Studying vertebrate topoisomerase 2 function using a conditional knockdown system in DT40 cells

DT40 is a B-cell lymphoma-derived avian cell line widely used to study cell autonomous gene function because of the high rates with which DNA constructs are homologously recombined into its genome. Here, we demonstrate that the power of the DT40 system can be extended yet further through the use of RNA interference as an alternative to gene targeting. We have generated and characterized stable DT40 transfectants in which both topo 2 genes have been in situ tagged using gene targeting, and from which the mRNA of both topoisomerase 2 isoforms can be conditionally depleted through the tetracycline-induced expression of short hairpin RNAs. The cell cycle phenotype of topo 2-depleted DT40 cells has been compared with that previously reported for other vertebrate cells depleted either of topo 2α through gene targeting, or depleted of both isoforms simultaneously by transient RNAi. In addition, the DT40 knockdown system has been used to explore whether excess catenation arising through topo 2 depletion is sufficient to trigger the G2 catenation (or decatenation) checkpoint, proposed to exist in differentiated vertebrate cells.     

Genetic analysis as a tool to investigate the molecular mechanisms underlying seed development in maize

BACKGROUND: In angiosperms the seed is the outcome of double fertilization, a process leading to the formation of the embryo and the endosperm. The development of the two seed compartments goes through three main phases: polarization, differentiation of the main tissues and organs and maturation. SCOPE: This review focuses on the maize kernel as a model system for developmental and genetic studies of seed development in angiosperms. An overview of what is known about the genetic and molecular aspects underlying embryo and endosperm formation and maturation is presented. The role played by embryonic meristems in laying down the plant architecture is discussed. The acquisition of the different endosperm domains are presented together with the use of molecular markers available for the detection of these domains. Finally the role of programmed cell death in embryo and endosperm development is considered. CONCLUSIONS: The sequence of events occurring in the developing maize seed appears to be strictly regulated. Proper seed development requires the co-ordinated expression of embryo and endosperm genes and relies on the interaction between the two seed components and between the seed and the maternal tissues. Mutant analysis is instrumental in unravelling the genetic control underlying the formation of each compartment as well as the molecular signals interplaying between the two compartments.     

Visualization of DNA replication in the vertebrate model system DT40 using the DNA fiber technique

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not only ensure faithful genome duplication in the face of endogenous and exogenous DNA damage but also prevent genomic instability, a recognized causative factor in tumor development. Here, we describe a simple and cost-effective fluorescence microscopy-based method to visualize DNA replication in the avian B-cell line DT40. This cell line provides a powerful tool to investigate protein function in vivo by reverse genetics in vertebrate cells(1). DNA fiber fluorography in DT40 cells lacking a specific gene allows one to elucidate the function of this gene product in DNA replication and genome stability. Traditional methods to analyze replication fork dynamics in vertebrate cells rely on measuring the overall rate of DNA synthesis in a population of pulse-labeled cells. This is a quantitative approach and does not allow for qualitative analysis of parameters that influence DNA synthesis. In contrast, the rate of movement of active forks can be followed directly when using the DNA fiber technique(2-4). In this approach, nascent DNA is labeled in vivo by incorporation of halogenated nucleotides (Fig 1A). Subsequently, individual fibers are stretched onto a microscope slide, and the labeled DNA replication tracts are stained with specific antibodies and visualized by fluorescence microscopy (Fig 1B). Initiation of replication as well as fork directionality is determined by the consecutive use of two differently modified analogues. Furthermore, the dual-labeling approach allows for quantitative analysis of parameters that influence DNA synthesis during the S-phase, i.e. replication structures such as ongoing and stalled forks, replication origin density as well as fork terminations. Finally, the experimental procedure can be accomplished within a day, and requires only general laboratory equipment and a fluorescence microscope.     

Transplacement mutagenesis: a novel in situ mutagenesis system using phage-plasmid recombination

Site-specific mutagenesis provides the ability to alter DNA with precision so that the function of any given gene can be more fully understood. Several methods of in vitro mutagenesis are time-consuming and imprecise, requiring the subcloning and sequencing of products. Here we describe a rapid, high fidelity method of in situ mutagenesis in bacteriophage lambda using transplacement. Using this method, mutations are transferred from oligonucleotides to target phages using a plasmid interface. A small (50 bp) homology region bearing a centred point mutation is generated from oligonucleotides and subcloned into a transplacement plasmid bearing positive and negative phage selectable markers. Following a positive/negative selection cycle of integrative recombination and excision, the point mutation is transferred precisely from plasmid to phage in a subset ( approximately 25-50%) of recombinants. As the fidelity of both oligonucleotide synthesis and phage-plasmid recombination is great, this approach is extremely reliable. Using transplacement, point mutations can be accurately deposited within large phage clones and we demonstrate the utility of this technique in the construction of gene targeting vectors in bacteriophages.     

