The Frequency of Homologous Recombination in Human ALT Cells

Instead of telomerase, some immortal cells use the alternative lengthening of telomeres pathway (ALT) to maintain their telomeres. There is good evidence that homologous recombination contributes to the ALT mechanism. Using an inducible GFP reporter system to measure the frequency of homologous recombination, we asked whether or not ALT cells exhibited a general change of the recombination machinery. Our results show that the frequency of homologous recombination for non-telomeric sequences in ALT cells is identical to that in telomerase positive cells, irrespective of whether the reporter was present at an intra-chromosomal location or next to a telomeric sequence. We conclude that the underlying recombination defect in ALT cells is restricted to telomeric sequences.     

The Effects of Translocations on Recombination Frequency in Caenorhabditis Elegans

In the nematode Caenorhabditis elegans, recombination suppression in translocation heterozygotes is severe and extensive. We have examined the meiotic properties of two translocations involving chromosome I, szT1(I;X) and hT1(I;V). No recombination was observed in either of these translocation heterozygotes along the left (let-362-unc-13) 17 map units of chromosome I. Using half-translocations as free duplications, we mapped the breakpoints of szT1 and hT1. The boundaries of crossover suppression coincided with the physical breakpoints. We propose that DNA sequences at the right end of chromosome I facilitate pairing and recombination. We use the data from translocations of other chromosomes to map the location of pairing sites on four other chromosomes. hT1 and szT1 differed markedly in their effect on recombination adjacent to the crossover suppressed region. hT1 had no effect on recombination in the adjacent interval. In contrast, the 0.8 map unit interval immediately adjacent to the szT1(I;X) breakpoint on chromosome I increased to 2.5 map units in translocation heterozygotes. This increase occurs in a chromosomal interval which can be expanded by treatment with radiation. These results are consistent with the suggestion that the szT1(I) breakpoint is in a region of DNA in which meiotic recombination is suppressed relative to the genomic average. We propose that DNA sequences disrupted by the szT1 translocation are responsible for determining the frequency of meiotic recombination in the vicinity of the breakpoint.     

On the Frequency of Undetectable Recombination Events

Simple analytical results show that many recombination events occur in such a way as to have no effect on the resultant DNA sequence. The proportion of these undetectable events depends on the population size, mutation rate and recombination rate and is quite large for reasonable values of these quantities. Efforts to estimate recombination rates and frequencies directly from DNA sequence data must, therefore, take this undetectable fraction into account.     

On Recombination between Close and Distant Markers in Phage Lambda

The contribution of parental DNA to progeny phages genetically recombinant for close markers, distant markers, or both simultaneously was studied in biparental and triparental replication-blocked crosses. The data are compatible with the previously proposed view that heterozygous overlaps at the sites of crossing over are sometimes about as long as the lambda chromosome. However, about half of the close marker recombinants have enjoyed triparental interactions, attenuating that conclusion and obscuring predictions of the long overlap model.     

The Effect of Oxygen on the Frequency of Somatic Recombination in DROSOPHILA MELANOGASTER

The influence of oxygen on the frequency of somatic recombination in the yellow singed system on the X chromosome of Drosophila melanogaster was studied under a variety of experimental conditions. Flies raised from egg to adult in atmospheres containing 70-90% oxygen were found to have significantly more mosaic spots on their abdominal tergites than were observed in flies which developed in air. First instar larvae X-rayed in from 0 to 100% oxygen demonstrated the existence of an oxygen effect for somatic recombination in the cells which form the abdominal hypoderm. The mosaic spot counts, beginning with the lowest numbers which were found in flies X-rayed in nitrogen, increased rapidly with rising oxygen tensions until the percentage in air was reached, then leveled off at the higher concentrations. Post-treatment with nitrogen of larvae X-rayed in air or oxygen created a substantially higher number of mosaic spots than were found when larvae, after being similarly irradiated, were instead placed into air or oxygen.     

