Gene targeting

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A chimeric mouse gene targeted for the agouti coat color gene, with its offspring ChimericMouseWithPups.jpg
A chimeric mouse gene targeted for the agouti coat color gene, with its offspring

Gene targeting is a biotechnological tool used to change the DNA sequence of an organism (hence it is a form of Genome Editing). It is based on the natural DNA-repair mechanism of Homology Directed Repair (HDR), including Homologous Recombination. Gene targeting can be used to make a range of sizes of DNA edits, from larger DNA edits such as inserting entire new genes into an organism, through to much smaller changes to the existing DNA such as a single base-pair change. Gene targeting relies on the presence of a repair template to introduce the user-defined edits to the DNA. The user (usually a scientist) will design the repair template to contain the desired edit, flanked by DNA sequence corresponding (homologous) to the region of DNA that the user wants to edit; hence the edit is targeted to a particular genomic region. In this way Gene Targeting is distinct from natural homology-directed repair, during which the ‘natural’ DNA repair template of the sister chromatid is used to repair broken DNA (the sister chromatid is the second copy of the gene). The alteration of DNA sequence in an organism can be useful in both a research context – for example to understand the biological role of a gene – and in biotechnology, for example to alter the traits of an organism (e.g. to improve crop plants).

Contents

Methods

Wild-type Physcomitrella and knockout mosses: Deviating phenotypes induced in gene-disruption library transformants. Physcomitrella wild-type and transformed plants were grown on minimal Knop medium to induce differentiation and development of gametophores. For each plant, an overview (upper row, scale bar corresponds to 1 mm) and a close-up (bottom row, scale bar equals 0.5 mm) is shown. A, Haploid wild-type moss plant completely covered with leafy gametophores and close-up of wild-type leaf. B-E, Different mutants. Physcomitrella knockout mutants.JPG
Wild-type Physcomitrella and knockout mosses: Deviating phenotypes induced in gene-disruption library transformants. Physcomitrella wild-type and transformed plants were grown on minimal Knop medium to induce differentiation and development of gametophores. For each plant, an overview (upper row, scale bar corresponds to 1 mm) and a close-up (bottom row, scale bar equals 0.5 mm) is shown. A, Haploid wild-type moss plant completely covered with leafy gametophores and close-up of wild-type leaf. B–E, Different mutants.

To create a gene-targeted organism, DNA must be introduced into its cells. This DNA must contain all of the parts necessary to complete the gene targeting. At a minimum this is the homology repair template, containing the desired edit flanked by regions of DNA homologous (identical in sequence to) the targeted region (these homologous regions are called “homology arms” ). Often a reporter gene and/or a selectable marker is also required, to help identify and select for cells (or “events”) where GT has actually occurred. It is also common practice to increase GT rates by causing a double-strand-break (DSB) in the targeted DNA region. [2] Hence the genes encoding for the site-specific-nuclease of interest may also be transformed along with the repair template. These genetic elements required for GT may be assembled through conventional molecular cloning in bacteria.

Gene targeting methods are established for several model organisms and may vary depending on the species used. To target genes in mice, the DNA is inserted into mouse embryonic stem cells in culture. Cells with the insertion can contribute to a mouse's tissue via embryo injection. Finally, chimeric mice where the modified cells make up the reproductive organs are bred. After this step the entire body of the mouse is based on the selected embryonic stem cell.

To target genes in moss, the DNA is incubated together with freshly isolated protoplasts and with polyethylene glycol. As mosses are haploid organisms, [3] moss filaments (protonema) can be directly screened for the target, either by treatment with antibiotics or with PCR. Unique among plants, this procedure for reverse genetics is as efficient as in yeast. [4] Gene targeting has been successfully applied to cattle, sheep, swine and many fungi.

The frequency of gene targeting can be significantly enhanced through the use of site-specific endonucleases such as zinc finger nucleases, [5] engineered homing endonucleases, [6] TALENS, or most commonly the CRISPR-Cas system. This method has been applied to species including Drosophila melanogaster, [5] tobacco, [7] [8] corn, [9] human cells, [10] mice [11] and rats. [11]

Comparison to other forms of genetic engineering

A Venn Diagram to show the relationship between three types of 'Genetic engineering'; Genetic Modification, Gene Targeting and Genome Editing. Genetic engineering subtypes.svg
A Venn Diagram to show the relationship between three types of 'Genetic engineering'; Genetic Modification, Gene Targeting and Genome Editing.

