Fidelity of meiotic gene conversion in yeast

Summary Gene conversion was studied in a sample of 3869 unselected meiotic tetrads obtained from three diploids, respectively; heterozygous for a single ochre mutant, heteroallelic for a pair of ochre alleles, and heterozygous for an ochre specific suppressor. Although the genetic system were sufficiently sensitive to detect single base changes at the mutant codon level, none were found among 36 conversions (1+:3m) of the ochre mutants and 153 conversions (3S:1+) of the suppressor locus. These findings lead to the conclusion that the informational transfer in gene conversion occurred with complete fidelity. Gene conversion conserved and did not generate new genetic information. The error level of conversion was estimated as less than 10^-2/N.P.     

Evolution of the segregation ratio: modification of gene conversion and meiotic drive

We compare the evolutionary pressures that direct the modification of gene conversion and meiotic drive at loci subject to purifying and overdominant viability selection. Gene conversion differs from meiotic drive in that modifers do not affect their own segregation ratios, even when linked to the viability locus. Segregation distortion generates gametic level disequilibria between alleles at the viability locus and modifiers of gene conversion and meiotic drive: enhancers of segregation distortion become positively associated with driven alleles. Suppression of gene conversion evolves if the driven allele is marginally disadvantageous (overdominant viability selection), and higher rates evolve if the driven alleles are relatively advantageous (purifying viability selection). Gametic disequilibria permit enhancers of meiotic drive that are linked to the driven locus to promote their own segregation. We attribute the failure of genetic modifiers of gene conversion and meiotic drive to maximinize mean fitness to the generation of such associations.     

Estimating meiotic gene conversion rates from population genetic data

Gene conversion plays an important part in shaping genetic diversity in populations, yet estimating the rate at which it occurs is difficult because of the short lengths of DNA involved. We have developed a new statistical approach to estimating gene conversion rates from genetic variation, by extending an existing model for haplotype data in the presence of crossover events. We show, by simulation, that when the rate of gene conversion events is at least comparable to the rate of crossover events, the method provides a powerful approach to the detection of gene conversion and estimation of its rate. Application of the method to data from the telomeric X chromosome of Drosophila melanogaster, in which crossover activity is suppressed, indicates that gene conversion occurs approximately 400 times more often than crossover events. We also extend the method to estimating variable crossover and gene conversion rates and estimate the rate of gene conversion to be approximately 1.5 times higher than the crossover rate in a region of human chromosome 1 with known recombination hotspots.     

Meiosis and sex chromosome aneuploidy: how meiotic errors cause aneuploidy; how aneuploidy causes meiotic errors

As a group, sex chromosome aneuploidies - the 47,XXY, 47,XYY, 47,XXX and 45,X conditions - constitute the most common class of chromosome abnormality in human live-births. Considerable attention has been given to the somatic abnormalities associated with these conditions, but less is known about their meiotic phenotypes; that is, how does sex chromosome imbalance influence the meiotic process. This has become more important with the advent of assisted reproductive technologies, because individuals previously thought to be infertile can now become biological parents. Indeed, there are several recent reports of successful pregnancies involving 47,XXY fathers, and suggestions that cryopreservation of ovarian tissue might impart fertility to at least some Turner syndrome individuals. Thus, the possible consequences of sex chromosome aneuploidy on meiotic chromosome segregation need to be explored.     

Creation of immunoglobulin diversity by intrachromosomal gene conversion

Not all vertebrates create an immunoglobulin repertoire through the recombination of individual members of variable (V), diversity (D) and joining (J) gene segment families. In chickens, for example, a diverse set of immunoglobulins is created by intrachromosomal gene conversion of the single variable gene segments of the immunoglobulin heavy and light chain genes. Recent evidence from other species such as the rabbit suggests that gene conversion may be a more widespread mechanism for the creation of immunologic diversity than previously supposed.     

Site specific induction of gene conversion: the effects of homozygosity of the ade6 mutant M26 of Schizosaccharomyces pombe on meiotic gene conversion.

Summary The ade6 mutant M26 of the yeast Schizosaccharomyces pombe uniquely influences both intragenic recombination and gene conversion of markers within its locus. To determine whether the marker effect of M26 is triggered by informational heterozygosity at that site, tetrads from the cross mat1-P mat2-P ade6-M26 Sup9 ura5xmat1-M mat2-O ade6-M26-M210 Sup9 ura5⁺ were analyzed and the conversion of the distal marker M210 scored. In a sample of 1005 tetrads 14 conversion tetrads were observed 8 of which were 3M26: 1M26-M210, 5 of which were 1M26:3M26-M210 and one of which was 2M26:1M26/M26-M210:1M26-M210. Since the 15.5 aberrant asci expected (frequency of an event at M26 X the probability that the M210 site will be included or (0.031+0.031) (0.25) (1005)=15.5) are not different from the 14 observed, the two doses of M26 act in an additive fashion in this cross. These results are consistent with an interpretation that conversion results from a sequence of events involving site specific breakage at M26, degradation of the broken strand, and the availability of an appropriate template which introduces new information as synthesis proceeds. This is congruent with the parity that is observed reflecting the fact intragenic recombination is signaled with equal probability on each of the strands due to the homozygosity of M26 in this cross. In addition, the single p.m.s. tetrad may be explained on the basis that hybrid DNA is formed, although its production is secondary and not a direct consequence of the processes leading to gene conversion. Given these results, it is possible to conclude that this marker effect is a result of the M26 leision itself and is not signaled as a consequence of specialized interactions involving the corresponding wild type nucleotide sequence.     