Genetic Recombination in Coprinus. IV. a Kinetic Study of the Temperature Effect on Recombination Frequency

At the restrictive conditions (35 degrees under continuous light) Coprinus lagopus is unable to initiate premeiotic S phase which takes place normally within 8-10 h of karyogamy. A shift-up to the restrictive conditions causes an arrest of the basidiocarps at this critical stage. A prolonged arrest causes a reversal to mitosis (Lu 1974b). Incubation of basidiocarps at the restrictive conditions before this critical stage causes no increase in recombination frequency (R.F.) in the loci studied. An arrest of 4 h at the critical stage still causes no R.F. increase, but 12-13 h and 18-19 h arrests cause increases of 50% and 90% over the controls, respectively. Thus R.F. can be increased even before the cells are fully committed to meiosis.-A 3-h heat treatment at the beginning of S phase (or 8 h before karyogamy) also causes some (30%) increase in R.F. while the same treatment at late S phase (or 3 h before karyogamy) causes a substantial (164%) increase in R.F. over the controls. A 3-h heat treatment before S phase causes no increase in R.F.-Pachytene is also responsive to temperature treatments (Lu 1969). The maximum R.f. increase is 100% by heat and 220% by cold treatment. The shortest time that can cause the maximum increase in recombination by high temperature is 3 h and that by cold treatment is 7 h. These durations are correlated with the length of the pachytene stage under the treatment conditions. The kinetic data show that the increase in R.F. caused by high and low temperatures follows two-hit kinetics and their rate of increase is almost identical. The higher increase in R.F. by low temperature can be attributed to the increased duration of pachytene and therefore R.F. is a function of time. The longer the homologous chromosomes are held together, the higher the recombination frequency.     

The Relationships among Transmission Frequency, Male Recombination and Progeny Production in DROSOPHILA MELANOGASTER

The T-007 second chromosome line, which was originally isolated in 1970 from a natural population of Drosophila melanogaster at Harlingen, south Texas, has previously been shown to be associated with several unusual genetic phenomena. In the present study, two characteristics, distorted transmission frequency and male recombination, were analyzed in relation to the progeny production of T-007 heterozygous individuals. The following points were established: (1) Distorted transmission frequency in the T-007 heterozygous male was mainly due to "elimination" of T-007 chromosomes among the progeny, while no such elimination occurred for the normal partner chromosome. (2) Transmission frequency and progeny production of the T-007 heterozygous females were normal, or at least almost normal. (3) The frequency of male recombination increased with an increasing degree of distortion. This was due to an increased number of recombinants produced per male and to a decreased number of progeny receiving the T-007 chromosome.     

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes.     

Dependence of Frequency of Homologous Recombination on the Homology Length

The frequency of homologous recombination is believed to be a linear function of the length (N bp) of homology between DNAs. Here, the N intercept is believed to be determined by a threshold length below which some physical constraint is effective. In the mammalian gene targeting systems, however, the frequency depends more steeply than linearly on the homology length. To explain both the linear dependence and the steeper dependence, we propose a model where the branch point of a reaction intermediate is assumed to ``walk randomly' along the homologous region until it is processed. The intermediate is assumed to be destroyed if the branch point ever reaches either end of the homology. In this model, the length dependence is governed by a parameter, h, which is defined as efficiency of processing of the intermediate and reflects unlikelihood of the destruction at either end of the homology. We find that the frequency is proportional to N(3) for smaller N and is a linear function of N for larger N. Where the shift from the N(3) dependence to the linear dependence takes place is determined by the parameter h. The range of N showing the N(3) dependence becomes narrower as h becomes larger. The dependence steeper than linear dependence, which is observed not only in the mammalian gene targeting system but also in bacteriophage T4, Escherichia coli and yeast systems, agrees well with the predicted N(3) dependence. The N intercept is determined not by physical (or structural) constraints but only by the parameter h in this model.     

High Frequency Repeat-Induced Point Mutation (Rip) Is Not Associated with Efficient Recombination in Neurospora

Duplicated DNA sequences in Neurospora crassa are efficiently detected and mutated during the sexual cycle by a process named repeat-induced point mutation (RIP). Linked, direct duplications have previously been shown to undergo both RIP and deletion at high frequency during premeiosis, suggesting a relationship between RIP and homologous recombination. We have investigated the relationship between RIP and recombination for an unlinked duplication and for both inverted and direct, linked duplications. RIP occurred at high frequency (42-100%) with all three types of duplications used in this study, yet recombination was infrequent. For both inverted and direct, linked duplications, recombination was observed, but at frequencies one to two orders of magnitude lower than RIP. For the unlinked duplication, no recombinants were seen in 900 progeny, indicating, at most, a recombination frequency nearly three orders of magnitude lower than the frequency of RIP. In a direct duplication, RIP and recombination were correlated, suggesting that these two processes are mechanistically associated or that one process provokes the other. Mutations due to RIP have previously been shown to occur outside the boundary of a linked, direct duplication, indicating that RIP might be able to inactivate genes located in single-copy sequences adjacent to a duplicated sequence. In this study, a single-copy gene located between elements of linked duplications was inactivated at moderate frequencies (12-14%). Sequence analysis demonstrated that RIP mutations had spread into these single-copy sequences at least 930 base pairs from the boundary of the duplication, and Southern analysis indicated that mutations had occurred at least 4 kilobases from the duplication boundary.     

