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PubMed1984

Sequence comparisons of non-allelic late histone genes and their early stage counterparts. Evidence for gene conversion within the sea urchin late stage gene family.

We have determined the nucleotide sequence of sea urchin (Lytechinus pictus) late stage H3 and H4 histone genes contained on the clone pLpH3H4 -21 and of the early stage H3 gene contained on the plasmid pLpA . Comparison of these differentially regulated histone genes with each other and with other L. pictus late and early stage histone H3 and H4 genes previously sequenced confirms that members of each histone gene family (early and late) are more homologous to each other than they are to members of other histone gene families. The spacer regions between two late H3-H4 gene pairs on the clones pLpH3H4 -19 and pLpH3H4 -21 have diverged to the point where they are no longer homologous. However, comparative analysis of the 5' flanking DNA has identified a sequence 5'C-T-C-A-T-G-T-A-T-T3' upstream of both late H4 genes and another, 5'A-G-A-T-T-C-A3', upstream of both H3 genes. Except for a short conserved sequence near the initiation codon, the transcribed 5' leaders of the late mRNAs differ in length and sequence in the two non-allelic late histone gene pairs. This divergence contrasts with the 95 to 96% conservation found between late histone gene coding sequences. The results suggest that there is intergenic exchange in the germline among members of the late histone gene family and that the unit of exchange is the individual gene rather than the heterotypic dimer which includes the common spacer DNA.

Animals↗
PubMed1988

Evidence for frequent gene conversion in the steroid 21-hydroxylase P-450(C21) gene: implications for steroid 21-hydroxylase deficiency.

Oligonucleotide probes specific for the deleterious mutations harbored in the P-450(C21)A pseudogene and oligonucleotide probes specific for the corresponding sequences in the B gene were prepared to examine the molecular lesions in the P-450(C21) gene of P-450(C21)-deficient patients. Using these gene-specific probes, we performed Southern blot analyses of genomic DNAs from 11 patients and eight normal individuals. At least one allele of the B gene (the 3.7-kb TaqI fragment) in a patient was inactivated by mutations caused by recombination with the A gene. The A genes in normal individuals and patients seemed to be replaced frequently (i.e., 10/19 individuals) in their 3' portions by B gene sequences. All of these alterations occurred without changing the characteristic length (3.2 kb) of the TaqI fragment of the A gene, a result strongly suggesting that frequent gene conversions and/or intragenic recombinations have happened in the P-450(C21) genes. Densitometric analysis of the autoradiograms from hybridization experiments revealed extensive variation (from one to five copies) in the copy number of the A gene (the 3.2-kb TaqI fragment) whereas that of the B gene (the 3.7-kb TaqI fragment) was relatively constant at two or three copies.

Adrenal Hyperplasia, Congenital↗
PubMed2006

Differential regulation of short- and long-tract gene conversion between sister chromatids by Rad51C.

The Rad51 paralog Rad51C has been implicated in the control of homologous recombination. To study the role of Rad51C in vivo in mammalian cells, we analyzed short-tract and long-tract gene conversion between sister chromatids in hamster Rad51C(-/-) CL-V4B cells in response to a site-specific chromosomal double-strand break. Gene conversion was inefficient in these cells and was specifically restored by expression of wild-type Rad51C. Surprisingly, gene conversions in CL-V4B cells were biased in favor of long-tract gene conversion, in comparison to controls expressing wild-type Rad51C. These long-tract events were not associated with crossing over between sister chromatids. Analysis of gene conversion tract lengths in CL-V4B cells lacking Rad51C revealed a bimodal frequency distribution, with almost all gene conversions being either less than 1 kb or greater than 3.2 kb in length. These results indicate that Rad51C plays a pivotal role in determining the "choice" between short- and long-tract gene conversion and in suppressing gene amplifications associated with sister chromatid recombination.

Animals↗
PubMed2003

C-terminal deletion of AID uncouples class switch recombination from somatic hypermutation and gene conversion.

Class-switch recombination (CSR), somatic hypermutation (SHM), and antibody gene conversion are distinct DNA modification reactions, but all are initiated by activation-induced cytidine deaminase (AID), an enzyme that deaminates cytidine residues in single-stranded DNA. Here we describe a mutant form of AID that catalyzes SHM and gene conversion but not CSR. When expressed in E. coli, AID(delta189-198) is more active in catalyzing cytidine deamination than wild-type AID. AID(delta189-198) also promotes high levels of gene conversion and SHM when expressed in eukaryotic cells, but fails to induce CSR. These results underscore an essential role for the C-terminal domain of AID in CSR that is independent of its cytidine deaminase activity and that is not required for either gene conversion or SHM.

