Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential

Sargent, R. Geoffrey; Kim, Soya; Gruenert, Dieter C.

doi:10.1089/oli.2010.0273

Cited by 21 publications

(23 citation statements)

References 258 publications

(292 reference statements)

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“…Successful targeted chromosomal deletions, duplications and inversions using ZFN [5, 9, 23–25] prompt us to investigate the possibility of targeted GSV using TALEN. We have previously shown that simultaneous expression of two TALENs could mediate heritable 792 bp segment deletion in silkworm, B. mori [11], which was also supported by similar investigations in livestock [12] and zebrafish [26].…”

Section: Discussionmentioning

confidence: 99%

Multiplex genomic structure variation mediated by TALEN and ssODN

Wang

Liu

et al. 2014

BMC Genomics

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BackgroundGenomic structure variation (GSV) is widely distributed in various organisms and is an important contributor to human diversity and disease susceptibility. Efficient approaches to induce targeted genomic structure variation are crucial for both analytic and therapeutic studies of GSV. Here, we presented an efficient strategy to induce targeted GSV including chromosomal deletions, duplications and inversions in a precise manner.ResultsUtilizing Transcription Activator-Like Effector Nucleases (TALEN) designed to target two distinct sites, we demonstrated targeted deletions, duplications and inversions of an 8.9 Mb chromosomal segment, which is about one third of the entire chromosome. We developed a novel method by combining TALEN-induced GSV and single stranded oligodeoxynucleotide (ssODN) mediated gene modifications to reduce unwanted mutations occurring during the targeted GSV using TALEN or Zinc finger nuclease (ZFN). Furthermore, we showed that co-introduction of TALEN and ssODN generated unwanted complex structure variation other than the expected chromosomal deletion.ConclusionsWe demonstrated the ability of TALEN to induce targeted GSV and provided an efficient strategy to perform GSV precisely. Furthermore, it is the first time to show that co-introduction of TALEN and ssODN generated unwanted complex structure variation. It is plausible to believe that the strategies developed in this study can be applied to other organisms, and will help understand the biological roles of GSV and therapeutic applications of TALEN and ssODN.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-41) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Multiplex genomic structure variation mediated by TALEN and ssODN

Wang

Liu

et al. 2014

BMC Genomics

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“…RDOs are a class of oligonucleotides used for gene targeting with a correction efficiency of approximately 50 %; however, the reproducibility of these studies has been limited in mammalian systems (Sargent et al 2011). TFOs are ssODNs that are typically 10-40 nt in length and bind to specific regions in duplex DNA as a third strand to form a triple helix.…”

Section: Missense Mutationsmentioning

confidence: 99%

“…TFOs are ssODNs that are typically 10-40 nt in length and bind to specific regions in duplex DNA as a third strand to form a triple helix. TFOs act in polypurine or polypyrimidine regions of DNA and bind DNA via Hoogsteen hydrogen bonds (Sargent et al 2011, Pauwels et al 2014.…”

Section: Missense Mutationsmentioning

confidence: 99%

New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals

Velho

Sperb‐Ludwig

Schwartz

2015

An. Acad. Bras. Ciênc.

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With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

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“…Our current knowledge on the basic mechanisms of OTNE originates from several studies performed exclusively on microorganisms and mammalian cells (Bonner and Kmiec 2009;Engstrom and Kmiec 2007;Sargent et al 2011). According to the widely accepted general model, after invading the targeted site of the duplex DNA, SDOs are hybridized to the complementary strand through transient D-loop formation.…”

Section: Introductionmentioning

confidence: 99%

Relaxed chromatin induced by histone deacetylase inhibitors improves the oligonucleotide-directed gene editing in plant cells

et al. 2017

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Improving efficiency of oligonucleotide-directed mutagenesis (ODM) is a prerequisite for wide application of this gene-editing approach in plant science and breeding. Here we have tested histone deacetylase inhibitor treatments for induction of relaxed chromatin and for increasing the efficiency of ODM in cultured maize cells.For phenotypic assay we produced transgenic maize cell lines expressing the non-functional Green Fluorescent Protein (mGFP) gene carrying a TAG stop codon. These transgenic cells were bombarded with corrective oligonucleotide as editing reagent to recover GFP expression. Repair of green fluorescent protein function was monitored by confocal fluorescence microscopy and flow cytometry was used for quantification of correction events. Sequencing PCR fragments of the GFP gene from corrected cells indicated a nucleotide exchange in the stop codon (TAG) from T to G nucleotide that resulted in the restoration of GFP function. We show that pretreatment of maize cells with sodium butyrate (5-10 mM) and nicotinamide (1-5 mM) as known inhibitors of 2 histone deacetylases can cause elevated chromatin sensitivity to DNase I that was visualized in agarose gels and confirmed by the reduced presence of intact PCR template for the inserted exogenous mGFP gene. Maize cells with more relaxed chromatin could serve as an improved recipient for targeted nucleotide exchange as indicated by an average of 2.67-3.62-fold increase in GFP-positive cells. Our results stimulate further studies on the role of the condition of the recipient cells in ODM and testing the application of chromatin modifying agents in other, programmable nuclease-based genome-editing techniques in higher plants.

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Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential

Cited by 21 publications

References 258 publications

Multiplex genomic structure variation mediated by TALEN and ssODN

Multiplex genomic structure variation mediated by TALEN and ssODN

New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals

Relaxed chromatin induced by histone deacetylase inhibitors improves the oligonucleotide-directed gene editing in plant cells

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