Genome Editing with Engineered Nucleases in Economically Important Animals and Plants: State of the Art in the Research Pipeline

doi:10.21775/cimb.021.041

Cited by 10 publications

(9 citation statements)

References 94 publications

(218 reference statements)

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“…Our literature search also covered publications of nGM applications that are near commercialization or already commercialized in some countries, such as a herbicide-resistant oilseed rape variety developed by ODM (Gocal et al, 2015). As seen in Sovova et al (2017) information on patents did not add significant information in terms of application and the potential for commercialization. We are thus confident that the sources we have considered sufficiently serve the purpose of this work.…”

Section: Literature Survey To Identify Applications Of Ngms With Relementioning

confidence: 94%

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

Eckerstorfer

Dolezel

Heissenberger

et al. 2019

Front. Bioeng. Biotechnol.

101

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The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.

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Section: Literature Survey To Identify Applications Of Ngms With Relementioning

confidence: 94%

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

Eckerstorfer

Dolezel

Heissenberger

et al. 2019

Front. Bioeng. Biotechnol.

101

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“…The advantage of meganucleases is their small size, making them appropriate to a majority of delivery methods [16]. However, the DNA-binding domain cannot be separated from the catalytic domain challenging the construction of MN [4]. MN have been applied successfully for genome editing in plants such as Arabidopsis [17], maize [18] and cotton [19].…”

Section: Meganucleasesmentioning

confidence: 99%

“…ZFN are generated by fusing two independent protein domains. A zinc-finger protein, which comprises up to six zinc-finger domains each able to identify a nucleotide triplet of a specific DNA sequence, is fused with a synthetic endonuclease domain (most frequently FokI) [4,9,29]. Since the nuclease is active as a dimer, two zinc-finger nucleases are necessary in close proximity to target and cut a sequence in the genome.…”

Section: Zinc-finger Nucleasesmentioning

confidence: 99%

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What is the available evidence for the application of genome editing as a new tool for plant trait modification and the potential occurrence of associated off-target effects: a systematic map protocol

et al. 2018

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Background: Plant breeding is a developing process and breeding methods have continuously evolved over time. In recent years, genome editing techniques such as clustered regularly interspaced short palindromic repeats/CRISPR associated proteins (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFN), meganucleases (MN) and oligonucleotide-directed mutagenesis (ODM) enabled a precise modification of DNA sequences in plants. Genome editing has already been applied in a wide range of plant species due to its simplicity, time saving and cost-effective application compared to earlier breeding techniques including classical mutagenesis. Although genome editing techniques induce much less unintended modifications in the genome (off-target effects) compared to classical mutagenesis techniques, off-target effects are a prominent point of criticism as they might cause genomic instability, cytotoxicity and cell death. Methods: The aim of this systematic map is to address the following primary question: "What is the available evidence for the application of genome editing as a new tool for plant trait modification and the potential occurrence of associated off-target effects"? The primary question will be considered by two secondary questions: One is aimed at the traits being modified by genome editing in plants and the other explores the occurrence of off-target effects. The systematic map will focus on model plants as well as on plants produced for agricultural production that were subjected to genome editing techniques. Academic and grey literature will be searched in English and German language. Inclusion/exclusion criteria were developed for the two secondary questions and will be applied on title/abstract and full text stage. Included studies will be catalogued in a searchable and open access database and study results will be summarized using descriptive statistics. Furthermore, the extracted data will serve as a preparatory step for further in-depth analysis, e.g. by a systematic review.

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“…The features of clustered regularly interspaced short palindromic repeats (CRISPR) were discovered serendipitously in the genomes of various bacteria and archaea during molecular biology studies ( Ishino et al, 1987 ; Mojica et al, 1993 ). The system was originally used as an adaptive immune defense system by bacteria against the invasion of foreign nucleic acids, such as viruses and plasmids ( Ishino et al, 1987 ; Sovova et al, 2017 ; Albitar et al, 2018 ). The immune process is divided into three stages: 1) adaptation: the invading nucleotide fragments are first captured by the host organism, and subsequently, a Cas integrase-derived nucleic acid sequence is inserted into the CRISPR array; 2) biogenesis: the CRISPR array is transcribed into a pre-crRNA (pre-crRNA) containing a spacer and a portion of the repeat, which is subsequently cleaved in the repeat to induce the generation of mature guide crRNA (gRNA); and 3) interference: mature crRNA-Cas complexes recognize specific sites on target nucleic acids through complementary base pairing, triggering Cas enzymes to catalyze the cleavage of effector complexes of invading nucleotides ( Debin Zhang et al, 2020 ; Makarova et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations

Huang

Chen

2022

Front. Bioeng. Biotechnol.

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Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.

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Genome Editing with Engineered Nucleases in Economically Important Animals and Plants: State of the Art in the Research Pipeline

Abstract: After induced mutagenesis and transgenesis,

Cited by 10 publications

References 94 publications

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

What is the available evidence for the application of genome editing as a new tool for plant trait modification and the potential occurrence of associated off-target effects: a systematic map protocol

The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations

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