Targeted Gene Insertion Research Articles

BurrH: a new modular DNA binding protein for genome engineering

The last few years have seen the increasing development of new DNA targeting molecular tools and strategies for precise genome editing. However, opportunities subsist to either improve or expand the current toolbox and further broaden the scope of possible biotechnological applications. Here we report the discovery and the characterization of BurrH, a new modular DNA binding protein from Burkholderia rhizoxinica that is composed of highly polymorphic DNA targeting modules. We also engineered this scaffold to create a new class of designer nucleases that can be used to efficiently induce in vivo targeted mutagenesis and targeted gene insertion at a desired locus.

Production of CMAH Knockout Preimplantation Embryos Derived From Immortalized Porcine Cells Via TALE Nucleases

Although noncancerous immortalized cell lines have been developed by introducing genes into human and murine somatic cells, such cell lines have not been available in large domesticated animals like pigs. For immortalizing porcine cells, primary porcine fetal fibroblasts were isolated and cultured using the human telomerase reverse transcriptase (hTERT) gene. After selecting cells with neomycin for 2 weeks, outgrowing colonized cells were picked up and subcultured for expansion. Immortalized cells were cultured for more than 9 months without changing their doubling time (~24 hours) or their diameter (< 20 µm) while control cells became replicatively senescent during the same period. Even a single cell expanded to confluence in 100 mm dishes. Furthermore, to knockout the CMAH gene, designed plasmids encoding a transcription activator-like effector nuclease (TALENs) pairs were transfected into the immortalized cells. Each single colony was analyzed by the mutation-sensitive T7 endonuclease I assay, fluorescent PCR, and dideoxy sequencing to obtain three independent clonal populations of cells that contained biallelic modifications. One CMAH knockout clone was chosen and used for somatic cell nuclear transfer. Cloned embryos developed to the blastocyst stage. In conclusion, we demonstrated that immortalized porcine fibroblasts were successfully established using the human hTERT gene, and the TALENs enabled biallelic gene disruptions in these immortalized cells.

Ligation-independent cloning and self-cleaving intein as a tool for high-throughput protein purification

The rapid production of purified recombinant proteins has become increasingly important for countless applications. Many purification methods involve expression of target proteins in fusion to purification tags, which often must be removed from the target proteins after purification. Recently, engineered inteins have been used to create convenient self-cleaving tags for tag removal. Although intein methods can greatly simplify protein purification, commercially available expression vectors still rely on conventional restriction/ligation cloning methods for target gene insertion. We have streamlined this process by introducing Ligation-Independent Cloning (LIC) capability to our intein expression plasmids, which provides a simple method for constructing self-cleaving tag-target gene fusions. In this work, we demonstrate efficient gene insertion via this system, as well as target protein expression and purification consistent with previously reported results. Through this newly developed system, arbitrary protein genes can be rapidly incorporated into self-cleaving tag expression vectors, and their products purified using convenient platform methods.

Sleeping Beauty transposon-based system for cellular reprogramming and targeted gene insertion in induced pluripotent stem cells

The discovery of direct cell reprogramming and induced pluripotent stem (iPS) cell technology opened up new avenues for the application of non-viral, transposon-based gene delivery systems. The Sleeping Beauty (SB) transposon is highly advanced for versatile genetic manipulations in mammalian cells. We established iPS cell reprogramming of mouse embryonic fibroblasts and human foreskin fibroblasts by transposition of OSKM (Oct4, Sox2, Klf4 and c-Myc) and OSKML (OSKM + Lin28) expression cassettes mobilized by the SB100X hyperactive transposase. The efficiency of iPS cell derivation with SB transposon system was in the range of that obtained with retroviral vectors. Co-expression of the miRNA302/367 cluster together with OSKM significantly improved reprogramming efficiency and accelerated the temporal kinetics of reprogramming. The iPS cells displayed a stable karyotype, and hallmarks of pluripotency including expression of stem cell markers and the ability to differentiate into embryoid bodies in vitro. We demonstrate Cre recombinase-mediated exchange allowing simultaneous removal of the reprogramming cassette and targeted knock-in of an expression cassette of interest into the transposon-tagged locus in mouse iPS cells. This strategy would allow correction of a genetic defect by site-specific insertion of a therapeutic gene construct into ‘safe harbor’ sites in the genomes of autologous, patient-derived iPS cells.

