonucleases has become more popular.

2.3. CRISPR/Cas System

The CRISPR (Clustered regularly interspaced short palindromic repeats) is a mysterious DNA sequence found in the prokaryotic genome (including bacteria and archaea) which is often palindromic, consisting of 29 nucleotides (nt), long identical tandem repeats separated by a unique spacer (32 nt in length) [41]. It is a kind of locus consisting of several CRISPR-associated conserved protein-coding genes (Cas) exclusively involved in the adaptive immunity of prokaryotes against bacteriophages. This CRISPR-mediated immunity is functionally related to eukaryotic RNA interference (RNAi) [42], with the additional advantage of the development of genetic memory from past encounters. The CRISPR can recognize the small CRISPR RNAs (crRNAs) transcribed from the genetic memory (acquired in the CRISPR repeats) and use these small guide RNAs to cleave the virus genome [43][44]. This mechanism of CRISPR is explored and exploited further. The programmable nature of the CRISPR system led to the design of the RNA-guided DNA endonucleases-based genome editing tool, which is popularly known as CRISPR/Cas.
The CRISPR/Cas-based genome editing works based on the RNA:DNA base-pairing principle to target the host DNA and is used as a novel system for precise genome manipulation in many organisms, including plants [45]. This technique is more robust and simpler compared to ZFN and TALEN [46]. It is inexpensive, easy to apply, and has high versatility with great accuracy, even when deployed for multiplex genome editing, i.e., for the manipulation of multiple genes at the same time [47]. It has been showcased in various model plants (Arabidopsis, tobacco, etc.) and crop plants (rice, wheat, maize, tomato, potato, and soybean) as well as woody plants (apple, poplar, etc.) for durable trait improvements, from achieving higher yield and quality to alleviating biotic and abiotic stress troubles [48][49][50].
This CRISPR/Cas system involves the creation of dsDNA breaks at a desirable specific site in the genome with the help of a guide RNA (20–23 nt long), which is designed to be complementary to the target sequences and binds with the one strand of genomic DNA, using Watson–Crick base pairing to facilitate the Cas endonucleases’ mediated cleavage of dsDNA [51]. The DSBs are then mended by the cellular repair machinery, involving HDR or NHEJ mechanism, and generate genomic modifications such as mutation via deletion and insertion [52].
Interestingly, there are different Cas endonucleases (class 1 and class 2) that vary in their structure, composition, functional targets. Out of them, class 2 of Cas endonucleases is most commonly used in genome editing (Table 2), and these nucleases are optimized for their wide-scale application in genome editing. With great functional variation in terms of specificity and nucleic acid target, they are extended for precise editing of both DNA and RNA. Further, improvisation has led to the emergence of some innovative techniques such as base editing, prime editing, etc. See Table 2 for more precise editing of single/few nucleotides. The utility of these techniques for the improvement of plant biotic stress tolerance has opened up a new avenue in rice improvement (Figure 1).

3. Future directions

In the present decennium, crop improvement is considered as a prime way for calorific and nutritional demands of every-second increasing mankind. However, various methods like hybridization, somaclonal variation, in vitro tissue culture, and mutagenesis require more manpower, time duration, efforts along with a high chance of failures in getting the “desirable traits”. The development of novel tools and technologies is indispensable for scientific advancement. In this regard, methodological advancements in the unprecedented toolbox of genome/gene-editing technology (including CRISPR/Cas9) offer immense opportunities for transforming agriculture science under the changing climate. This also offers unlimited potential for improving existing crops in a short time and de novo domesticating new crops in the fast and forward direction. Among all these technologies, Programmable nucleases are at the epicentre of the explosive growth of the genome-editing field. Within these nucleases, CRISPR-associated protein 9 (Cas9), Cas12a nucleases and their derivatives have been most precise, easy to handle, and also employed for avoiding backcrossing of a huge number of inbred lines. The new CRISPR/Cas systems may enable researchers to overcome the limitations of Protospacer Adjacent Motif sequences, target specificities, large protein size of Cas9, and multi-genes editing. In addition, CRISPR/Cas based cis-regulatory element sequences alternation holds a great promise for the development of future-ready crops. Single-nucleotide polymorphism (SNPs) and microRNA (mRNA) both play a very important role in gene expression and their functions in a plant which are closely associated with many agronomic traits. The latest base editing and prime editing tools offer a wider application of CRISPR technologies to create SNPs in the genome and alteration of microRNA binding genomic regions thus altering the function of gene and regulatory region which can be implemented to create improved crop varieties. Besides generating modifications in target genes, CRISPR/Cas can also be used to restructure and engineer chromosomes. Introduction of duplications, inversions of large regions within a chromosome, or translocations between chromosomes, can lead to the breakage of linkages, providing useful genetic materials for crop breeding. Taking these points in a frame together, researchers can affirm those genome editing technologies holds the promise of improving crops.