Animals↗
PubMed1983

Evolution of a finite population under gene conversion.

Evolution at a multiallelic locus under the joint action of gene conversion, mutation, selection, and random genetic drift is studied. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. Under the assumption that all four evolutionary forces are weak, a diffusion approximation is established for the dynamics of the gene frequencies. For two alleles, the inclusion of gene conversion merely alters one of the two selection parameters of the thoroughly investigated diffusion process without conversion. Therefore, all results for this classical process, some of which are reviewed and extended here, are immediately applicable to the biologically more general problem. Small conversional disparities can dramatically affect the fixation probability (and hence the rate of gene substitution) and can greatly reduce the mean conditional fixation time of a new mutant. The mean absorption and fixation times are often sufficiently short to imply that biased gene conversion can be an important mechanism for the loss of genetic variability in and the genetic divergence of isolated populations.

Alleles↗
PubMed1999

Efficient antibody diversification by gene conversion in vivo in the absence of selection for V(D)J-encoded determinants.

Antibody diversification in the bursa of Fabricius occurs by gene conversion: pseudogene-derived sequences replace homologous sequences in rearranged immunoglobulin genes. Bursal cells expressing a truncated immunoglobulin mu heavy chain, introduced by retroviral gene transfer, bypass normal requirements for endogenous surface immunoglobulin expression. Immunoglobulin light chain rearrangements in such cells undergo gene conversion under conditions where the products are not selected based on their ability to encode a functional protein. The efficiency with which gene conversion maintains a productive reading frame exceeds 97% under such non-selective conditions. By analysis of donor pseudogene usage we demonstrate that bursal cell development is not driven by a restricted set of antigenic specificities. We further demonstrate that gene conversion can restore a productive reading frame to out-of-frame VJ(L) junctions, providing a rationale for the elimination of cells containing non-productive VJ(L) rearrangements prior to the onset of gene conversion in normal bursal cell development.

Animals↗
PubMed1994

Radiation-induced mitotic gene conversion frequency in yeast is modulated by the conditions allowing DNA double-strand break repair.

Repair of DNA double-strand breaks (DSB) involves recombinational processes which may lead to gene conversion (intragenic recombination). Using the diploid yeast mutant rad54-3 heteroallelic for his1 (his1-7/his1-1) and temperature conditional for DSB rejoining, radiation induced gene conversion was investigated as dependent on DSB repair under different postirradiation conditions. Gene conversion is negligible under conditions preventing DSB repair (36 degrees C). In contrast, gene conversion is observed when cells are incubated at the permissive temperature (23 degrees C) both under growth and nongrowth conditions. However, there is a much higher yield of convertants for cells incubated under growth as opposed to nongrowth conditions. These results can most plausibly be explained by the cell cycle regulated enhancement of the expression of genes such as PMS and POL3 known to be involved in gene conversion processes and/or the enhanced recombination in transcriptionally active genes. 'Nutrient stress' inducible responses and/or cell cycle specific recombination pathways leading to gene conversion events preferentially in S-phase cells seem to be less likely.

Cell Survival↗
PubMed2026

High levels of mitotic gene conversion are needed to effectively purge deleterious mutations in asexual organisms.

Self-fertilisation and asexual reproduction are both hypothesised to cause long-term extinction due to inefficient selection against deleterious mutations. Self-fertilisation can counter these effects through creating homozygous genotypes and purging deleterious mutations. Although complete asexuality lacks meiotic gene exchange, mitotic gene conversion creates homozygous regions that could limit deleterious mutation accumulation in an analogous manner. We compare mutation accumulation in self-fertilising and facultative sexual populations subject to mitotic gene conversion, and quantify the efficacy of purging in the latter. We first show analytically that purging is most effective with high levels of asexuality and gene conversion, and when deleterious mutations are recessive. We further show using simulations that, when mitotic gene conversion becomes sufficiently high in obligate asexuals, there is a reduction in the mutation count and a jump in homozygosity, reflecting purging. However, this mechanism is not necessarily as efficient at purging under high self-fertilisation, and elevated rates of mitotic gene conversion seem to be needed for widespread purging compared to empirical estimates. If gene conversion rates are allowed to evolve, then elevated rates that increase mean fitness can arise, but only if there is sufficient variance in the gene conversion rate. Conversely, if gene conversion rates are already high and rates are not constrained then they will slightly decrease, reducing mean fitness.