Transcription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering

The ability to precisely engineer plant genomes offers much potential for advancing basic and applied plant biology. Here, we describe methods for the targeted modification of plant genomes using transcription activator-like effector nucleases (TALENs). Methods were optimized using tobacco (Nicotiana tabacum) protoplasts and TALENs targeting the acetolactate synthase (ALS) gene. Optimal TALEN scaffolds were identified using a protoplast-based single-strand annealing assay in which TALEN cleavage creates a functional yellow fluorescent protein gene, enabling quantification of TALEN activity by flow cytometry. Single-strand annealing activity data for TALENs with different scaffolds correlated highly with their activity at endogenous targets, as measured by high-throughput DNA sequencing of polymerase chain reaction products encompassing the TALEN recognition sites. TALENs introduced targeted mutations in ALS in 30% of transformed cells, and the frequencies of targeted gene insertion approximated 14%. These efficiencies made it possible to recover genome modifications without selection or enrichment regimes: 32% of tobacco calli generated from protoplasts transformed with TALEN-encoding constructs had TALEN-induced mutations in ALS, and of 16 calli characterized in detail, all had mutations in one allele each of the duplicate ALS genes (SurA and SurB). In calli derived from cells treated with a TALEN and a 322-bp donor molecule differing by 6 bp from the ALS coding sequence, 4% showed evidence of targeted gene replacement. The optimized reagents implemented in plant protoplasts should be useful for targeted modification of cells from diverse plant species and using a variety of means for reagent delivery.

In vivo genome editing restores haemostasis in a mouse model of haemophilia

Editing of the human genome to correct disease-causing mutations is a promising approach for the treatment of genetic disorders. Genome editing improves on simple gene-replacement strategies by effecting in situ correction of a mutant gene, thus restoring normal gene function under the control of endogenous regulatory elements and reducing risks associated with random insertion into the genome. Gene-specific targeting has historically been limited to mouse embryonic stem cells. The development of zinc finger nucleases (ZFNs) has permitted efficient genome editing in transformed and primary cells that were previously thought to be intractable to such genetic manipulation. In vitro, ZFNs have been shown to promote efficient genome editing via homology-directed repair by inducing a site-specific double-strand break (DSB) at a target locus, but it is unclear whether ZFNs can induce DSBs and stimulate genome editing at a clinically meaningful level in vivo. Here we show that ZFNs are able to induce DSBs efficiently when delivered directly to mouse liver and that, when co-delivered with an appropriately designed gene-targeting vector, they can stimulate gene replacement through both homology-directed and homology-independent targeted gene insertion at the ZFN-specified locus. The level of gene targeting achieved was sufficient to correct the prolonged clotting times in a mouse model of haemophilia B, and remained persistent after induced liver regeneration. Thus, ZFN-driven gene correction can be achieved in vivo, raising the possibility of genome editing as a viable strategy for the treatment of genetic disease.

90. Targeted Gene Insertion in Human Chromosomes Using a Homing Endonuclease

90. Targeted Gene Insertion in Human Chromosomes Using a Homing Endonuclease

Contribution of outer membrane protein K36 to antimicrobial resistance and virulence in Klebsiella pneumoniae

Loss of outer membrane protein (Omp) is commonly encountered in multidrug-resistant Klebsiella pneumoniae. However, little is known about the association between Omp loss and virulence. In the present study, this association was investigated in K. pneumoniae. An OmpK36-deficient mutant (DeltaOmpK36) was derived from a virulent clinical isolate by targeted gene insertion. Antimicrobial susceptibility was tested by microbroth dilution and disc diffusion. Virulence was assessed by serum resistance, phagocytosis, clearance of viable bacteria in the liver and lethality in mice following inoculation with bacteria. Susceptibility tests showed that DeltaOmpK36 contributed to the resistance to cefazolin and cefoxitin but not to resistance to late-generation cephalosporins. In vitro assays demonstrated that loss of OmpK36 decreased the resistance to neutrophil phagocytosis and increased the resistance to serum killing during the first hour of the assay, but did not influence the growth rate when compared with the parental strain. Intraperitoneal injection of similar doses ( approximately 4 x 10(4) cfu) of the parental strain and DeltaOmpK36 led to significantly fewer viable bacteria in the liver 24 h post-inoculation in DeltaOmpK36-inoculated mice. In the mice LD(50) (the bacterial dose that caused 50% death) assay, the parental strain was approximately 100-fold more lethal ( approximately 10(3) cfu) than the DeltaOmpK36 mutant ( approximately 10(5) cfu). Loss of OmpK36 in K. pneumoniae resulted in increased antimicrobial resistance, increased susceptibility to neutrophil phagocytosis, increased resistance to serum killing and reduced virulence.

