Targeting multi-cellular organisms

A review on advanced methods in plant gene targeting

Plant genetic engineering is one of the most significant tools implemented in the modern molecular crop breeding techniques. The conventional approaches of plant genetic transformation include Agrobacterium tumefaciens, particle bombardment, DNA uptake into protoplast. The transgenic events derived by these methods carry the transgenes that are integrated at random sites in the plant genome. Novel techniques that mediate integration of foreign genes at specific pre-determined locations circumvent many problems associated with the existing methods of gene transfer. The recent years have witnessed the emergence of gene targeting techniques by employing zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindrome repeats (CRISPR). The present review focuses on the various approaches and their performance of plant gene targeting and suggests future directions in the important areas of plant molecular biology.

PCR-mediated one-step deletion of targeted chromosomal regions in haploid Saccharomyces cerevisiae

Chromosome rearrangements, especially chromosomal deletions, have been exploited as important resources for functional analysis of genomes. To facilitate this analysis, we applied a previously developed method for chromosome splitting for the direct deletion of a designed internal or terminal chromosomal region carrying many nonessential genes in haploid Saccharomyces cerevisiae. The method, polymerase chain reaction (PCR)-mediated chromosomal deletion (PCD), consists of a two-step PCR and one transformation per deletion event. In this paper, we show that the PCD method efficiently deletes internal regions in a single transformation. Of the six chromosomal regions targeted for deletion by this method, five regions (16 to 38 kb in length) containing 10 to 19 nonessential genes were successfully eliminated at high efficiency. The one targeted region on chromosome XIII that was not deleted was subsequently found to contain sequences essential for yeast growth. While 14 individual genes in this region have been reported to be nonessential, synthetic lethal interactions may occur among these nonessential genes. Phenotypic analysis showed that four deletion strains still exhibited normal growth while possible synthetic growth defects were observed in another strain harboring a 19-gene deletion on chromosome XV. These results demonstrate that the PCD method is a useful tool for deleting genes and for analyzing their functions in defined chromosomal regions.

Neurogenetics of courtship and mating in Drosophila

The reproductive biology of Drosophila melanogaster is described and critically discussed, primarily with regard to genetic studies of sex-specific behavior and its neural underpinnings. The investigatory history of this system includes, in addition to a host of recent neurobiological analyses of reproductive phenotypes, studies of mating as well as the behaviors leading up to that event. Courtship and mating have been delved into mostly with regard to male-specific behavior and biology, although a small number of studies has also pointed to the neural substrates of female reproduction. Sensory influences on interactions between courting flies have long been studied, partly by application of mutants and partly by surgical experiments. More recently, molecular-genetic approaches to sensations passing between flies in reproductive contexts have aimed to "dissect" further the meaning of separate sensory modalities. Notable among these are olfactory and contact-chemosensory stimuli, which perhaps have received an inordinate amount of attention in terms of the possibility that they could comprise the key cues involved in triggering and sustaining courtship actions. But visual and auditory stimuli are heavily involved as well--appreciated mainly from older experiments, but analyzable further using elementary approaches (single-gene mutations mutants and surgeries), as well as by applying the molecularly defined factors alluded to above. Regarding regulation of reproductive behavior by components of Drosophila's central nervous system (CNS), once again significant invigoration of the relevant inquiries has been stimulated and propelled by identification and application of molecular-genetic materials. A distinct plurality of the tools applied involves transposons inserted in the fly's chromosomes, defining "enhancer-trap" strains that can be used to label various portions of the nervous system and, in parallel, disrupt their structure and function by "driving" companion transgenes predesigned for these experimental purposes. Thus, certain components of interneuronal routes, functioning along pathways whose starting points are sensory reception by the peripheral nervous system (PNS), have been manipulated to enhance appreciation of sexually important sensory modalities, as well as to promote understanding of where such inputs end up within the CNS: Where are reproductively related stimuli processed, such that different kinds of sensation would putatively be integrated to mediate sex-specific behavioral readouts? In line with generic sensory studies that have tended to concentrate on chemical stimuli, PNS-to-CNS pathways focused upon in reproductive experiments relying on genic enhancers have mostly involved smell and taste. Enhancer traps have also been applied to disrupt various regions within the CNS to ask about the various ganglia, and portions thereof, that contribute to male- or female-specific behavior. These manipulations have encompassed structural or functional disruptions of such regions as well as application of molecular-genetic tricks to feminize or masculinize a given component of the CNS. Results of such experiments have, indeed, identified certain discrete subsets of centrally located ganglia that, on the one hand, lead to courtship defects when disrupted or, on the other, must apparently maintain sex-specific identity if the requisite courtship actions are to be performed. As just implied, perturbations of certain neural tissues not based on manipulating "sex factors" might lead to reproductive behavioral abnormalities, even though changing the sexual identity of such structures would not necessarily have analogous consequences. It has been valuable to uncover these sexually significant subsets of the Drosophila nervous system, although it must be said that not all of the transgenically based dissection outcomes are in agreement. Thus, the good news is that not all of the CNS is devoted to courtship control, whereby any and all locales disrupted might have led to sex-specific deficits; but the bad news is that the enhancer-trap approach to these matters has not led to definitive homing-in on some tractable number of mutually agreed-upon "courtship centers" within the brain or within the ventral nerve cord (VNC). The latter neural region, which comprises about half of the fly's CNS, is underanalyzed as to its sex-specific significance: How, for example, are various kinds of sensory inputs to posteriorly located PNS structures processed, such that they eventually end up modulating brain functions underlying courtship? And how are sex-specific motor outputs mediated by discrete collections of neurons within VNC ganglia--so that, for instance, male-specific whole-animal motor actions and appendage usages are evoked? These behaviors can be thought of as fixed action patterns. But it is increasingly appreciated that elements of the fly's reproductive behavior can be modulated by previous experience. In this regard, the neural substrates of conditioned courtship are being more and more analyzed, principally by further usages of various transgenic types. Additionally, a set of molecular neurogenetic experiments devoted to experience-dependent courtship was based on manipulations of a salient "sex gene" in D. melanogaster. This well-defined factor is called fruitless (fru). The gene, its encoded products, along with their behavioral and neurobiological significance, have become objects of frenetic attention in recent years. How normal, mutated, and molecularly manipulated forms of fru seem to be generating a good deal of knowledge and insight about male-specific courtship and mating is worthy of much attention. This previews the fact that fruitless matters are woven throughout this chapter as well as having a conspicuous section allocated to them. Finally, an acknowledgment that the reader is being subjected to lengthy preview of an article about this subject is given. This matter is mentioned because--in conjunction with the contemporary broadening and deepening of this investigatory area--brief summaries of its findings are appearing with increasing frequency. This chapter will, from time to time, present our opinion that a fair fraction of the recent minireviews are replete with too many catch phrases about what is really known. This is one reason why the treatment that follows not only attempts to describe the pertinent primary reports in detail but also pauses often to discuss our views about current understandings of sex-specific behavior in Drosophila and its underlying biology.

