Transcription enhances intrachromosomal homologous recombination in mammalian cells

Misrejoining of DNA double-strand breaks in primary and transformed human and rodent cells: a comparison between the HPRT region and other genomic locations

Many studies of radiation response and mutagenesis have been carried out with transformed human or rodent cell lines. To study whether the transfer of results between different cellular systems is justified with regard to the repair of radiation-induced DNA double-strand breaks (DSBs), two assays that measure the joining of correct DSB ends and total rejoining in specific regions of the genome were applied to primary and cancer-derived human cells and a Chinese hamster cell line. The experimental procedure involves Southern hybridization of pulsed-field gel electrophoresis blots and quantitative analysis of specific restriction fragments detected by a single-copy probe. The yield of X-ray-induced DSBs was comparable in all cell lines analyzed, amounting to about 1 x 10(-2) breaks/Mbp/Gy. For joining correct DSB ends following an 80 Gy X-ray exposure all cell lines showed similar kinetics and the same final level of correctly rejoined breaks of about 50%. Analysis of all rejoining events revealed a considerable fraction of unrejoined DSBs (15-20%) after 24 h repair incubation in the tumor cell line, 5-10% unrejoined breaks in CHO cells and complete DSB rejoining in primary human fibroblasts. To study intragenomic heterogeneity of DSB repair, we analyzed the joining of correct and incorrect break ends in regions of different gene density and activity in human cells. A comparison of the region Xq26 spanning the hypoxanthine guanine phosphoribosyl transferase locus with the region 21q21 revealed identical characteristics for the induction and repair of DSBs, suggesting that there are no large variations between Giemsa-light and Giemsa-dark chromosomal bands.

The magnocellular neurons of the hypothalamo-neurohypophyseal system display remarkable neuropeptidergic phenotypes leading to novel insights in neuronal cell biology

For decades the magnocellular neurons of the hypothalamo-neurophypophyseal system (HNS), in which either vasopressin or oxytocin are produced and released into the bloodstream, have been playing a pivotal role in fundamental discoveries in the nervous system. The primary structure of vasopressin and oxytocin was the first of all neuropeptides to be published, i.e., in the 1950s by the Nobel prize laureate Du Vigneaud. Moreover, many trend-setting discoveries have their origin in the HNS, which abundantly expresses vasopressin and oxytocin, clearly displays its function and is relatively easily to manipulate. Examples are the phenomenon of coexpression of neuropeptides, patch-clamping of nerve endings, axonal transport of RNA, neuroglia interactions and the behavioral effects. An extraordinarily intriguing example is the homozygous Brattleboro rat, which lacks vasopressin by a germ-line mutation, and has disclosed many of the fundamental characteristics of peptidergic neurons, and neurons in general. In this chapter we will discuss a few of them, in particular the recent data on mutations in vasopressin RNA. It is to be expected that the HNS will retain its informative role in the next decades.

Positive-negative selection and T-DNA stability in Arabidopsis transformation

We have analysed the application of positive-negative selection for the selection of homologous recombination interactions between the chromosome and a T-DNA molecule after transformation of plant cells. Two different genomic loci in a cell suspension of Arabidopsis thaliana were chosen to study gene targeting events. One was the chalcone synthase (CHS) gene present as a single copy and the second an hemizygous chromosomally inserted T-DNA containing the hpt gene, conferring resistance to hygromycin, flanked by CHS sequences. The target lines were transformed with replacement-type T-DNA vectors which contained a positive selectable marker flanked by the regions of the CHS gene and a negative selectable marker to counter-select random insertions. As negative marker we used the Escherichia coli codA gene encoding cytosine deaminase, conferring upon the cells sensitivity to 5-flourocytosine (5-FC). Doubly selected transformants represent 1-4% of the primary transformed cells. Targeting events were not found at the chalcone synthase locus nor at the artificial hpt locus in a total of 4379 doubly selected calli, corresponding to at least 109,475 individual primary transformants. We show by PCR and Southern analysis that the 5-FC resistance in the majority of these cells is associated with substantial deletions of the T-DNA molecule from the right-border end.