Life history influences how fire affects genetic diversity in two lizard species

‘Fire mosaics’ are often maintained in landscapes to promote successional diversity in vegetation with little understanding of how this will affect ecological processes in animal populations such as dispersal, social organization and re‐establishment. To investigate these processes, we conducted a replicated, spatiotemporal landscape genetics study of two Australian woodland lizard species [Amphibolurus norrisi (Agamidae) and Ctenotus atlas (Scincidae)]. Agamids have a more complex social and territory structure than skinks, so fire might have a greater impact on their population structure and thus genetic diversity. Genetic diversity increased with time since fire in C. atlas and decreased with time since fire in A. norrisi. For C. atlas, this might reflect its increasing population size after fire, but we could not detect increased gene flow that would reduce the loss of genetic diversity through genetic drift. Using landscape resistance analyses, we found no evidence that postfire habitat succession or topography affected gene flow in either species and we were unable to distinguish between survival and immigration as modes of postfire re‐establishment. In A. norrisi, we detected female‐biased dispersal, likely reflecting its territorial social structure and polygynous mating system. The increased genetic diversity in A. norrisi in recently burnt habitat might reflect a temporary disruption of its territoriality and increased male dispersal, a hypothesis that was supported with a simulation experiment. Our results suggest that the effects of disturbance on genetic diversity will be stronger for species with territorial social organization.     

Bayesian population genomic inference of crossing over and gene conversion

Meiotic recombination is a fundamental cellular mechanism in sexually reproducing organisms and its different forms, crossing over and gene conversion both play an important role in shaping genetic variation in populations. Here, we describe a coalescent-based full-likelihood Markov chain Monte Carlo (MCMC) method for jointly estimating the crossing-over, gene-conversion, and mean tract length parameters from population genomic data under a Bayesian framework. Although computationally more expensive than methods that use approximate likelihoods, the relative efficiency of our method is expected to be optimal in theory. Furthermore, it is also possible to obtain a posterior sample of genealogies for the data using this method. We first check the performance of the new method on simulated data and verify its correctness. We also extend the method for inference under models with variable gene-conversion and crossing-over rates and demonstrate its ability to identify recombination hotspots. Then, we apply the method to two empirical data sets that were sequenced in the telomeric regions of the X chromosome of Drosophila melanogaster. Our results indicate that gene conversion occurs more frequently than crossing over in the su-w and su-s gene sequences while the local rates of crossing over as inferred by our program are not low. The mean tract lengths for gene-conversion events are estimated to be ～70 bp and 430 bp, respectively, for these data sets. Finally, we discuss ideas and optimizations for reducing the execution time of our algorithm.     

Evolution of the rat kallikrein gene family: Gene conversion leads to functional diversity

Summary Kallikrein-like simple serine proteases are encoded by closely related members of a gene family in several mammalian species. Molecular cloning and genomic Southern blot analysis after conventional and pulsed-field gel electrophoresis indicate that the rat kallikrein gene family comprises 15–20 members, probably closely linked at a single locus. Determination of the nucleotide sequences of the rGK-3,-4, and-6 genes here completes sequence data for a total of nine rat kallikrein family members. Comparison of the rat gene sequences to each other and to those of human and mouse kallikrein family genes reveals patterns of relatedness indicative of concerted evolution. Analysis of nucleotide sequence variants in kallikrein family members shows that most sequence variants are shared by multiple family members; the patterns of shared variants are complex and indicate multiple short gene conversions between family members. Sequence exchanges between family members generate novel assortments of variants in amino acid coding regions that may affect substrate specificity and thereby contribute to the diversity of enzyme activity. Furthermore, small sequence exchanges also may play a role in generating the diverse patterns of tissue-specific expression of rat family members. These analyses indicate an important role for gene conversion in the evolution of the functional diversity of these duplicated genes.     