Figure 1. Schematic illustration representing the genome editing strategies adopted for the enhancement of disease resistance in rice. Different approaches are functional knockout of the host S genes via either deletion/mutation/replace of the coding sequences, modification of single nucleotide polymorphisms in the recessive allele of R genes through base editing, targeted modification of non-coding regulatory RNAs (miRNAs) by Cas13, replacement of central regulators like NPR1, engineering the promoter cis-elements by multiplex editing, modification of negative TFs of plant defense, metabolic engineering of secondary metabolite (lignin) synthesis to favor plant defense, etc. These strategies have been applied to intervene in the different steps of pathogenesis events of fungi, bacteria, and viruses.
Table 2. Advancements in genome editing tools and their variants are available for rice improvement.
Genome Editing Tools Variants Features Function Application References
ZFN - Engineered protein, containing a zinc finger domain and endonuclease domain Protein-dependent cleavage of any genomic DNA sequence Editing of any DNA sequence [53]
TALEN - Customized protein-containing DNA binding domain of transcriptional activator-like effector (TALE) and FokI restriction enzyme Protein-dependent cleavage of any genomic DNA sequence Editing of any DNA sequence [39]
CRISPR/Cas Cas9 A ribonucleoprotein complex containing a DNA endonuclease (Cas9) enzyme fused with guide RNAs (gRNAs) RNA-guided cleavage of dsDNA sequence complementary to the gRNA; Efficient genome editing with limited target site and potential off-target effect due to long size of sgRNA (100 nt) Genome editing with multiplex facility [54]
Cas12 A ribonucleoprotein complex containing a DNA endonuclease (Cas12/Cpf1) enzyme fused with crRNA (CRISPR-derived RNA), but not tracrRNA RNA-guided cleavage of ssDNA and dsDNA sequence with high cleavage efficiency and less off-target effect due to short crRNA (40--45 nt) molecules Precise genome editing [55]
Cas13 A ribonucleoprotein complex containing an RNA endonuclease (Cas13) enzyme fused with crRNA RNA-guided cleavage of ssRNA sequence; suitable multiplex editing Robust management of RNA viruses [56]
Base editing A ribonucleoprotein complex containing catalytically inactive Cas9 nickase
and a cytidine deaminase domain fused with a single gRNA
G-C to A-T conversion at desired locations in the genome Nucleotide substitutions; with the limitation of limited PAM site and frequent off-target effect [57]
Prime editing A ribonucleoprotein complex containing a
Cas9 nickase fused with reverse transcriptase (RT) and a prime editing guide RNA (pegRNA)
Targeted small insertions, deletions, and base transition by ‘search-and-replace’ method
using the pegRNA sequence
Specific nucleotide substitution via gene knock-in at targeted genomic site [58]

References

  1. Li, H.; Yang, Y.; Hong, W.; Huang, M.; Wu, M.; Zhao, X. Applications of genome editing technology in the targeted therapy of human diseases: Mechanisms, advances, and prospects. Signal Transduct. Target. Ther. 2020, 5, 1.
