Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment

Triplex-forming oligonucleotides (TFOs) are synthetic DNA code-reading molecules that have been demonstrated to function to some extent in chromatin within cell nuclei. Here we have investigated the impact of DNA nuclear environment on the efficiency of TFO binding. For this study we have used locked nucleic acid-containing TFOs (TFO/LNAs) and we report the development of a rapid PCR-based method to quantify triplex formation. We have first compared triplex formation on genes located at different genomic sites and containing the same oligopyrimidine•oligopurine sequence. We have shown that efficient TFO binding is possible on both types of genes, expressed and silent. Then we have further investigated when gene transcription may influence triplex formation in chromatin. We have identified situations where for a given gene, increase of transcriptional activity leads to enhanced TFO binding: this was observed for silent or weakly expressed genes that are not or are only slightly accessible to TFO. Such a transcriptional dependence was observed for integrated and endogenous loci, and chemical and biological activations of transcription. Finally, we provide evidence that TFO binding is sequence-specific as measured on mutated target sequences and that up to 50% of chromosomal targets can be covered by the TFO/LNA in living cells

High doses of CRISPR/Cas9 ribonucleoprotein efficiently induce gene knockout with low mosaicism in the hydrozoan Clytia hemisphaerica through microhomology-mediated deletion

Targeted mutagenesis using CRISPR/Cas9 technology has been shown to be a powerful approach to examine gene function in diverse metazoan species. One common drawback is that mixed genotypes, and thus variable phenotypes, arise in the F0 generation because incorrect DNA repair produces different mutations amongst cells of the developing embryo. We report here an effective method for gene knockout (KO) in the hydrozoan Clytia hemisphaerica, by injection into the egg of Cas9/sgRNA ribonucleoprotein complex (RNP). Expected phenotypes were observed in the F0 generation when targeting endogenous GFP genes, which abolished fluorescence in embryos, or CheRfx123 (that codes for a conserved master transcriptional regulator for ciliogenesis) which caused sperm motility defects. When high concentrations of Cas9 RNP were used, the mutations in target genes at F0 polyp or jellyfish stages were not random but consisted predominantly of one or two specific deletions between pairs of short microhomologies flanking the cleavage site. Such microhomology-mediated (MM) deletion is most likely caused by microhomology-mediated end-joining (MMEJ), which may be favoured in early stage embryos. This finding makes it very easy to isolate uniform, largely non-mosaic mutants with predictable genotypes in the F0 generation in Clytia, allowing rapid and reliable phenotype assessment

A hybrid CMV-H1 construct improves efficiency of PEI-delivered shRNA in the mouse brain

RNA-interference-driven loss of function in specific tissues in vivo should permit analysis of gene function in temporally and spatially defined contexts. However, delivery of efficient short hairpin RNA (shRNA) to target tissues in vivo remains problematic. Here, we demonstrate that efficiency of polyethylenimine (PEI)-delivered shRNA depends on the regulatory sequences used, both in vivo and in vitro. When tested in vivo, silencing of a luciferase target gene by shRNA produced from a hybrid construct composed of the CMV enhancer/promoter placed immediately upstream of an H1 promoter (50%) exceeds that obtained with the H1 promoter alone (20%). In contrast, in NIH 3T3 cells, the H1 promoter was more efficient than the hybrid construct (75 versus 60% inhibition of target gene expression, respectively). To test CMV-H1 shRNA efficiency against an endogenous gene in vivo, we used shRNA against thyroid hormone receptor α1 (TRα1). When vectorized in the mouse brain, the hybrid construct strongly derepressed CyclinD1-luciferase reporter gene expression, CyclinD1 being a negatively regulated thyroid hormone target gene. We conclude that promoter choice affects shRNA efficiency distinctly in different in vitro and in vivo situations and that a hybrid CMV-H1 construct is optimal for shRNA delivery in the mouse brain

Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities

Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5′-conjugation of an intercalating agent, an acridine derivative. In vitro a stable triplex was formed with the TFO-acridine conjugate: by SPR measurements at 37°C and neutral pH, the dissociation equilibrium constant was found in the nanomolar range and the triplex half-life ∼10 h (50-fold longer compared with the unconjugated TFO/LNA). Moreover to further understand DNA binding of (T,C)-containing TFO/LNAs, hybridization studies were performed at different pH values: triplex stabilization associated with pH decrease was mainly due to a slower dissociation process. Finally, biological activity of pyrimidine TFO/LNAs was evaluated in a cellular context: it occurred at concentrations ∼0.1 μM for acridine-conjugated TFO/LNA (or ∼2 μM for the unconjugated TFO/LNA) whereas the corresponding phosphodiester TFO was inactive, and it was demonstrated to be triplex-mediated

Stable transmission of targeted gene modification using single-stranded oligonucleotides with flanking LNAs

Targeted mutagenesis directed by oligonucleotides (ONs) is a promising method for manipulating the genome in higher eukaryotes. In this study, we have compared gene editing by different ONs on two new target sequences, the eBFP and the rd1 mutant photoreceptor βPDE cDNAs, which were integrated as single copy transgenes at the same genomic site in 293T cells. Interestingly, antisense ONs were superior to sense ONs for one target only, showing that target sequence can by itself impart strand-bias in gene editing. The most efficient ONs were short 25 nt ONs with flanking locked nucleic acids (LNAs), a chemistry that had only been tested for targeted nucleotide mutagenesis in yeast, and 25 nt ONs with phosphorothioate linkages. We showed that LNA-modified ONs mediate dose-dependent target modification and analyzed the importance of LNA position and content. Importantly, when using ONs with flanking LNAs, targeted gene modification was stably transmitted during cell division, which allowed reliable cloning of modified cells, a feature essential for further applications in functional genomics and gene therapy. Finally, we showed that ONs with flanking LNAs aimed at correcting the rd1 stop mutation could promote survival of photoreceptors in retinas of rd1 mutant mice, suggesting that they are also active in vivo

Homology-directed repair in rodent zygotes using Cas9 and TALEN engineered proteins

International audienceThe generation of genetically-modified organisms has been revolutionized by the development of new genome editing technologies based on the use of gene-specific nucleases, such as meganucleases, ZFNs, TALENs and CRISPRs-Cas9 systems. The most rapid and cost-effective way to generate genetically-modified animals is by microinjection of the nucleic acids encoding gene-specific nucleases into zygotes. However, the efficiency of the procedure can still be improved. In this work we aim to increase the efficiency of CRISPRs-Cas9 and TALENs homology-directed repair by using TALENs and Cas9 proteins, instead of mRNA, microinjected into rat and mouse zygotes along with long or short donor DNAs. We observed that Cas9 protein was more efficient at homology-directed repair than mRNA, while TALEN protein was less efficient than mRNA at inducing homology-directed repair. Our results indicate that the use of Cas9 protein could represent a simple and practical methodological alternative to Cas9 mRNA in the generation of genetically-modified rats and mice as well as probably some other mammals

Sequence-specific DNA cleavage mediated by bipyridine polyamide conjugates

The design of molecules that damage a selected DNA sequence provides a formidable opportunity for basic and applied biology. For example, such molecules offer new prospects for controlled manipulation of the genome. The conjugation of DNA-code reading molecules such as polyamides to reagents that induce DNA damages provides an approach to reach this goal. In this work, we showed that a bipyridine conjugate of polyamides was able to induce sequence-specific DNA breaks in cells. We synthesized compounds based on two polyamide parts linked to bipyridine at different positions. Bipyridine conjugates of polyamides were found to have a high affinity for the DNA target and one of them produced a specific and high-yield cleavage in vitro and in cultured cells. The bipyridine conjugate studied here, also presents cell penetrating properties since it is active when directly added to cell culture medium. Harnessing DNA damaging molecules such as bipyridine to predetermined genomic sites, as achieved here, provides an attractive strategy for targeted genome modification and DNA repair studies