The relationship between gene targeting, gene editing and genetic modification is outlined in the Venn diagram below. It displays how 'Genetic engineering' encompasses all 3 of these techniques. Genome editing is characterised by making small edits to the genome at a specific location, often following cutting of the target DNA region by a site-specific-nuclease such as CRISPR. [12] Genetic modification usually describes the insertion of a transgene (foreign DNA, i.e. a gene from another species) into a random location within the genome. [13] [14] Gene-targeting is a specific biotechnological tool that can lead to small changes to the genome at a specific site [2] - in which case the edits caused by gene-targeting would count as genome editing. However gene targeting is also capable of inserting entire genes (such as transgenes) at the target site if the transgene is incorporated into the homology repair template that is used during gene-targeting. [15] [16] In such cases the edits caused by gene-targeting would, in some jurisdictions, be considered as equivalent to Genetic Modification as insertion of foreign DNA has occurred. [16]

Gene targeting is one specific form of genome editing tool. Other genome editing tools include targeted mutagenesis, base editing and prime editing, all of which create edits to the endogenous DNA (DNA already present in the organism) at a specific genomic location. [17] [18] This site-specific or ‘targeted’ nature of genome editing is typically what makes genome-editing different to traditional ‘genetic modification’ which inserts a transgene at a non-specific location in the organisms' genome, as well as gene-editing making small edits to the DNA already present in the organisms, verses genetic modification insertion 'foreign' DNA from another species. [19] [20]

Because gene editing makes smaller changes to endogenous DNA, many mutations created through genome-editing could in theory occur through natural mutagenesis or, in the context of plants, through mutation breeding which is part of conventional breeding (in contrast the insertion of a transgene to create a Genetically Modified Organism (GMO) could not occur naturally). However, there are exceptions to this general rule; as explained in the introduction, GT can introduce a range of possible size of edits to DNA; from very small edits such as changing, inserting or deleting 1 base-pair, through to inserting much longer DNA sequences, which could in theory include insertion of an entire transgene. [16] However, in practice GT is more commonly used to insert smaller sequences. The range of edits possible through GT can make it challenging to regulate (see Regulation).

Possible DNA repair outcomes after cutting by CRISPR, leading to gene editing. Both strands of DNA are cut by CRISPR-Cas (or other site-specific nuclease) to create a double-strand-break (DSB). The DSB is then repaired through two alternative DNA repair pathways (NHEJ or HR) to lead to random mutations at the cut site ("targeted mutagenesis") or specific mutations if a repair template is supplied that contains those specific edits ("gene targeting"). Gene targeting mechanism vs non homologous end joining.svg
Possible DNA repair outcomes after cutting by CRISPR, leading to gene editing. Both strands of DNA are cut by CRISPR-Cas (or other site-specific nuclease) to create a double-strand-break (DSB). The DSB is then repaired through two alternative DNA repair pathways (NHEJ or HR) to lead to random mutations at the cut site ("targeted mutagenesis") or specific mutations if a repair template is supplied that contains those specific edits ("gene targeting").

The two most established forms of gene editing are gene-targeting and targeted-mutagenesis. While gene targeting relies on the Homology Directed Repair (HDR) (also called Homologous Recombination, HR) DNA repair pathway, targeted-mutagenesis uses Non-Homologous-End-Joining (NHEJ) of broken DNA. NHEJ is an error-prone DNA repair pathway, meaning that when it repairs the broken DNA it can insert or delete DNA bases, creating insertions or deletions (indels). The user cannot specify what these random indels will be, hence they cannot control exactly what edits are made at the target site. However they can control where these edits will occur (i.e. dictate the target site) through using a site-specific nuclease (previously Zinc Finger Nucleases & TALENs, now commonly CRISPR) to break the DNA at the target site. A summary of gene-targeting through HDR (also called Homologous Recombination) and targeted mutagenesis through NHEJ is shown in the figure below.

The more newly developed gene-editing techniques of prime editing and base editing, [18] based on CRISPR-Cas methods, are alternatives to gene targeting, which can also create user-defined edits at targeted genomic locations. However each is limited in the length of DNA sequence insertion possible; base editing is limited to single base pair conversions [21] while prime editing can only insert sequences of up to ~44bp. [22] [23] Hence GT remains the primary method of targeted (location-specific) insertion of long DNA sequences for genome engineering.  

Comparison with gene trapping

Gene trapping is based on random insertion of a cassette, while gene targeting manipulates a specific gene. Cassettes can be used for many different things while the flanking homology regions of gene targeting cassettes need to be adapted for each gene. This makes gene trapping more easily amenable for large scale projects than targeting. On the other hand, gene targeting can be used for genes with low transcriptions that would go undetected in a trap screen. The probability of trapping increases with intron size, while for gene targeting, small genes are just as easily altered.