Polarity of meiotic gene conversion is 5′ to 3′ within the niaD gene of Aspergillus nidulans

We have examined polarity of meiotic gene conversion in the niiA-niaD gene cluster of Aspergillus nidulans in two-point crosses. The type and position of the mutations represented by the niaD alleles and the correlation between the relative frequency of gene conversion and the physical position of these mutations were determined. We show that polarity of meiotic gene conversion is 5′ to 3′ (transcribed strand) within the niaD gene. Additional crosses involving a niiA allele and a niaD allele show little polarity of gene conversion, which suggests that the recombination events leading to restoration of the niaD gene are initiated upstream of the coding region of the niaD gene but within the niiA-niaD gene cluster, possibly within the intergenic promoter region.     

A yeast centromere acts in cis to inhibit meiotic gene conversion of adjacent sequences

The centromere of chromosome III (CEN3) of yeast has been examined for its ability to inhibit meiotic recombination in adjacent sequences. The effect of the centromere was investigated when it was adjacent to both of the recombining sequences (homozygous) or adjacent to only one of the two recombining DNA segments (hemizygous). When homozygous, CEN3 exerts a bidirectional repression of crossing over and a strong inhibition of gene conversion. This suggests that CEN3 reduces the frequency of crossing over by interfering with the initiation of proximal recombination events. When hemizygous, CEN3 impairs the ability of adjacent sequences to act as the recipient of genetic information during gene conversion. These results support the idea that the initiating event in yeast meiotic recombination involves the recipient molecule.     

Gene conversion: a non-Mendelian process integral to meiotic recombination

Meiosis is undoubtedly the mechanism that underpins Mendelian genetics. Meiosis is a specialised, reductional cell division which generates haploid gametes (reproductive cells) carrying a single chromosome complement from diploid progenitor cells harbouring two chromosome sets. Through this process, the hereditary material is shuffled and distributed into haploid gametes such that upon fertilisation, when two haploid gametes fuse, diploidy is restored in the zygote. During meiosis the transient physical connection of two homologous chromosomes (one originally inherited from each parent) each consisting of two sister chromatids and their subsequent segregation into four meiotic products (gametes), is what enables genetic marker assortment forming the core of Mendelian laws. The initiating events of meiotic recombination are DNA double-strand breaks (DSBs) which need to be repaired in a certain way to enable the homologous chromosomes to find each other. This is achieved by DSB ends searching for homologous repair templates and invading them. Ultimately, the repair of meiotic DSBs by homologous recombination physically connects homologous chromosomes through crossovers. These physical connections provided by crossovers enable faithful chromosome segregation. That being said, the DSB repair mechanism integral to meiotic recombination also produces genetic transmission distortions which manifest as postmeiotic segregation events and gene conversions. These processes are non-reciprocal genetic exchanges and thus non-Mendelian.Subject terms: Eukaryote, Genome     

Silk moth chorion pseudogenes: Hallmarks of genomic evolution by sequence duplication and gene conversion

The part of the genetic locus of the domesticated silk moth,Bombyx mori, in which high cysteine (Hc) chorion genes of late developmental specificity reside contains regions encompassing genelike sequences which exhibit properties distinct from those of functional Hc genes. One of these regions has been characterized and shown to contain a chorion pseudogene, ψHcB.15, which shares pronounced similarities with a transcribed chorion pseudogene, ψHcB.12/13, which was characterized previously. Both pseudogenes are homologous to HcB chorion genes but bear multiple single nucleotide substitutions and short segmental mutations (insertions and deletions) which introduce translational frame shifts and termination codons in the coding regions. Structural characteristics unique to the two pseudogenes suggest that ψHcB.15 was generated first from a functional HcB gene and gave rise subsequently to ψHcB 12/13 as a result of a sequence duplication event. The two pseudogenes can be distinguished from each other by the presence of distinct regions of similarity to the consensus sequence of functional HcB genes which appear to have arisen from gene-conversionmediated correctional events. These findings lend support to the hypothesis that chorion pseudogene sequences represent reservoirs of genetic information that participates in the evolution of the chorion locus rather than relics of inactivated genes passively awaiting extinction. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

同一染色体上基因转换在HLA多态性形成中的作用

摘要: 人类白细胞抗原(Human leukocyte antigens, HLA)是人类基因组中已知多态性最高的基因家族, 为人类面对异源多变的外界生物分子所必须。以往对HLA多态性形成的研究多集中在互换式重组机制上, 文章研究了基因转换这一重要的多态性形成机制在HLA-DRB基因多态性形成中的作用。应用已知的各基因座的等位基因序列对其进行多态性分析表明, HLA-DRB是一高度多态的基因家族。用Ester Betran模型检测到32个基因转换的区域, 最小的基因转换区域长2 bp, 最远差异位点间隔为204 bp。在71~75、18~221等几个区域上出现基因转换的频数高, 成为基因转换的热点。进一步的分析显示, 71~75、205~217等热点区域分别与东方人、高加索人这两个人群密切相关, 提示基因转换的热点可能具有一定的人群特异性