Gene conversion in transgenic maize plants expressing FLP/FRT and Cre/loxP site-specific recombination systems

DNA recombination reactions (site-specific and homologous) were monitored in the progeny of transgenic maize plants by bringing together two recombination substrates (docking sites and shuttle vectors) in the zygotes. In one combination of transgenic events, the recombination marker gene (yellow fluorescent protein gene, YFP) was activated in 1%-2% of the zygotes receiving both substrates. In other crosses, chimeric embryos and plants were identified, indicative of late recombination events taking place after the first mitotic division of the zygotes. The docking site structure remained unchanged; therefore, all recovered recombination events were classified as gene conversions. The recombinant YFP-r gene segregated as a single locus in subsequent generations. The recombination products showed evidence of homologous recombination at the 5' end of the YFP marker gene and recombinational rearrangements at the other end, consistent with the conclusion that DNA replication was involved in generation of the recombination products. Here, we demonstrate that maize zygotes are efficient at generating homologous recombination products and that the homologous recombination pathways may successfully compete with other possible DNA repair/recombination mechanisms such as site-specific recombination. These results indicate that maize zygotes provide a permissive environment for homologous recombination, offering a new strategy for gene targeting in maize.

Modification of endogenous natural genes by gene targeting in rice and other higher plants

The capability to modify a genomic sequence into a designed sequence is a powerful tool for biologists and breeders to elucidate the function of an individual gene and its cis-acting elements of multigene families in the genome. Gene targeting refers to the alteration of a specific DNA sequence in an endogenous gene at its original locus in the genome. In higher plants, however, the overwhelming occurrence of the random integration of transgenes by non-homologous end-joining is the main obstacle to develop efficient gene targeting. Two approaches have been undertaken to modify a genomic sequence in higher plants- chimeric RNA/DNA oligonucleotide-directed gene targeting to generate a site-specific base conversion, and homologous recombination-dependent gene targeting to produce either a base change or a gene replacement in a sequence-specific manner. The successful and reproducible targeting of an endogenous gene by homologous recombination, independently of gene-specific selection by employing a strong positive-negative selection, has been demonstrated for the first time in rice, an important staple food and a model plant for other cereal species. This review addresses the current status of targeting of an endogenous natural gene in rice and other higher plants and discusses possible models for Agrobacterium- mediated gene targeting by homologous recombination using a strong positive-negative selection.

Enhancing gene targeting efficiency in higher plants: rice is on the move

Meeting the challenge of routine gene targeting (GT) in higher plants is of crucial interest to researchers and plant breeders who are currently in need of a powerful tool to specifically modify a given locus in a genome. Higher plants have long been considered the last lineage resistant to targeting technology. However, a recent report described an efficient method of T-DNA-mediated targeted disruption of a non-selectable locus in rice [Terada et al., Nat Biotechnol 20: 1030-1034 (2002)]. Though this study was an obvious breakthrough, further improvement of GT frequencies may derive from a better understanding of the natural mechanisms that control homologous recombination (HR) processes. In this review, we will focus on what is known about HR and the factors which may hamper the development of routine GT by HR in higher plants. We will also present the current strategies envisaged to overcome these limitations, such as expression of recombination proteins and refinements in the design of the transformation vector.