Separation of Linked Markers in Chinese Hamster Cell Hybrids: Mitotic Recombination Is Not Involved

A search for mitotic recombination was carried out using mutant subclones of cultured Chinese hamster ovary cells. Recombination events were sought between the linked loci specifying the enzymes hypoxanthine phosphoribosyl transferase and glucose-6-phosphate dehydrogenase. It was shown by fluctuation analysis that markers at these two loci co-segregate from doubly heterozygous pseudotetraploid hybrid cells more than 90% of the time. The minority class of segregants, which had lost one marker without losing the other, were genetically analyzed to distinguish between the possibilities of mitotic recombination and deletion of chromosomal material. Nine clones in which a linkage disruption had occured were studied, using further cell hybridization and segregation. In three cases, a recessive lethal loss of genetic information was indicated, suggesting the deletion mechanism. In six cases, it was demonstrated that no new linkage relationships had been established concomitant with linkage disruption. Thus, in all nine clones, the evidence indicated that mitotic recombination was not involved in the events that disrupted linkage between these two loci. If mitotic recombination takes place at all in this system, the rate must be less than about 10^-6 per cell per generation.     

Evolution of Mutational Robustness in the Yeast Genome: A Link to Essential Genes and Meiotic Recombination Hotspots

Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential) genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG) clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i) the evolution of non-random distributions of meiotic crossovers, (ii) the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii) the evolution of EG enrichment in pericentromeric regions and (iv) the associated absence of meiotic crossovers (cold centromeres). Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new aspect of the evolution of genome architectures that complements insights about molecular constraints, such as the interference of pericentromeric crossovers with chromosome segregation.     

Effects of Ploidy and Recombination on Evolution of Robustness in a Model of the Segment Polarity Network

Many genetic networks are astonishingly robust to quantitative variation,allowing these networks to continue functioning in the face of mutation andenvironmental perturbation. However, the evolution of such robustness remainspoorly understood for real genetic networks. Here we explore whether and howploidy and recombination affect the evolution of robustness in a detailedcomputational model of the segment polarity network. We introduce a novelcomputational method that predicts the quantitative values of biochemicalparameters from bit sequences representing genotype, allowing our model tobridge genotype to phenotype. Using this, we simulate 2,000 generations ofevolution in a population of individuals under stabilizing and truncationselection, selecting for individuals that could sharpen the initial pattern ofengrailed and wingless expression. Robustness was measured by simulating amutation in the network and measuring the effect on the engrailed and winglesspatterns; higher robustness corresponded to insensitivity of this pattern toperturbation. We compared robustness in diploid and haploid populations, witheither asexual or sexual reproduction. In all cases, robustness increased, andthe greatest increase was in diploid sexual populations; diploidy and sexsynergized to evolve greater robustness than either acting alone. Diploidyconferred increased robustness by allowing most deleterious mutations to berescued by a working allele. Sex (recombination) conferred a robustnessadvantage through “survival of the compatible”: thosealleles that can work with a wide variety of genetically diverse partnerspersist, and this selects for robust alleles.     

The Coalescent Process in Models with Selection and Recombination

The statistical properties of the process describing the genealogical history of a random sample of genes at a selectively neutral locus which is linked to a locus at which natural selection operates are investigated. It is found that the equations describing this process are simple modifications of the equations describing the process assuming that the two loci are completely linked. Thus, the statistical properties of the genealogical process for a random sample at a neutral locus linked to a locus with selection follow from the results obtained for the selected locus. Sequence data from the alcohol dehydrogenase (Adh) region of Drosophila melanogaster are examined and compared to predictions based on the theory. It is found that the spatial distribution of nucleotide differences between Fast and Slow alleles of Adh is very similar to the spatial distribution predicted if balancing selection operates to maintain the allozyme variation at the Adh locus. The spatial distribution of nucleotide differences between different Slow alleles of Adh do not match the predictions of this simple model very well.