Protein purification involving a unique auto-cleavage feature of a repeated EAAAK peptide

Protein purification generally requires many steps of column chromatography that typically involve ion-exchange, hydrophobic-interaction and gel-filtration separations. More sophisticated purification of protein might be achieved through an application of affinity binding on a functionalized gel such as a nickel column, glutathione-modified column, maltose-modified gel column or others. Of several drawbacks existing in these methods, fusion proteins are commonly obtained, protease digestion might be necessary to remove the fusion moiety; a costly gel is employed for affinity binding, etc. Here we report that an expression vector derived from pREST was constructed to compose the gene of the chitin-binding protein (CBP) and the nucleotide sequence of the (EAAAK)(5) peptide linker following restriction sites for target gene insertion. Fusion proteins were expressed with E. coli and purified with a chitin column. The (EAAAK)(5) linker is shown to possess a pH-dependent auto-cleavage feature. In the range pH 6-7, the target protein becomes automatically released from the fusion protein without proteolytic treatment. Although the mechanism of this auto-cleavage property of an (EAAAK)(5) linker is unclear, this feature has been successfully employed for many cases of protein purification without the tag of a fusion protein.

Protein purification involving a unique auto-cleavage feature of a repeated EAAAK peptide

Protein purification generally requires many steps of column chromatography that typically involve ion-exchange, hydrophobic-interaction and gel-filtration separations. More sophisticated purification of protein might be achieved through an application of affinity binding on a functionalized gel such as a nickel column, glutathione-modified column, maltose-modified gel column or others. Of several drawbacks existing in these methods, fusion proteins are commonly obtained, protease digestion might be necessary to remove the fusion moiety; a costly gel is employed for affinity binding, etc. Here we report that an expression vector derived from pREST was constructed to compose the gene of the chitin-binding protein (CBP) and the nucleotide sequence of the (EAAAK) 5 peptide linker following restriction sites for target gene insertion. Fusion proteins were expressed with E. coli and purified with a chitin column. The (EAAAK) 5 linker is shown to possess a pH-dependent auto-cleavage feature. In the range pH 6–7, the target protein becomes automatically released from the fusion protein without proteolytic treatment. Although the mechanism of this auto-cleavage property of an (EAAAK) 5 linker is unclear, this feature has been successfully employed for many cases of protein purification without the tag of a fusion protein.

325. Identification of Homing Endonuclease Cleavage Sites in Human Chromosome: Implication for Targeted Gene Insertion

325. Identification of Homing Endonuclease Cleavage Sites in Human Chromosome: Implication for Targeted Gene Insertion

Targeted gene insertion for molecular medicine

Genomic insertion of a functional gene together with suitable transcriptional regulatory elements is often required for long-term therapeutical benefit in gene therapy for several genetic diseases. A variety of integrating vectors for gene delivery exist. Some of them exhibit random genomic integration, whereas others have integration preferences based on attributes of the targeted site, such as primary DNA sequence and physical structure of the DNA, or through tethering to certain DNA sequences by host-encoded cellular factors. Uncontrolled genomic insertion bears the risk of the transgene being silenced due to chromosomal position effects, and can lead to genotoxic effects due to mutagenesis of cellular genes. None of the vector systems currently used in either preclinical experiments or clinical trials displays sufficient preferences for target DNA sequences that would ensure appropriate and reliable expression of the transgene and simultaneously prevent hazardous side effects. We review in this paper the advantages and disadvantages of both viral and non-viral gene delivery technologies, discuss mechanisms of target site selection of integrating genetic elements (viruses and transposons), and suggest distinct molecular strategies for targeted gene delivery.

Citations

Citations

Using Satellite Tobacco Mosaic Virus Vectors for Gene Silencing

This unit describes the use of satellite tobacco mosaic virus (STMV) vectors in combination with native TMV particles for inducing transient gene silencing in tobacco plants. Target gene fragment selection and insertion, virus delivery procedures, and phenotype screening of silenced plants are described in detail. All critical parameters for tobacco plant cultivation, virus infection, and RNA silencing efficiency are discussed.

