New Frontiers for Site-Directed RNA Editing: Harnessing Endogenous ADARs.

RNA editing activity can be exploited for the restoration of disease-causing nonsense and missense mutations and as a tool to manipulate the transcriptome in a simple and programmable way. The general concept is called site-directed RNA editing and has high potential for translation into the clinics. Due to its different mode of action RNA editing may well complement gene editing and other gene therapy options. In this method chapter, we particularly highlight RNA editing strategies that harness endogenous ADARs. Such strategies circumvent the delivery and expression of engineered editases and are notably precise and simple. This is particularly true if endogenous ADARs are recruited with chemically modified antisense oligonucleotides, an approach we call RESTORE (recruiting endogenous ADAR to specific transcripts for oligonucleotide-mediated RNA editing). To foster the research and development of RESTORE we now report a detailed protocol for the procedure of editing reactions, and a protocol for the generation of partly chemically modified RESTORE ASOs with a combination of in vitro transcription and ligation.

[A new milestone in human embryo editing]. / CRISPR sur embryons humains : une nouvelle étape - Chroniques génomiques.

Viable human embryos carrying a disease mutation have now been corrected by CRISPR-Cas9 editing. Although the correction is not perfect, and the embryos have not been implanted, this brings us closer to human germline editing and to the associated ethical questions.

[The CRISPR case, « ready-made ¼ mutations and Lamarckian evolution of an adaptive immunity system]. / Le cas CRISPR, mutations « ready-made ¼ et évolution lamarckienne d'un système immunitaire adaptatif.

Since genetics has shown that mutation predates selection, biology has developed within the Darwinian paradigm framework. However, a mechanism that produces favorable mutations preferentially in response to adaptive constraints has been recently identified. This mechanism, the CRISPR-Cas adaptive immunity system, is considered as a bona fide example of Lamarckian evolution, even if it only reflects loosely Lamarck's ideas. This unusual evolutionary process is made possible by two prokaryotic properties: i) somatic and germinal cells are not distinct sets of cells; ii) Archae and Bacteria very frequently integrate DNA fragments from the environment, and they therefore have access to a source of "ready-made" useful genetic information. The CRISPR-Cas is a defense system against viruses and plasmids that is based on the integration of genomic fragments of these infectious agents into the host genome, and that protects the host against subsequent infections. Therefore, this mechanism does produce advantageous mutations by integrating DNA from the environment and allowing its transmission to descendants. In conclusion, most of the time evolution relies on purely Darwinian processes, i.e. mutations occurring at random, but in a small minority of cases the occurrence of mutations is more or less biased, and is therefore more or less Lamarckian. Although they are rare, such processes are nevertheless important to our understanding of the plurality of modes of evolution.

The expanding footprint of CRISPR/Cas9 in the plant sciences.

CRISPR/Cas9 has evolved and transformed the field of biology at an unprecedented pace. From the initial purpose of introducing a site specific mutation within a genome of choice, this technology has morphed into enabling a wide array of molecular applications, including site-specific transgene insertion and multiplexing for the simultaneous induction of multiple cleavage events. Efficiency, specificity, and flexibility are key attributes that have solidified CRISPR/Cas9 as the genome-editing tool of choice by scientists from all areas of biology. Within the field of plant biology, several CRISPR/Cas9 technologies, developed in other biological systems, have been successfully implemented to probe plant gene function and to modify specific crop traits. It is anticipated that this trend will persist and lead to the development of new applications and modifications of the CRISPR technology, adding to an ever-expanding collection of genome-editing tools. We envision that these tools will bestow plant researchers with new utilities to alter genome complexity, engineer site-specific integration events, control gene expression, generate transgene-free edited crops, and prevent or cure plant viral disease. The successful implementation of such utilities will represent a new frontier in plant biotechnology.

Progress of targeted genome modification approaches in higher plants.

Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.

Preferential protection of domains II and III of bacillus thuringiensis cry1Aa toxin by brush border membrane vesicles / Protección preferencial de los dominios II y III de la toxina cry1Aa de bacillus thuringiensis en vesículas de membrana de borde de cepillo

The surface exposed Leucine 371 on loop 2 of domain II, in Cry1Aa toxin, was mutated to Lysine to generate the trypsin-sensitive mutant, L371K. Upon trypsin digestion L371K is cleaved into approximately 37 and 26 kDa fragments. These are separable on SDS-PAGE, but remain as a single molecule of 65 kDa upon purification by liquid chromatography. The larger fragment is domain I and a portion of domain II (amino acid residues 1 to 371). The smaller 26-kDa polypeptide is the remainder of domain II and domain III (amino acids 372 to 609). When the mutant toxin was treated with high dose of M. sexta gut juice both fragments were degraded. However, when incubated with M. sexta BBMV, the 26 kDa fragment (domains II and III) was preferentially protected from gut juice proteases. As previously reported, wild type Cry1Aa toxin was also protected against degradation by gut juice proteases when incubated with M. sexta BBMV. On the contrary, when mouse BBMV was added to the reaction mixture neither Cry1Aa nor L371K toxins showed resistance to M. sexta gut juice proteases and were degraded. Since the whole Cry1Aa toxin and most of the domain II and domain III of L371K are protected from proteases in the presence of BBMV of the target insect, we suggest that the insertion of the toxin into the membrane is complex and involves all three domains.