Applications

Applications in mammalian systems

Gene targeting was developed in mammalian cells in the 1980s, [24] [25] [26] with diverse applications possible as a result of being able to make specific sequence changes at a target genomic site, such as the study of gene function or human disease, particularly in mice models. [27] Indeed, gene targeting has been widely used to study human genetic diseases by removing ("knocking out"), or adding ("knocking in"), specific mutations of interest. [28] [29] Previously used to engineer rat cell models, [30] [31] advances in gene targeting technologies enable a new wave of isogenic human disease models. These models are the most accurate in vitro models available to researchers and facilitate the development of personalized drugs and diagnostics, particularly in oncology. [32] Gene targeting has also been investigated for gene therapy to correct disease-causing mutations. However the low efficiency of delivery of the gene-targeting machinery into cells has hindered this, with research conducted into viral vectors for gene targeting to try and address these challenges. [33]

Applications in yeast and moss

Gene targeting is relatively high efficiency in yeast, bacterial and moss (but is rare in higher eukaryotes). Hence gene targeting has been used in reverse genetics approaches to study gene function in these systems. [34] [35] [36] [37] [38]

Applications in plant genome engineering

Gene targeting (GT), or homology-directed repair (HDR), is used routinely in plant genome engineering to insert specific sequences, [39] with the first published example of GT in plants in the 1980s. [15] However, gene targeting is particularly challenging in higher plants due to the low rates of Homologous Recombination, or Homology Directed Repair, in higher plants and the low rate of transformation (DNA uptake) by many plant species. [40] However, there has been much effort to increase the frequencies of gene targeting in plants in the past decades, [39] [40] [41] [42] as it is very useful to be able to introduce specific sequences in the plant genome for plant genome engineering. The most significant improvement to gene targeting frequencies in plants was the induction of double-strand-breaks through site specific nucleases such as CRISPR, as described above. Other strategies include in planta gene targeting, whereby the homology repair template is embedded within the plant genome and then liberated using CRISPR cutting; [43] upregulation of genes involved in the homologous recombination pathway; downregulation of the competing Non-Homologous-End-Joining pathway; [39] increasing copy numbers of the homologous repair template; [44] and engineering Cas variants to be optimised for plant tissue culture. [45] Some of these approaches have also been used to improve gene targeting efficiencies in mammalian cells. [46]

Plants that have been gene-targeted include Arabidopsis thaliana (the most commonly used model plant), rice, tomato, maize, tobacco and wheat. [40]

Technical challenges

Gene targeting holds enormous promise to make targeted, user-defined sequence changes or sequence insertions in the genome. However its primary applications - human disease modelling and plant genome engineering - are hindered by the low efficiency of homologous recombination in comparison to the competing non-homologous end joining in mammalian and higher plant cells. [47] As described above, there are strategies that can be employed to increase the frequencies of gene targeting in plants and mammalian cells. [37] In addition, robust selection methods that allow the selection or specific enrichment of cells where gene targeting has occurred can increase the rates of recovery of gene-targeted cells. [48]

2007 Nobel Prize

Mario R. Capecchi, Martin J. Evans and Oliver Smithies were awarded the 2007 Nobel Prize in Physiology or Medicine for their work on "principles for introducing specific gene modifications in mice by the use of embryonic stem cells", or gene targeting. [49]

Regulation of Gene Targeted organisms

As explained above, Gene Targeting is technically capable of creating a range of sizes of genetic changes; from single base-pair mutations through to insertion of longer sequences, including potentially transgenes. This means that products of gene targeting can be indistinguishable from natural mutation, or can be equivalent to GMOs due to their insertion of a transgene (see Venn diagram above). Hence regulating products of Gene Targeting can be challenging and different countries have taken different approaches or are reviewing how to do so as part of broader regulatory reviews into the products of gene-editing. [50] [51] [52] Broadly adopted classifications split gene-edited organisms into 3 classes of "SDN1-3", referring to Site Directed Nucleases (such as CRISPR-Cas) that are used to generate gene-edited organisms. [53] [16] These SDN classifications can guide national regulations as to which class of SDN they will consider to be ‘GMOs’ and therefore which are subject to potentially strict regulations. 