Increased transcription decreases the spontaneous mutation rate at the thymidine kinase locus in human cells

Transcription increases DNA repair efficiency and modulates the distribution of certain types of DNA damage. Furthermore, increased transcription level stimulates spontaneous mutation rate in yeast. We explored whether transcription level affects spontaneous mutation rate in human cells. We first developed two thymidine kinase (tk) inducible human cell lines using the Gal4-Estrogen receptor system. In our TK6i-G3 and G9 tk heterozygous cell lines, the active tk allele is linked to an inducible promoter element. Tk mRNA is induced following treatment with estrogen. Spontaneous mutation rate was significantly decreased in human cell lines after induction in contrast to the report in yeast. Thus, humans may have evolved different or additional mechanisms to deal with transcription related spontaneous mutagenesis.

The yeast HRS1 gene is involved in positive and negative regulation of transcription and shows genetic characteristics similar to SIN4 and GAL11

We provide genetic evidence that HRS1/PGD1, a yeast gene previously identified as a suppressor of the hyper-recombination phenotype of hpr1, has positive and negative roles in transcriptional regulation. We have analyzed three differently regulated promoters, GAL1, PHO5 and HSP26, by beta-galactosidase assays of lacZ-fused promoters and by Northern analysis of the endogenous genes. Transcription of these promoters was derepressed in hrs1delta mutants under conditions in which it is normally repressed in wild type. Under induced conditions it was either strongly reduced or significantly enhanced depending on the promoter system analyzed. Constitutive transcription was not affected, as determined in ADH1 and TEF2. In addition, Hrs1p was required for mating-factor expression, telomere-linked DNA silencing and DNA supercoiling of plasmids. Furthermore, hrs1delta suppressed Ty-insertion mutations and conferred a Gal- phenotype. Many of these phenotypes also result from mutations in GAL11, SIN4 or RGR1, which encode proteins of the RNA polII mediator. We also show that gal11delta and sin4delta partially suppress the hyper-rec phenotype of hpr1 mutants, although to a lesser extent than hrs1delta. Our results provide new evidence for the connection between hpr1delta-induced deletions and transcription. We discuss the possibility that Hrs1p might be a component of the RNA polII transcription machinery.

Parameters controlling the rate of gene targeting frequency in the protozoan parasite Leishmania

In this study we investigated the role of several parameters governing the efficiency of gene targeting mediated by homologous recombination in the protozoan parasite Leishmania. We evaluated the relative targeting frequencies of different replacement vectors designed to target several sequences within the parasite genome. We found that a decrease in the length of homologous sequences <1 kb on one arm of the vector linearly influences the targeting frequency. No homologous recombination was detected, however, when the flanking homologous regions were <180 bp. A requirement for a very high degree of homology between donor and target sequences was found necessary for efficient gene targeting in Leishmania , as targeted recombination was strongly affected by base pair mismatches. Targeting frequency increased proportionally with copy number of the target only when the target was part of a linear amplicon, but remained unchanged when it was present on circles. Different chromosomal locations were found to be targeted with significantly variable levels of efficiency. Finally, different strains of the same species showed differences in gene targeting frequency. Overall, gene targeting mediated by homologous recombination in Leishmania shares similarities to both the yeast and the mammalian recombination systems.

Are ABL and BCR imprinted?

An increasing number of clinical observations and genetic experiments have shown that some parts of the genome behave differently depending on whether they are of paternal or maternal origin. This phenomenon is known as “genomic imprinting” and has been defined as “a reversible process whereby a gamete-specific modification in the parental generation can sometimes lead to functional differences between maternal and paternal genomes in diploid cells of the offspring” [1]. The accumulating evidence for its important role in cancer predisposition syndromes as well as for the pathogenesis of certain types of sporadic tumors prompted us to investigate whether imprinting may also be instrumental in selecting particular parental chromosome regions involved in balanced rearrangements, such as the leukemia-specific translocation t(9;22) [2]. Several reports have analyzed the expression, the methylation and the replication patterns of the two genes, ABL and BCR, on chromosomes 9 and 22, respectively, which are affected by this translocation [3-6]. Although not directly comparable, the results of these studies seem to invalidate our cytogenetic observations. We therefore review this controversial issue and provide some possible explanations for the contradictory results.