Vectorisation d'oligonucleotides par la vitamine b2

Les oligonucléotides antisens et leurs analogues, tels que les Peptide Nucleic Acids (PNA), ont la capacité d'inhiber ou de moduler l'expression d'un gène cible, de manière spécifique de séquence. Leur utilisation pour des applications thérapeutiques est cependant limitée par leur faible internalisation cellulaire ou leur mauvaise localisation intracellulaire, etnécessite le développement de stratégies efficaces de vectorisation. La Riboflavine, ou vitamine B2, est une vitamine essentielle qui a les caractéristiques requises pour être potentiellement utilisée en tant qu'agent ciblant de vectorisation. Le travail accompli au cours de ce projet de thèse a permis de démontrer la capacité de deux dérivés de la Riboflavine, la Flavine et le Lumichrome, à induire une internalisation par endocytose de PNA conjugués, dans plusieurs lignées cellulaires. En outre, un phénomène d'internalisation photochimique induit par la Rhodamine a été mis en évidence avec des double-conjugués Flavine ou Lumichrome - PNA - Rhodamine et conduit à une sortie efficace des endosomes de ces conjugués. Ce travail de thèse a donc permis de caractériser un conjugué trifonctionnel pour l'internalisation et lalibération cytoplasmique de molécules bioactives.Antisense oligonucleotides and analogs, such as Peptide Nucleic Acids (PNA), are valuable tools to inhibit or modulate gene expression in a sequence-specific manner. Their successful application for therapeutic purposes is however hampered by poor cellular uptake or incorrect intracellular localization, and requires the development of efficient delivery strategies.Riboflavin, or vitamin B2, is an essential vitamin that could potentially be used as a targeting delivery ligand. We demonstrate in this PhD work the ability of two Riboflavin derivatives, Flavin and Lumichrome, to promote endocytosis-mediated internalization of PNA conjugates in several cell lines. Furthermore, a phenomenon of Photochemical Internalization produced by Rhodamine has been characterized using Flavin or Lumichrome - PNA - Rhodamine conjugatesand is responsible for an efficient release of these conjugates from endosomes. This PhD work has thus led to the characterization of a trifunctional conjugate for the internalization and cytoplasmic delivery of bioactive molecules.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Les "Locked Nucleic Acids" pour la stratégie anti-gène (de la fixation sur l'ADN aux applications fonctionnelles)

Nous avons caractérisé des oligonucléotides capables de former une triple-hélice (OFT) chimiquement modifiés sous forme de Locked Nucleic Acids (LNA), les OFT/LNA : 1/ Propriétés anti-gènes: Les OFT/LNA sont capables de former in vitro des complexes très stables et sélectifs de la séquence d ADN cible. Cette stabilité thermodynamique permet la formation intracellulaire d un triplexe stable. 2/ Fixation dans la chromatine Nous avons montré que la fixation des OFT/LNA est spécifique de la séquence ciblée (jusqu à 50% de fixation) et que son efficacité est corrélée à l accessibilité de la chromatine, l OFT/LNA se fixant mieux sur les régions décompactées. 3/ Induction de coupures double-brin ciblées Ces ligands de l AD (OFT/LNA) ont été couplés à un agent de coupure, la phénanthroline (OP) pour obtenir des coupures double-brin de façon spécifique dans les cellules. Le taux de modification spécifique est de 50% sur cible épisomale. La coupure endogène est en cours de caractérisation.We have studied triplex-forming oligonucleotides (TFO), chemically modified as Locked Nucleic Acids (LNA), the TFO/LNA: 1/ Anti-gene properties TFO/LNA are able to form highly stable and specific complexes on the DNA target sequence in vitro. This thermodynamic stability leads to stable triplex formation in cells. 2/ Binding in the chromatine structure We have characterized TFO/LNA binding in chromatin and evaluated the cellular factors driving binding efficiency. We have shown that about 50% of the chromosomal target can be covered by the TFO specifically, and that the efficiency of TFO binding in chromatin was correlated to chromatin accessibility: TFO did bind more efficiently to unfolded chromatin regions. 3/ Induction of targeted DNA damages We have studied TFO covalently linked to a cleaving agent, the phenanthroline (OP). In cells, DNA modifications occur specifically at 50% of the episomal target plasmid. We are presently running experiments on chromosomally located target sites.PARIS-Museum Hist.Naturelle (751052304) / SudocSudocFranceF