  2. Khalil, A.M. The genome editing revolution: Review. J. Genet. Eng. Biotechnol. 2020, 18, 68.
  3. Valin, H.; Sands, R.D.; Van der Mensbrugghe, D.; Nelson, G.C.; Ahammad, H.; Blanc, E.; Bodirsky, B.; Fujimori, S.; Hasegawa, T.; Havlik, P.; et al. The future of food demand: Understanding differences in global economic models. Agri. Econ. 2014, 45, 51–67.
  4. United Nations, Department of Economic and Social Affairs, Population Division, World Population Prospects 2019: Highlights (ST/ESA/SER.A/423). Available online: https://population.un.org/wpp/Publications/Files/WPP2019_Highlights.pdf (accessed on 9 January 2022).
  5. Ahmar, S.; Gill, R.A.; Jung, K.H.; Faheem, A.; Qasim, M.U.; Mubeen, M.; Zhou, W. Conventional and molecular techniques from simple breeding to speed breeding in crop plants: Recent advances and future outlook. Int. J. Mol. Sci. 2020, 21, 2590.
  6. Low, L.-Y.; Yang, S.-K.; Kok, D.-X.A.; Ong-Abdullah, J.; Tan, N.-P.; Lai, K.-S. Transgenic plants: Gene constructs, vector and transformation method. In New Visions in Plant Science; Çelik, Ö., Ed.; IntechOpen: London, UK, 2018.
  7. Xu, K.; Segal, D.J.; Zhang, Z. Precise genome editing techniques and applications. Front. Genet. 2020, 11, 412.
  8. Kamburova, V.S.; Nikitina, E.V.; Shermatov, S.E.; Buriev, Z.T.; Kumpatla, S.P.; Emani, C.; Abdurakhmonov, I.Y. Genome editing in plants: An overview of tools and applications. Inter. J. Agron. 2017, 2017, 15.
  9. Achary, V.M.M.; Reddy, M.K. CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice. Sci. Rep. 2021, 11, 21941.
  10. Mishra, R.; Joshi, R.K.; Zhao, K. Genome editing in rice: Recent advances, challenges, and future implications. Front. Plant. Sci. 2018, 9, 1361.
  11. Zafar, K.; Sedeek, K.E.M.; Rao, G.S.; Khan, M.Z.; Amin, I.; Kamel, R.; Mukhtar, Z.; Zafar, M.; Mansoor, S.; Mahfouz, M.M. Genome editing technologies for rice improvement: Progress, prospects, and safety concerns. Front. Genome Ed. 2020, 2, 5.
  12. Mehta, S.; Lal, S.K.; Sahu, K.P.; Venkatapuram, A.K.; Kumar, M.; Sheri, V.; Varakumar, P.; Vishwakarma, C.; Yadav, R.; Jameel, M.R.; et al. CRISPR/Cas9-Edited Rice: A New Frontier for Sustainable Agriculture. In New Frontiers in Stress Management for Durable Agriculture; Rakshit, A., Singh, H., Singh, A., Singh, U., Fraceto, L., Eds.; Springer: Singapore, 2020; pp. 427–458.
  13. Tabassum, J.; Ahmad, S.; Hussain, B.; Mawia, A.M.; Zeb, A.; Ju, L. Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives. Agronomy 2021, 11, 1359.
  14. Wada, N.; Ueta, R.; Osakabe, Y.; Osakabe, K. Precision genome editing in plants: State-of-the-art in CRISPR/Cas9-based genome engineering. BMC Plant Biol. 2020, 20, 1–12.
  15. Ceasar, S.A.; Rajan, V.; Prykhozhij, S.V.; Berman, J.N.; Ignacimuthu, S. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9. Biochim. Biophys. Acta Bioenerg. 2016, 1863, 2333–2344.