The effect of transcription on genetic recombination in poxvirus-infected cells

We have examined the effects of transcription on recombination frequencies in poxvirus-infected cells. A synthetic poxviral promoter was shown to function as a hybrid early/late transcription element when fused to a luciferase reporter gene, and then cloned into genetically-marked recombination substrates. These lambda DNA substrates were transfected into cells infected with Shope fibroma virus (SFV) and the recombinants detected by recovering the transfected DNA, packaging it in vitro into infectious particles, and then assaying the yield of recombinants on Escherichia coli. Controls showed that the poxviral promoter conferred no replicative advantage, or disadvantage, on molecules encoding the promoter. Furthermore, the promoter had no detectable effect on the recombination frequency when recombination was measured in the interval immediately adjacent to the promoter-insertion site. However, the promoter did appear to stimulate recombination at a distance, in a manner that appeared to be dependent on the level of transcription, and the effect was observed regardless of whether or not the promoter was present on one or both of the recombinational substrates. The peak of recombinational enhancement was centered about 500 bp away from the promoter element, where the frequency of recombination was 30-50% higher than that seen when the recombinational substrates lacked the promoter. Possible explanations for these observations are discussed.

The influence of a (GT)29 microsatellite sequence on homologous recombination in the hamster adenine phosphoribosyltransferase gene

Several DNA sequence elements are thought to stimulate homologous recombination, illegitimate recombination, or both in mammalian cells. Some are implicated by their recurrence around rearrangement breakpoints, others by their effects on recombination of extrachromosomal plasmids. None of these sequences, however, has been tested on the chromosome in a defined context. In this paper we show how the adenine phosphoribosyltransferase locus in CHO cells can be used to study the recombinogenic potential of defined DNA sequences. As an example we have measured the effect on homologous recombination of a dinucleotide repeat, (GT)29, which has been shown to stimulate homologous recombination in extrachromosomal vectors 3-20 fold. On the chromosome at the adenine phosphoribosyltransferase locus, however, this sequence shows no capacity to stimulate recombination or to influence the distribution of recombination events.

Somatic mutations in the brain: relationship to aging?

Genetic instability is generally thought to underlie the process of aging and is predominantly associated with meiosis and mitosis. This review will discuss DNA damage and repair, somatic mutations and somatic recombination events in non-dividing neurons in relation to aging. In general it can be concluded that mutagenesis operates at high frequency in the brain. Present data do not provide clear evidence for accumulating DNA damage or a change in DNA repair activity in the brain with age. However, a linear age-related increase in frameshift mutations has been shown to occur in vasopressin neurons of the rat, revealing a novel post-mitotic mechanism.

Unstable integration of transfected DNAs into embryonal carcinoma cells

Plasmid DNA can be efficiently transfected into embryonal carcinoma cells but it is difficult to isolate clones of cells stably expressing genes present on the transfected plasmids. Even in clonal populations derived from transfected cells, the introduced genes are expressed in some but not all cells. Cotransfection with a region of the Pgk-1 gene results in more efficient, stable cotransformation due to increased numbers of copies of the transfected plasmids integrated into the genomic DNA. The PgK-1 genomic sequences did not allow the plasmid DNA to replicate autonomously but seemed to enhance the ligation of transfected plasmids before their integration into the host genome. Our results suggest a model in which the plasmid DNAs are able to integrate and subsequently excise from the host genome by recombination events enhanced by transcription through the tandemly repeated sequences of the transfected plasmids.

Intragenic regions of the murine Pgk-1 locus enhance integration of transfected DNAs into genomes of embryonal carcinoma cells

Introduction of recombinant genes into mammalian cells in culture has been an important procedure in establishing the molecular mechanisms of various cellular processes. The efficiency with which plasmid borne recombinant genes are expressed following stable integration into genomes of embryonal carcinoma cells is low. Using the P19 embryonal carcinoma cells as recipients, we found that constructs carrying the promoter and intragenic regions of the murine Pgk-1 gene were expressed with high efficiency. This elevated expression was associated with increased numbers of copies of the transfected plasmid DNA stably associated with the genomes of recipient cells. The elevated plasmid copy numbers may result from enhanced ligation of transfected plasmids because cotransfected plasmids were also integrated in increased numbers. The enhanced integration and expression of transfected plasmids required active transcription through an intragenic region of Pgk-1, perhaps resulting in more recombinogenic plasmid DNAs.