Introducing specific antibodies into electropermeabilized cells is a valuable tool for eliminating specific cell functions

A technique is established for the role of intracellular proteins to be eliminated and thereby gives information about their specific role in signal transduction within cells. Rat pancreatic islets as well as INS-1 cells (an insulin secreting cell line) were electrically permeabilized in order to introduce high molecular weight compounds. Optimized conditions were five exposures with 15-s intervals, τ=200 ms, an electric field of 1·36 kV per 0·4 cm in a specific permeabilization buffer at a calculated Ca⁺⁺ concentration of 5×10⁻⁸ M . In electroporation control experiments the spectrophotometrically measured uptake of the cell membrane-impermeable propidium iodide, FITC-labelled dextran (MW∼4000) and FITC-labelled antibodies (MW∼150,000) was established as being 81·5±5·0, 82·7±3·0 and 81·0±1·0 per cent of maximum, respectively. These data were corroborated qualitatively by visualizing microscopically the fluorescence of the FITC-labelled compounds in islets as well as in INS-1 cells. The cells appear to reseal since control experiments indicated a short-lived outflow of lactate dehydrogenase (MW of 140,000 which is similar to that of antibodies) and of insulin for the first 15–20 min. After electroporation the cells were functionally intact, i.e. responded to the stimulus carbachol (CCh). Only 18·0±10·1 per cent of cells had not resealed after 2 h (propidium iodide uptake measured at various time intervals after electroporation). As was shown recently the effect of specific compounds such as CCh and CCK₈ on insulin release was eliminated selectively by antibodies against specific G proteins thus proving this method to be a valuable tool. In conclusion, adding antibodies to electrically permeabilized cells is a valuable tool for eliminating a specific cell function in order to elucidate the specific role of intracellular compounds. This method can probably be used for testing the specific role of other proteins in cell functions. © 1997 John Wiley & Sons, Ltd.     

The chicken HPRT gene: a counter selectable marker for the DT40 cell line

We describe the cloning, characterisation and chromosomal mapping of the chicken hprt gene together with the construction of two counter selectable hprt-/- DT40 derived cell lines. One of these cell lines contains a stably integrated gene encoding a conditionally active cre recombinase and thus allows efficient manipulation of targeted loci by site-specific recombination. These cell lines will enhance the utility of the hyper-recombinogenic DT40 cell line as a system for the genetic analysis of cell autonomous functions in vertebrates and as a tool for mammalian chromosome engineering.     

WI-38 cell long-term quiescence model system: A valuable tool to study molecular events that regulate growth

A number of cell culture model systems have been used to study the regulation of cell cycle progression at the molecular level. In this paper we describe the WI-38 cell long-term quiescence model system. By modulating the length of time that WI-38 cells are density arrested, it is possible to proportionately alter the length of the prereplicative or G-1 phase which the cell traverses after growth factor stimulation in preparation for entry into DNA synthesis. Through studies aimed at understanding the cause and molecular nature of the prolongation of the prereplicative phase, we have determined that gene expression plays an important role in establishing growth factor “competence” and that once the cell becomes “competent” there is a defined order to the molecular events that follow during the remainder of G-1. More specifically, we have determined that the prolongation represents a delay in the ability of long term quiescent cells to become fully “competent” to respond to growth factors which regulate progression through G-1 into S. This prolongation appears to occur as a result of changes during long term quiescence in the ability of immediate early G-1 specific genes (such as c-myc) to activate the expression of early G-1 specific genes (such as ornithine decarboxylase). While ODC is the first and thus far only growth associated gene identified as a target of c-myc (and the Myc/Max protein complex), it is likely that further studies in this model system will reveal other early G-1 growth regulatory genes. We anticipate that future follow-up studies in this model system will provide additional valuable information abuot the function of growth-regulatory genes in controlling growth factor responsiveness and cell cycle progression.     