Historically the European Union (EU) has broadly been opposed to Genetic Modification technology, on grounds of its precautionary principle. In 2018 the European Court of Justice (ECJ) ruled that gene-edited crops (including gene-targeted crops) should be considered as genetically modified [55] and therefore were subject to the GMO Directive, which places significant regulatory burdens on GMO use. However this decision was received negatively by the European scientific community. [56] In 2021 the European Commission deemed that current EU legislation governing Genetic Modification and Gene-Editing techniques (or NGTs – New Genomic Techniques) was ‘not fit for purpose’ and needed adapting to reflect scientific and technological progress. [57] In July 2023 the European Commission published a proposal to change rules for certain products of gene-editing to reduce the regulatory requirements for organisms developed with gene-editing that contained genetic changes that could have occurred naturally. [58]

See also

Related Research Articles

Gene knockouts are a widely used genetic engineering technique that involves the targeted removal or inactivation of a specific gene within an organism's genome. This can be done through a variety of methods, including homologous recombination, CRISPR-Cas9, and TALENs.

Gene knockdown is an experimental technique by which the expression of one or more of an organism's genes is reduced. The reduction can occur either through genetic modification or by treatment with a reagent such as a short DNA or RNA oligonucleotide that has a sequence complementary to either gene or an mRNA transcript.

<span class="mw-page-title-main">Germline mutation</span> Inherited genetic variation

A germline mutation, or germinal mutation, is any detectable variation within germ cells. Mutations in these cells are the only mutations that can be passed on to offspring, when either a mutated sperm or oocyte come together to form a zygote. After this fertilization event occurs, germ cells divide rapidly to produce all of the cells in the body, causing this mutation to be present in every somatic and germline cell in the offspring; this is also known as a constitutional mutation. Germline mutation is distinct from somatic mutation.

<span class="mw-page-title-main">Homologous recombination</span> Genetic recombination between identical or highly similar strands of genetic material

Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids.

Gene editing may refer to:

A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis, has the potential to change the phenotype of an organism. Transgene describes a segment of DNA containing a gene sequence that has been isolated from one organism and is introduced into a different organism. This non-native segment of DNA may either retain the ability to produce RNA or protein in the transgenic organism or alter the normal function of the transgenic organism's genetic code. In general, the DNA is incorporated into the organism's germ line. For example, in higher vertebrates this can be accomplished by injecting the foreign DNA into the nucleus of a fertilized ovum. This technique is routinely used to introduce human disease genes or other genes of interest into strains of laboratory mice to study the function or pathology involved with that particular gene.

Recombineering is a genetic and molecular biology technique based on homologous recombination systems, as opposed to the older/more common method of using restriction enzymes and ligases to combine DNA sequences in a specified order. Recombineering is widely used for bacterial genetics, in the generation of target vectors for making a conditional mouse knockout, and for modifying DNA of any source often contained on a bacterial artificial chromosome (BAC), among other applications.

<span class="mw-page-title-main">Zinc-finger nuclease</span> Artificial enzymes

Zinc-finger nucleases (ZFNs) are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target specific desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes. By taking advantage of endogenous DNA repair machinery, these reagents can be used to precisely alter the genomes of higher organisms. Alongside CRISPR/Cas9 and TALEN, ZFN is a prominent tool in the field of genome editing.

<span class="mw-page-title-main">Insert (molecular biology)</span>

In Molecular biology, an insert is a piece of DNA that is inserted into a larger DNA vector by a recombinant DNA technique, such as ligation or recombination. This allows it to be multiplied, selected, further manipulated or expressed in a host organism.

Microhomology-mediated end joining (MMEJ), also known as alternative nonhomologous end-joining (Alt-NHEJ) is one of the pathways for repairing double-strand breaks in DNA. As reviewed by McVey and Lee, the foremost distinguishing property of MMEJ is the use of microhomologous sequences during the alignment of broken ends before joining, thereby resulting in deletions flanking the original break. MMEJ is frequently associated with chromosome abnormalities such as deletions, translocations, inversions and other complex rearrangements.

Meganucleases are endodeoxyribonucleases characterized by a large recognition site ; as a result this site generally occurs only once in any given genome. For example, the 18-base pair sequence recognized by the I-SceI meganuclease would on average require a genome twenty times the size of the human genome to be found once by chance. Meganucleases are therefore considered to be the most specific naturally occurring restriction enzymes.

<span class="mw-page-title-main">Transcription activator-like effector nuclease</span> Enzymes that cleave DNA in specific ways

Transcription activator-like effector nucleases (TALEN) are restriction enzymes that can be engineered to cut specific sequences of DNA. They are made by fusing a TAL effector DNA-binding domain to a DNA cleavage domain. Transcription activator-like effectors (TALEs) can be engineered to bind to practically any desired DNA sequence, so when combined with a nuclease, DNA can be cut at specific locations. The restriction enzymes can be introduced into cells, for use in gene editing or for genome editing in situ, a technique known as genome editing with engineered nucleases. Alongside zinc finger nucleases and CRISPR/Cas9, TALEN is a prominent tool in the field of genome editing.