  16. Okamoto, S.; Amaishi, Y.; Maki, I.; Enoki, T.; Mineno, J. Highly efficient genome editing for single-base substitutions using optimized ssODNs with Cas9-RNPs. Sci. Rep. 2019, 9, 1–11.
  17. Hsu, P.D.; Lander, E.S.; Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014, 157, 1262–1278.
  18. Chakraborty, C.; Teoh, S.L.; Das, S. The smart programmable CRISPR technology: A next-generation genome editing tool for investigators. Curr. Drug Targets 2017, 18, 1653–1663.
  19. Bortesi, L.; Fischer, R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol. Adv. 2015, 33, 41–52.
  20. Mao, Z.; Bozzella, M.; Seluanov, A.; Gorbunova, V. Comparison of nonhomologous end joining and homologous recombination in human cells. DNA Repair 2008, 7, 1765–1771.
  21. Lieber, M.R. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 2010, 79, 181–211.
  22. Rouet, P.; Smih, F.; Jasin, M. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol. Cell. Biol. 1994, 14, 8096–8106.
  23. Puchta, H. The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution. J. Exp. Bot. 2005, 56, 1–14.
  24. Miyaoka, Y.; Berman, J.R.; Cooper, S.B.; Mayerl, S.J.; Chan, A.H.; Zhang, B.; Karlin-Neumann, G.A.; Conklin, B.R. Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Sci. Rep. 2016, 6, 23549.
  25. Mengiste, T.; Paszkowski, J. Prospects for the precise engineering of plant genomes by homologous recombination. Biol. Chem. 1999, 380, 749–758.
  26. Vergunst, A.C.; Hooykaas, P.J.J. Recombination in the plant genome and its application in biotechnology. Crit. Rev. Plant. Sci. 1999, 18, 1–31.
  27. Randhawa, S.; Sengar, S. The evolution and history of gene editing technologies. Prog. Mol. Biol. Transl. Sci. 2021, 178, 1–62.
  28. Kim, Y.G.; Cha, J.; Chandrasegaran, S. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. USA 1996, 93, 1156–1160.
  29. Porteus, M.H.; Carroll, D. Gene targeting using zinc-finger nucleases. Nat. Biotechnol. 2005, 23, 967–973.
  30. Bitinaite, J.; Wah, D.A.; Aggarwal, A.K.; Schildkraut, I. FokI dimerization is required for DNA cleavage. Proc. Natl. Acad. Sci. USA 1998, 95, 10570–10575.
  31. Wolfe, S.A.; Nekludova, L.; Pabo, C.O. DNA recognition by Cys2His2 Zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 183–212.
  32. Urnov, F.D.; Rebar, E.J.; Holmes, M.C.; Zhang, H.S.; Gregory, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 2010, 11, 636–646.
  33. Petolino, J.F. Genome editing in plants via designed zinc-finger nucleases. Vitr. Cell. Dev. Biol. Plant. 2015, 51, 1–8.
  34. Pattanayak, V.; Ramirez, C.L.; Joung, J.K.; Liu, D.R. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat. Methods 2011, 8, 765–770.
  35. Boch, J.; Scholze, H.; Schornack, S.; Landgraf, A.; Hahn, S.; Kay, S.; Lahaye, T.; Nickstadt, A.; Bonas, U. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 2009, 326, 1509–1512.
  36. Moscou, M.J.; Bogdanove, A.J. A simple cipher governs DNA recognition by TAL effectors. Science 2009, 326, 1501.
  37. Jankele, R.; Svoboda, P. TAL effectors: Tools for DNA targeting. Brief. Funct. Genom. 2014, 13, 409–419.
  38. Mak, A.N.; Bradley, P.; Bogdanove, A.J.; Stoddard, B.L. TAL effectors: Function, structure, engineering and applications. Curr. Opin. Struct. Biol. 2013, 23, 93–99.