Somatic cell nuclear transfer

Nuclear transfer research became front-page news when the birth of Dolly, the cloned ewe, was reported by Ian Wilmut and Keith Campbell in 1997. Since Dolly’s birth, offspring from many other species have been produced using somatic cell nuclear transfer. While Dolly’s birth transformed embryology research, her death in February 2003 marked the beginning of the next phase of research and development. This period will determine the scale of the commercial and societal benefits that accrue from somatic cell nuclear transfer and transgenics. Proof of concept for many of the potential benefits of somatic cell nuclear transfer has already been demonstrated. Desirable genotypes have been cloned, further insights into the nuclear reprogramming process have been achieved, and precision gene insertions/deletion has been demonstrated. It is likely that nuclear transfer can be adapted to ‘copy’ individuals from any mammalian species. Offspring have been produced using cells from sheep, mice, cattle, goats, pigs, rabbits and a cat. It appears very likely that copying of other species such as horses will follow shortly. However, early results from monkeys suggest that somatic cell nuclear transfer in primates may require further intensive study before the likelihood of success can be predicted. The nuclear transfer process is far less efficient at producing healthy offspring than the natural process of combining a sperm with an egg. Fewer normal embryos, fetuses and offspring are produced from somatic cell nuclear transfer than from other assisted breeding techniques. The reasons for this appear to be related to abnormal expression of key developmental genes. Many of these genes are imprinted genes, which rely on correct methylation patterns of the genome that are established in the first week of life. Research into this area not only aids further development of the nuclear transfer technique but is also important for basic research into understanding the nuclear reprogramming process in mammals. The combination of nuclear transfer with gene insertion/deletion techniques has permitted a quantum leap in the efficiency of producing livestock with an additional ‘value adding’ gene. This has resulted in more economical production of animals that carry a specific valuable gene, such as a gene to enable production of novel or valuable proteins in their milk. Precision gene insertions or deletions will become more available in the near term so that this technique will become as important for testing gene function for agricultural applications as it is in mice for biomedical uses. Our challenge for the next decade is to fine-tune the somatic cell nuclear transfer technique so as to achieve more normal development rates. At the same time we need to increase the efficiency of targeted gene insertion or deletion so that the 2 techniques can be effectively combined to utilise the information on gene function created by livestock gene discovery programs.

Engineering of the rpl23 gene cluster to replace the plastid RNA polymerase alpha subunit with the Escherichia coli homologue.

The Escherichia coli RNA polymerase (RNAP) alpha, beta, and beta' core subunits are evolutionarily conserved among bacteria and plastids, and the plastid specificity factors form a functional holoenzyme with the E. coli core. To investigate whether the E. coli core subunits may form a functional hybrid enzyme with the plastid core subunits, we replaced the tobacco plastid RNAP alpha subunit gene (rpoA) with the E. coli alpha subunit gene by targeted gene insertion. The transplastomic tobacco plants look similar to tobacco rpoA deletion mutants in that they are chlorophyll-deficient and nonphotoautotrophic. In addition, they lack transcripts from promoters recognized by the E. coli-like plastid RNA polymerase. These results indicate that evolutionary conservation between the E. coli and plastid RNA polymerase alpha subunits is insufficient to allow substitution of the tobacco alpha subunit with its bacterial counterpart. Interestingly, the cyanobacterial alpha subunits are as different as the E. coli alpha subunits; and therefore it is unlikely that replacement of the tobacco alpha subunit with cyanobacterial alpha subunits would yield a functional enzyme. Replacement of plastid rpoA with the E. coli RNA polymerase alpha subunit gene represents the first engineering of a plastid operon in higher plants.

Conditional gene knockout using cre recombinase.

The directed introduction of null mutations into defined genes has proven invaluable in elucidating gene function in a variety of experimental organisms. In the last decade or so this approach has been extended to mice (1) by the combined use of homologous recombination in murine embryonic stem (ES) cells to precisely target a mutation to a desired gene and subsequent derivation of mice carrying the targeted gene alteration from the genetically manipulated ES cells (e.g., by injection of gene- modified ES cells into blastocysts with subsequent germline transmission). In most instances null, or knockout (KO), mutations have been generated in mice by either simple insertion of a neo selectable marker in the target gene or neo insertion coupled with deletion of a critical region of the target gene. Targeted null mutations in a gene of interest, however, can lead to embryonic lethality in mice, thus obscuring the particular role of that gene in a target tissue or in the adult.

Current and future prospects for xenotransplantation.