The DT40 web site: sampling and connecting the genes of a B cell line

Thousands of new vertebrate genes have been discovered and genetic systems are needed to address their functions at the cellular level. The chicken B cell line DT40 allows efficient gene disruptions due to its high homologous recombination activity. However, cloning the gene of interest is often cumbersome, since relatively few chicken cDNA sequences are present in the public databases. In addition, the accumulation of multiple mutations within the same cell clone is limited by the consumption of one drug-resistance marker for each transfection. Here, we present the DT40 web site (http://genetics.hpi.uni-hamburg.de/dt40.html), which includes a comprehensive database of chicken bursal ESTs to identify disruption candidate genes and recyclable marker cassettes based on the loxP system. These freely available resources greatly facilitate the analysis of genes and genetic networks.     

Liposome-entrapped tyrosinase: a tool to investigate the regulation of the Raper-Mason pathway

The effect of the entrapment of mushroom tyrosinase (EC 1.14.18.1) within liposomes on the enzyme activity and Km vs. L-3,4-dihydroxyphenylalanine is reported in the present work; the effect of cholesterol insertion within liposome membranes on the enzyme activity has also been studied. The oxidation rates of various monophenols and diphenols by free and liposome-integrated mushroom tyrosinase were measured and the oxidation latencies vs. different substrates investigated. The different substrates are apparently oxidized according to the properties of the substituents as electron donors or acceptors; the Km values vs. L-3,4-dihydroxyphenylalanine calculated on measuring O2 consumption are higher than those calculated on measuring the dopachrome production rates. It is interesting that natural substrates of tyrosinase are oxidized according to a negative catalysis by the liposome-entrapped enzyme; this point is discussed in relation to the well known cytotoxicity of some intermediates of the Raper-Mason pathway.     

PCNA ubiquitination and REV1 define temporally distinct mechanisms for controlling translesion synthesis in the avian cell line DT40

Translesion synthesis (TLS) is a potentially mutagenic method of bypassing DNA damage encountered during replication that requires the recruitment of specialized DNA polymerases to stalled replication forks or postreplicative gaps. Current models suggest that TLS is activated by monoubiquitination of the DNA sliding clamp PCNA. However, in higher organisms, fully effective TLS also requires a noncatalytic function of the Y family polymerase REV1. Using the genetically tractable chicken cell line DT40, we show that TLS at stalled replication forks requires that both the translesion polymerase-interaction domain and ubiquitin-binding domain in the C terminus of REV1 are intact. Surprisingly, however, PCNA ubiquitination is not required to maintain normal fork progression on damaged DNA. Conversely, PCNA ubiquitination is essential for filling postreplicative gaps. Thus, PCNA ubiquitination and REV1 play distinct roles in the coordination of DNA damage bypass that are temporally separated relative to replication fork arrest.     

Use of DT40 conditional-knockout cell lines to study chromosomal passenger protein function

The CPC [chromosomal passenger complex; INCENP (inner centromere protein), Aurora B kinase, survivin and borealin] is implicated in many mitotic processes. In the present paper we describe how we generated DT40 conditional-knockout cell lines for incenp1 and survivin1 to better understand the role of these CPC subunits in the control of Aurora B kinase activity. These lines enabled us to reassess current knowledge of survivin function and to show that INCENP acts as a rheostat for Aurora B activity.     

MEKK1 is essential for DT40 cell apoptosis in response to microtubule disruption

Vinblastine and other microtubule-damaging agents, such as nocodazole and paclitaxel, cause cell cycle arrest at the G2/M transition and promote apoptosis in eukaryotic cells. The roles of these drugs in disrupting microtubule dynamics and causing cell cycle arrest are well characterized. However, the mechanisms by which these agents promote apoptosis are poorly understood. We disrupted the MEKK1 kinase domain in chicken bursal B-cell line DT40 by homologous recombination and have shown that it is essential for both vinblastine-mediated apoptosis and vinblastine-mediated c-Jun N-terminal protein kinase activation. In addition, our data indicate that vinblastine-mediated apoptosis in DT40 cells requires new protein synthesis but does not require G2/M arrest, suggesting that vinblastine-mediated cell cycle arrest and apoptosis are two independent processes.     