  39. Joung, J.K.; Sander, J.D. TALENs: A widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 2013, 14, 49–55.
  40. Gaj, T.; Gersbach, C.A.; Barbas, C.F., III. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013, 31, 397–405.
  41. Chaudhary, K.; Chattopadhyay, A.; Pratap, D. The evolution of CRISPR/Cas9 and their cousins: Hope or hype? Biotechnol. Lett. 2018, 43, 2329.
  42. Makarova, K.S.; Grishin, N.V.; Shabalina, S.A.; Wolf, Y.I.; Koonin, E.V. 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. 2006, 1, 7.
  43. Barrangou, R.; Fremaux, C.; Deveau, H.; Richards, M.; Boyaval, P.; Moineau, S.; Romero, D.A.; Horvath, P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315, 1709–1712.
  44. Brouns, S.J.; Jore, M.M.; Lundgren, M.; Westra, E.R.; Slijkhuis, R.J.; Snijders, A.P.; Dickman, M.J.; Makarova, K.S.; Koonin, E.V.; van der Oost, J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008, 321, 960–964.
  45. Mushtaq, M.; Ahmad Dar, A.; Skalicky, M.; Tyagi, A.; Bhagat, N.; Basu, U.; Bhat, B.A.; Zaid, A.; Ali, S.; Dar, T.-U.-H.; et al. CRISPR-based genome editing tools: Insights into technological breakthroughs and future challenges. Genes 2021, 12, 797.
  46. Ahmad, H.I.; Ahmad, M.J.; Asif, A.R.; Adnan, M.; Iqbal, M.K.; Mehmood, K.; Muhammad, S.A.; Bhuiyan, A.A.; Elokil, A.; Du, X.; et al. A review of CRISPR-based genome editing: Survival, evolution, and challenges. Curr. Issues Mol. Biol. 2018, 28, 47–68.
  47. Mccarty, N.S.; Graham, A.E.; Studená, L.; Ledesma-Amaro, R. Multiplexed CRISPR technologies for gene editing and transcriptional regulation. Nat. Commun. 2020, 11, 1281.
  48. Arora, L.; Narula, A. Gene editing and crop improvement using CRISPR-Cas9 system. Front. Plant Sci. 2017, 8, 1932.
  49. Jaganathan, D.; Ramasamy, K.; Sellamuthu, G.; Jayabalan, S.; Venkataraman, G. CRISPR for crop improvement: An update review. Front. Plant Sci. 2018, 9, 985.
  50. Montecillo, J.A.V.; Chu, L.L.; Bae, H. CRISPR-Cas9 system for plant genome editing: Current approaches and emerging developments. Agronomy 2020, 10, 1033.
  51. Jiang, F.; Doudna, J.A. CRISPR-Cas9 structures and mechanisms. Annu. Rev. Biophys. 2017, 46, 505–529.
  52. Shin, H.Y.; Wang, C.; Lee, H.K.; Yoo, K.H.; Zeng, X.; Kuhns, T.; Yang, C.M.; Mohr, T.; Liu, C.; Hennighausen, L. CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nat. Commun. 2017, 8, 15464.
  53. Carroll, D. Genome engineering with zinc-finger nucleases. Genetics 2011, 188, 773–782.
  54. Wolf, S.; Wu, W.; Jones, C.; Perwitasari, O.; Mahalingam, S.; Tripp, R.A.; Chan, M.C. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 2014, 343, 1247997.
  55. 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. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 2015, 163, 759–771.
  56. Mahas, A.; Aman, R.; Mahfouz, M. CRISPR-Cas13d mediates robust RNA virus interference in plants. Genome Biol. 2019, 20, 263.
  57. Rees, H.A.; Liu, D.R. Base editing: Precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 2018, 19, 770–788.
  58. Matsoukas, I.G. Prime editing: Genome editing for rare genetic diseases without double-strand breaks or donor DNA. Front. Genet. 2020, 11, 528.
More
Information
Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register : , ,
View Times: 675
Revisions: 3 times (View History)
Update Date: 08 Mar 2022
1000/1000
Video Production Service