<span class="mw-page-title-main">Genome editing</span> Type of genetic engineering

Genome editing, or genome engineering, or gene editing, is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the genome of a living organism. Unlike early genetic engineering techniques that randomly inserts genetic material into a host genome, genome editing targets the insertions to site-specific locations. The basic mechanism involved in genetic manipulations through programmable nucleases is the recognition of target genomic loci and binding of effector DNA-binding domain (DBD), double-strand breaks (DSBs) in target DNA by the restriction endonucleases, and the repair of DSBs through homology-directed recombination (HDR) or non-homologous end joining (NHEJ).

<span class="mw-page-title-main">Genetic engineering techniques</span> Methods used to change the DNA of organisms

Genetic engineering techniques allow the modification of animal and plant genomes. Techniques have been devised to insert, delete, and modify DNA at multiple levels, ranging from a specific base pair in a specific gene to entire genes. There are a number of steps that are followed before a genetically modified organism (GMO) is created. Genetic engineers must first choose what gene they wish to insert, modify, or delete. The gene must then be isolated and incorporated, along with other genetic elements, into a suitable vector. This vector is then used to insert the gene into the host genome, creating a transgenic or edited organism.

<span class="mw-page-title-main">Cas9</span> Microbial protein found in Streptococcus pyogenes M1 GAS

Cas9 is a 160 kilodalton protein which plays a vital role in the immunological defense of certain bacteria against DNA viruses and plasmids, and is heavily utilized in genetic engineering applications. Its main function is to cut DNA and thereby alter a cell's genome. The CRISPR-Cas9 genome editing technique was a significant contributor to the Nobel Prize in Chemistry in 2020 being awarded to Emmanuelle Charpentier and Jennifer Doudna.

<span class="mw-page-title-main">Gene drive</span> Way to propagate genes throughout a population

A gene drive is a natural process and technology of genetic engineering that propagates a particular suite of genes throughout a population by altering the probability that a specific allele will be transmitted to offspring. Gene drives can arise through a variety of mechanisms. They have been proposed to provide an effective means of genetically modifying specific populations and entire species.

No-SCAR genome editing is an editing method that is able to manipulate the Escherichia coli genome. The system relies on recombineering whereby DNA sequences are combined and manipulated through homologous recombination. No-SCAR is able to manipulate the E. coli genome without the use of the chromosomal markers detailed in previous recombineering methods. Instead, the λ-Red recombination system facilitates donor DNA integration while Cas9 cleaves double-stranded DNA to counter-select against wild-type cells. Although λ-Red and Cas9 genome editing are widely used technologies, the no-SCAR method is novel in combining the two functions; this technique is able to establish point mutations, gene deletions, and short sequence insertions in several genomic loci with increased efficiency and time sensitivity.

Off-target genome editing refers to nonspecific and unintended genetic modifications that can arise through the use of engineered nuclease technologies such as: clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9, transcription activator-like effector nucleases (TALEN), meganucleases, and zinc finger nucleases (ZFN). These tools use different mechanisms to bind a predetermined sequence of DNA (“target”), which they cleave, creating a double-stranded chromosomal break (DSB) that summons the cell's DNA repair mechanisms and leads to site-specific modifications. If these complexes do not bind at the target, often a result of homologous sequences and/or mismatch tolerance, they will cleave off-target DSB and cause non-specific genetic modifications. Specifically, off-target effects consist of unintended point mutations, deletions, insertions inversions, and translocations.

<span class="mw-page-title-main">CRISPR gene editing</span> Gene editing method

CRISPR gene editing (CRISPR, pronounced "crisper", refers to "clustered regularly interspaced short palindromic repeats") is a genetic engineering technique in molecular biology by which the genomes of living organisms may be modified. It is based on a simplified version of the bacterial CRISPR-Cas9 antiviral defense system. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added in vivo.

Prime editing is a 'search-and-replace' genome editing technology in molecular biology by which the genome of living organisms may be modified. The technology directly writes new genetic information into a targeted DNA site. It uses a fusion protein, consisting of a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase enzyme, and a prime editing guide RNA (pegRNA), capable of identifying the target site and providing the new genetic information to replace the target DNA nucleotides. It mediates targeted insertions, deletions, and base-to-base conversions without the need for double strand breaks (DSBs) or donor DNA templates.

References

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