Mouse chimeras as a system to investigate development,cell and tissue function,disease mechanisms and organ regeneration

Chimeras are organisms composed of at least two genetically distinct cell lineages originating from different zygotes. In the laboratory, mouse chimeras can be produced experimentally; various techniques allow combining different early stage mouse embryos with each other or with pluripotent stem cells. Identification of the progeny of the different lineages in chimeras permits to follow cell fate and function, enabling correlation of genotype with phenotype. Mouse chimeras have become a tool to investigate critical developmental processes, including cell specification, differentiation, patterning and the function of specific genes. In addition, chimeras can also be generated to address biological processes in the adult, including mechanisms underlying diseases or tissue repair and regeneration. This review summarizes the different types of chimeras and how they have been generated and provides examples of how mouse chimeras offer a unique and powerful system to investigate questions pertaining to cell and tissue function in the developing and adult organism.Key words: chimera, developmental chimera, aggregation, blastocyst injection, embryonic stem cells, induced pluripotent stem cells, complementation, regeneration     

Mouse chimeras as a system to investigate development,cell and tissue function,disease mechanisms and organ regeneration

Chimeras are organisms composed of at least two genetically distinct cell lineages originating from different zygotes. In the laboratory, mouse chimeras can be produced experimentally; various techniques allow combining different early stage mouse embryos with each other or with pluripotent stem cells. Identification of the progeny of the different lineages in chimeras permits to follow cell fate and function, enabling correlation of genotype with phenotype. Mouse chimeras have become a tool to investigate critical developmental processes, including cell specification, differentiation, patterning, and the function of specific genes. In addition, chimeras can also be generated to address biological processes in the adult, including mechanisms underlying diseases or tissue repair and regeneration. This review summarizes the different types of chimeras and how they have been generated and provides examples of how mouse chimeras offer a unique and powerful system to investigate questions pertaining to cell and tissue function in the developing and adult organism.     

Paternal sex in parthenogenetic planarians: a tool to investigate the accumulation of deleterious mutations

Clonally reproducing organisms are expected to accumulate slightly deleterious mutations, and this has been demonstrated in RNA viruses, bacteria and unicellular algae. In this paper we present evidence for increased embryo mortality in obligate parthenogenetic strains of the freshwater flatworm Schmidtea polychroa, possibly indicating the action of deleterious mutations. The inheritance of this fitness defect was tested by crossing parthenogens with sexuals. This is possible because both forms are simultaneous hermaphrodites that produce fertile sperm. The resulting sexual offspring showed significantly increased embryo mortality in comparison to offspring of a sexual × sexual cross. Alternatives to a mutation explanation of these results, like the degeneration of male traits in parthenogens, are being discussed. In conclusion, these results lend support to the hypothesis that sex is advantageous to a multicellular organism because it prevents the accumulation of deleterious mutations.     

Protein evolution by hypermutation and selection in the B cell line DT40

Genome-wide mutations and selection within a population are the basis of natural evolution. A similar process occurs during antibody affinity maturation when immunoglobulin genes are hypermutated and only those B cells which express antibodies of improved antigen-binding specificity are expanded. Protein evolution might be simulated in cell culture, if transgene-specific hypermutation can be combined with the selection of cells carrying beneficial mutations. Here, we describe the optimization of a GFP transgene in the B cell line DT40 by hypermutation and iterative fluorescence activated cell sorting. Artificial evolution in DT40 offers unique advantages and may be easily adapted to other transgenes, if the selection for desirable mutations is feasible.     

FTIR spectroscopy: A new valuable tool to classify the effects of polyphenolic compounds on cancer cells

Polyphenolic compounds are an important part of human diet and regular consumption of fruits, vegetables and tea is associated with reduced risk of cancer. Dietary polyphenols display a vast array of cellular effects but the large number of data published in the literature makes it difficult to determine the main mechanisms of action associated and to identify molecules with original mechanisms. Therefore, there is an increasing demand for more systemic approaches in order to obtain a global insight of the biochemical processes mediated by polyphenols. Here, we used Fourier transform infrared (FTIR) spectroscopy to analyze cancer cells exposed in vitro to 6 polyphenols: 3 natural well documented polyphenols (curcumin, epigallocatechin gallate (EGCG) and quercetin) and 3 synthetic molecules with a very closely related chemical structure. Statistical analyses on FTIR spectra allowed the comparison of global effects of the 6 compounds and evidenced some common or different features in the cell perturbations among natural and synthetic molecules. Interestingly, marked metabolic changes induced by polyphenols closely related from a chemical point of view were identified. Furthermore, many metabolic changes could be detected as early as after 2 h incubation with the drugs.