La superficie de la toxina Cry1Aa, en el asa 2 del dominio II contiene expuesta la leucina 371, la cual fue modificada a lisina produciendo una mutante sensible a la tripsina, L371K. Esta mutante produce dos fragmentos de 37 y 26 kDa por acción de la tripsina que son separables por SDS-PAGE, pero que a la purificación por cromatografía líquida se mantienen como una sola molécula de 65 kDa. El fragmento grande contiene al dominio I y una parte del dominio II (aminoácidos 1 al 371). El polipéptido de 26 kDa contiene la parte restante del dominio II y dominio III (aminoácidos 372 al 609). Cuando la toxina mutante fue tratada con dosis altas de jugo intestinal de Manduca sexta, ambos fragmentos fueron degradados. Sin embargo, cuando fueron incubados en VMBC de M. sexta, el fragmento de 26 kDa fue protegido preferencialmente de las proteasas intestinales. Como se ha reportado, la toxina silvestre Cry1Aa también es protegida de la degradación de las proteasas cuando es incubada en VMBC de M. sexta. Sin embargo, cuando se adicionó VMBC de ratón a la mezcla de reacción, ni la toxina Cry1Aa ni la mutante L371K mostraron resistencia a las proteasas y fueron degradadas. Dado que la toxina completa de Cry1Aa y casi todo de los dominios II y III de L371K están protegidos de proteasas en presencia de VMBC del insecto, este estudio sugiere que la inserción de la toxina en la membrana involucra los tres dominios.

Progress and prospects: techniques for site-directed mutagenesis in animal models.

In the past 2 years, new gene-targeting approaches using adeno-associated virus and designer zinc-finger nucleases have been successfully applied to the production of genetically modified ferrets, pigs, mice and zebrafish. Gene targeting using these tools has been combined with somatic cell nuclear transfer and germ cell transplantation to generate gene-targeted animal models. These new technical advances, which do not require the generation of embryonic stem cell-derived chimeras, will greatly accelerate the production of non-mouse animal models for biomedical research.

Protein design by directed evolution.

While nature evolved polypeptides over billions of years, protein design by evolutionary mimicry is progressing at a far more rapid pace. The mutation, selection, and amplification steps of the evolutionary cycle may be imitated in the laboratory using existing proteins, or molecules created de novo from random sequence space, as starting templates. However, the astronomically large number of possible polypeptide sequences remains an obstacle to identifying and isolating functionally interesting variants. Intelligently designed libraries and improved search techniques are consequently important for future advances. In this regard, combining experimental and computational methods holds particular promise for the creation of tailored protein receptors and catalysts for tasks unimagined by nature.

Protein engineers turned evolutionists.

When generating novel tailor-made proteins, protein engineers routinely apply the principles of 'Darwinian' evolution. However, laboratory evolution of proteins also has the potential to test evolutionary theories and reproduce evolutionary scenarios, thus reconstructing putative protein intermediates and providing a glimpse of 'protein fossils'. This commentary describes research at the interface of applied and fundamental molecular evolution, and provides a personal view of how synergy between fundamental and applied experiments indicates novel and more efficient ways of generating new proteins in the laboratory.

Dissecting protein structure and function using directed evolution.

To characterize the contributions of individual amino acids to the structure or function of a protein, researchers have adopted directed evolution approaches, which use iterated cycles of mutagenesis and selection or screening to search vast areas of sequence space for sets of mutations that provide insights into the protein of interest.

GM maize from site-specific recombination technology, what next?

The term plant genetic engineering has long conveyed a highly efficient and precise process for the manipulation of plant genomes. For nearly two decades, research on recombinase-based applications has steadily advanced the surgical capabilities of plant genome rearrangements. Once considered interesting laboratory exercises, a first crop plant derived from this type of DNA acrobatics is heading to market. Originally configured for a specific application, to remove a selectable marker, it could be the first of more to come - and not just market-free plants.

[Site specific mutagenesis by homologous recombination in embryonic stem cells]. / Mutagenèse dirigée par recombinaison homologue dans les cellules ES.

Twenty years ago, the production of mice whose genomes have been deliberatly modified revolutionised biology. Indeed, it is now possible to eliminate a gene's expression to various levels in desired locations, and also to broadcast these genetic modifications created in vitro to the progeny. The isolation and culture of embryonic stem cells (ES) and the discovery of the mechanism of homologous recombination between two sequences of DNA in the 80's, have contributed to the development of site-directed mutagenesis. Today, site specific mutagenesis by homologous recombination in embryonic stem cells is a powerful technique and is widely used throughout the world. In parallel, new techniques to invalidate targeted genes are emerging. These genetics tools, which we will introduce, allow for a better understanding of a gene's function both in fundamental and clinical research. It is now possible to create murine models of human genetic diseases including Lesch-Nhyan syndrome, Adenomatous Polyposis and Duchenne muscular dystrophy which we will discuss as examples.