The transplantation of organs and tissues between animal species, or xenotransplantation, is the focus of a growing field of research, owing primarily to the increasing shortage of allogeneic donor organs. The pig stands out as the most suitable donor animal for humans; however, xenografts (e.g. pig organs) used for human transplantation are normally destroyed by the host within minutes by hyperacute xenograft rejection. An improved understanding of the immune recognition and rejection of xenografts has resulted in new therapies that can partially overcome hyperacute rejection (HAR), delayed xenograft rejection (DXR) or acute vascular xenograft rejection. Strategies to diminish immunogenicity following xenotransplantation can be divided into two approaches: those directed at the recipient (e.g. antibodies or complement depletion or inhibition and tolerance induction) and those directed at the donor (e.g. transgenic modifications to express human complement-regulatory proteins or removal or displacement of alphaGal epitopes). DXR is likely to be controlled by transgenic inhibition of endothelial cell activation (e.g. inhibition of NF-kappaB). Transgenic pigs required for xenotransplantation will soon be generated at a greater efficiency and precision using nuclear transfer and cloning when compared to pronuclear injection. Of greater significance is that nuclear transfer offers the ability to target gene insertion selectively to specific gene loci and to delete specific genes in the pig. Experimental pig-to-primate organ xenotransplantation is currently under way, and results show increased transplant function from minutes to days and weeks. The final therapeutic regimen that allows survival of a discordant xenograft is likely to involve a combination of 'modified' functional genes in the donor organ, the development of immunological tolerance to pig antigens and administration of novel therapeutic agents, including immunosuppressants, that can control natural killer (NK) cell and monocyte mediated responses.

Introduction

The transplantation of organs and tissues between animal species, orxenotransplantation, is the focus of a growing field of research, owingprimarily to the increasing shortage of allogeneic donor organs. The pigstands out as the most suitable donor animal for humans; however, xenografts(e.g. pig organs) used for human transplantation are normally destroyed by thehost within minutes by hyperacute xenograft rejection. An improvedunderstanding of the immune recognition and rejection of xenografts hasresulted in new therapies that can partially overcome hyperacute rejection(HAR), delayed xenograft rejection (DXR) or acute vascular xenograftrejection. Strategies to diminish immunogenicity following xenotransplantationcan be divided into two approaches: those directed at the recipient (e.g.antibodies or complement depletion or inhibition and tolerance induction) andthose directed at the donor (e.g. transgenic modifications to express humancomplement-regulatory proteins or removal or displacement of αGalepitopes). DXR is likely to be controlled by transgenic inhibition ofendothelial cell activation (e.g. inhibition of NF-κB). Transgenic pigsrequired for xenotransplantation will soon be generated at a greaterefficiency and precision using nuclear transfer and cloning when compared topronuclear injection. Of greater significance is that nuclear transfer offersthe ability to target gene insertion selectively to specific gene loci and todelete specific genes in the pig. Experimental pig-to-primate organxenotransplantation is currently under way, and results show increasedtransplant function from minutes to days and weeks. The final therapeuticregimen that allows survival of a discordant xenograft is likely to involve acombination of ‘modified’ functional genes in the donor organ, thedevelopment of immunological tolerance to pig antigens and administration ofnovel therapeutic agents, including immunosuppressants, that can controlnatural killer (NK) cell and monocyte mediated responses.

Light-responsive and transcription-enhancing elements regulate the plastid psbD core promoter.

The psbD operon of higher plant plastids is regulated transcriptionally through the activity of an upstream light-responsive promoter. To identify promoter elements important for the regulation, portions of the tobacco psbD 5' region were fused to the reporter gene, uidA, and were introduced into the tobacco plastid genome by targeted gene insertion. Examination of uidA mRNA accumulation in dark-adapted and light-treated transplastomic plants revealed that a 107 bp segment of psbD 5' sequence was sufficient to promote light-responsive expression of the reporter gene in vivo. The 107 bp promoter region contains three pairs of short, repeated sequences upstream of the core promoter -10/-35 elements. Deletion of the upstream-most A-rich sequences resulted in a 5-fold decrease in reporter gene mRNA accumulation, but did not affect the light response. Additional removal of the second and third repeated elements further reduced the promoter strength approximately 30-fold and almost eliminated the light-dependent accumulation of uidA transcripts. These data indicate that the architecture of chloroplast promoters is more complex than previously assumed, and may comprise general enhancer and regulatory elements in addition to the core promoter motifs. Transcriptional regulation of psbD may be mediated by the chloroplast proteins which were shown to interact with the repeated sequences.