P element excision and repair by non-homologous end joining occurs in both G1 and G2 of the cell cycle

P element excision generates a DNA double-strand break at the transposon donor site. Genetic studies have demonstrated a strong bias toward repair of P element-induced DNA breaks by homologous recombination with the sister chromatid, suggesting that P element excision occurs after DNA replication, in G2 of the cell cycle. We developed methods to arrest Drosophila tissue culture cells and assay P element excision in either G1- or G2-arrested cells. Dacapo or tribbles transgene expression arrests cells in either G2 or G2, respectively. RNA-mediated gene interference (RNAi) directed against cyclin E or cyclin A arrests cells in G1 or G2, respectively. P element excision occurs efficiently in both G1- and G2-arrested cells, suggesting that cell cycle regulation of P element transposase does not occur in our somatic cell system. DNA double-strand break repair occurs by two predominant mechanisms: homologous recombination (HR) and non-homologous end joining (NHEJ). HR is thought to be restricted to the post-replicative, G2, phase of the cell cycle, while NHEJ may occur throughout the cell cycle. Our results indicate that NHEJ repair of an extrachromasomal plasmid substrate occurs at least as efficiently in G2-arrested cells as in asynchronous cells or in G1-arrested cells.

Emerging technologies for gene manipulation in Drosophila melanogaster

The popularity of Drosophila melanogaster as a model for understanding eukaryotic biology over the past 100 years has been accompanied by the development of numerous tools for manipulating the fruitfly genome. Here we review some recent technologies that will allow Drosophila melanogaster to be manipulated more easily than any other multicellular organism. These developments include the ability to create molecularly designed deletions, improved genetic mapping technologies, strategies for creating targeted mutations, new transgenic approaches and the means to clone and modify large fragments of DNA.

A tale of two integrations, transgene and T-DNA: gene targeting by homologous recombination in rice

The first successful and reproducible gene targeting by homologous recombination, without the concomitant occurrence of ectopic events, has been reported. This will be a powerful approach for the characterization of gene function in rice, an important crop and a model for other cereal species. Models have been proposed to explain gene replacement by homologous recombination, including a possible model for Agrobacterium-mediated gene targeting using a strong positive-negative selection.

Generation of double gene disruptions in Dictyostelium discoideum using a single antibiotic marker selection

Gene targeting is a powerful molecular genetic technique that has been widely used to understand specific gene function in vivo. This technique allows the ablation of an endogenous gene by recombination between an introduced DNA fragment and the homologous target gene. However, when multiple gene disruptions are needed, the availability of only a limited number of marker genes becomes a complication. Here we describe a new approach to perform double gene disruptions in Dictyostelium discoideum by simultaneous transfection of two gene targeting cassettes followed by performing clonal selection against only one marker gene. The subsequent PCR-based screens of blasticidin-resistant clones revealed the integration of both the selected and the nonselected targeting cassettes at their original respective loci creating complete gene disruptions. For the genes we have tested in these studies (myosin heavy chain kinases B and C), the efficiency of the double gene targeting event is found in the range of 2%-5% of all blasticidin-resistant colonies following the transfection step. This approach for the simultaneous disruptions of multiple genes should prove to be a valuable tool for other laboratories interested in creating multiple gene disruptants in Dictyostelium or other organisms where a limited number of selectable markers are available.

Tethering Naturally Occurring Peptide Toxins for Cell-Autonomous Modulation of Ion Channels and Receptors In Vivo

The physiologies of cells depend on electrochemical signals carried by ion channels and receptors. Venomous animals produce an enormous variety of peptide toxins with high affinity for specific ion channels and receptors. The mammalian prototoxin lynx1 shares with alpha-bungarotoxin the ability to bind and modulate nicotinic receptors (nAChRs); however, lynx1 is tethered to the membrane via a GPI anchor. We show here that several classes of neurotoxins, including bungarotoxins and cobratoxins, retain their selective antagonistic properties when tethered to the membrane. Targeted elimination of nAChR function in zebrafish can be achieved with tethered alpha-bungarotoxin, silencing synaptic transmission without perturbing synapse formation. These studies harness the pharmacological properties of peptide toxins for use in genetic experiments. When combined with specific methods of cell and temporal expression, the extension of this approach to hundreds of naturally occurring peptide toxins opens a new landscape for cell-autonomous regulation of cellular physiology in vivo.

Homologous gene targeting in Caenorhabditis elegans by biolistic transformation

Targeted homologous recombination is a powerful approach for genome manipulation that is widely used for gene alteration and knockouts in mouse and yeast. In Caenorhabditis elegans, several methods of target-selected mutagenesis have been implemented but none of them provides the opportunity of introducing exact predefined changes into the genome. Although anecdotal cases of homologous gene targeting in C.elegans have been reported, no practical technique of gene targeting has been developed so far. In this work we demonstrate that transformation of C.elegans by microparticle bombardment (biolistic transformation) can result in homologous recombination between introduced DNA and the chromosomal locus. We describe a scaled up version of biolistic transformation that can be used as a method for homologous gene targeting in the worm.

Genome-wide insertional mutagenesis of Arabidopsis thaliana

Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.