Genetic recombination of nucleosomal templates is mediated by transcription

An in vitro system has been developed to examine the influence of transcription on genetic rearrangement. Using a homologous pairing assay, the transfer of one strand of a nucleosomal template onto a recipient DNA molecule was monitored as a function of RNA polymerase activity. Transcriptionally inactive nucleosomal DNA was refractory to homologous pairing. Homologous pairing was catalyzed, however, by the eukaryotic recombinase, rec1, when the nucleosomal template was being transcribed. The reaction was found to be dependent on the presence of rec1, RNA polymerase, NTPs and RNA synthesis. Heteroduplex formation between a short DNA duplex fragment assembled into a nucleosome and a single-stranded circle relied also on the presence of sequence homology between the duplex and the circle. The results of this study lend support to the notion that transcriptionally active regions within a chromosome are more apt to serve as sites of genetic recombination.

High-frequency loss of specific immunoglobulin production in hybridoma cell lines bearing a chromosomal immunoglobulin kappa gene modified by homologous recombination

We have examined the stability of trinitrophenyl (TNP) -specific IgM production in hybridoma cell lines in which homologous recombination was used to change the variable region of an endogenous chromosomal immunoglobulin kappa gene to one specific for TNP. Mutant hybridomas that have lost TNP-specific IgM production are detected with a frequency of approximately 1%. Characterization of the mutant cells reveals a variety of gross rearrangements in the recombinant kappa TNP gene as well as in the endogenous kappa and muTNP genes.

Replacement-like recombination induced by an integration vector with a murine homology flank at the immunoglobulin heavy-chain locus in mouse and rat hybridoma cells

Vectors for homologous recombination are commonly designed as replacement or integration constructs. We have evaluated integration vectors for the substitution of the immunoglobulin heavy-chain constant region by various human isotypes in mouse and rat hybridomas. It is known that under certain circumstances replacement vectors exhibit a lower target efficiency and can be incorporated by integration events. Conversely, we show here that an integration vector can undergo a replacement event despite having free homologous adjacent DNA ends, which would be expected to initiate integration according to the double-strand break repair model. Moreover, in cases of replacement recombination the 5' crossover is not necessarily located within the homology region, thereby giving rise to a truncated gene product. Whether or not the replacement leads to such deletions is clearly dependent on the isotypes involved in the targeting reaction. The fact that the vector is correctly targeted to the heavy-chain locus, but that the homology region is not always the site of recombination, points to a novel recombination mechanism that may be specific for the immunoglobulin loci and that seems to be predominant even in the presence of the free homologous adjacent ends of an integration vector. Furthermore we demonstrate that homologous recombination at the heavy-chain locus is also possible between sequences from different species. The implications of our findings for the production of chimeric antibodies are discussed.

Protein tracking-induced supercoiling of DNA: a tool to regulate DNA transactions in vivo?

An interplay between DNA-dependent biological processes appears to be crucial for cell viability. At the molecular level, this interplay relies heavily on the communication between DNA-bound proteins, which can be facilitated and controlled by the dynamic structure of double-stranded DNA. Hence, DNA structural alterations are recognized as potential tools to transfer biological information over some distance within a genome. Until recently, however, direct evidence for DNA structural information as a mediator between cellular processes was lacking. This changed when the concept of transient waves of DNA supercoiling, induced by proteins tracking along the right-handed DNA double helix, came into the limelight. Indeed, a number of observations now suggest that helix tracking-induced DNA structural information might be exploited to participate in the regulation of a variety of DNA transactions in vivo.

Chromosome bands--flavours to savour

The mammalian chromosome is longitudinally heterogeneous in structure and function and this is the basis for the specific banding patterns produced by various chromosome staining techniques. The two most frequently used techniques are G, or Giemsa banding and R, or reverse banding. Each type of stained band is characterised by variations in gene density, time of replication, base composition, density of repeat sequences, and chromatin packaging. It is increasingly apparent that R and G bands, which are complementary to each other, represent separate compartments of the euchromatic human genome, with R bands containing the vast majority of genes. R bands are also more GC-rich, contain a higher density of Alu repeats, and replicate earlier in S phase, than G bands. These properties may be interdependent and may have coevolved.