Self-fertilisation↗
PubMed1994

Long-tract mitotic gene conversion in yeast: evidence for a triparental contribution during spontaneous recombination.

In Saccharomyces cerevisiae, spontaneous mitotic gene conversion at one site is statistically correlated with recombination at other loci. In general, coincident conversion frequencies are highest for tightly linked markers and decline as a function of intermarker distance. Paradoxically, a significant fraction of mitotic gene convertants exhibits concomitant nonreciprocal segregation for multiple and widely spaced markers. We have undertaken a detailed genetic analysis of this class of mitotic recombinants. Our results indicate that mitotic gene conversion in yeast is frequently associated with nonreciprocal segregation of markers centromere-distal to the selected site of conversion. In addition, distal markers are often found to be mosaic within the product colonies. These observations, and others described here, suggest that a percentage of gene conversion in vegetative yeast cells is coupled to a chromosome break and repair mechanism. This hypothesis was further tested using a strain trisomic for chromosome VII which was specially marked to detect homolog-dependent repair events. An association between mitotic gene conversion events and the production of broken chromosomes which are repaired by a homologous-pairing-copy mechanism was supported.

Chromosome Mapping↗
PubMed1990

Effect of gene conversion on variances of digenic identity measures.

The variances and covariances of digenic descent measures are studied for a two-locus model incorporating mutation, gene conversion, recombination, drift, and finite sampling. Gene conversion can occur between allelic pairs of genes or between non-allelic pairs on the same or different gametes within individuals. Most interest therefore centers on pairs of genes, and five digenic identity measures are required. The behavior over time of these measures is studied, with an emphasis on the effects of gene conversion. Because of the stochastic nature of the forces of drift, recombination, mutation, and conversion, the actual identity status of gene pairs can vary from expectation among replicate populations. To study this variation we compute the expected variances and covariances of the measures, and show that this requires the introduction of trigenic and quadrigenic measures. Allowing for conversion between genes on different gametes requires a large number of these higher-order measures.

Gene Conversion↗
PubMed1992

Closely linked H2B genes in the marine copepod, Tigriopus californicus indicate a recent gene duplication or gene conversion event.

Two nonallelic histone gene clusters were characterized in the marine copepod, Tigriopus californicus. The DNA sequence of one of the clusters reveals six genes in the contiguous arrangement of H2B, H1, H3, H4, H2B and H2A. The order of genes within the second cluster is H3, H4, H2B and H2A. There is no evidence for the presence of an H1 gene in this cluster. Comparison of the three copepod H2B genes reveals a high degree of similarity between the 5' upstream regions and between the amino terminal halves of the two H2B genes found within the same cluster. From these data we infer that gene duplication and/or gene conversion events occurred within this cluster in the recent past.

Alleles↗
PubMed2003

Contractions and expansions of CAG/CTG trinucleotide repeats occur during ectopic gene conversion in yeast, by a MUS81-independent mechanism.

CAG/CTG trinucleotide repeat tracts expand and contract at a high rate during gene conversion in Saccharomyces cerevisiae. In order to characterize the mechanism responsible for such rearrangements, we built an experimental system based on the use of the rare cutter endonuclease I-SceI, to study the fate of trinucleotide repeat tracts during meiotic or mitotic (allelic or ectopic) gene conversion. After double-strand break (DSB) induced meiotic recombination, (CAG)(98) and (CAG)(255) are rearranged in 5% and 52% of the gene conversions, respectively, with similar proportions of contractions and expansions. No evidence of a meiotic hot spot activity associated with trinucleotide repeats could be found. When gene conversion is induced by a DSB during mitotic growth of the cells, no rearrangement of the repeat tracts is detected when the donor sequence is allelic to the recipient site of the DSB. However, when the donor sequence is at an ectopic location, frequent contractions and expansions of the repeat tract are found. No crossing-over associated with gene conversion could be detected. Mutants for the MUS81 gene, involved in the resolution of recombination intermediates, show a frequency of rearrangements identical with that of the wild-type strain. We concluded that trinucleotide repeat rearrangements occur frequently during ectopic but not during allelic recombination, by a mechanism that does not require crossover formation.

Alleles↗
PubMed1990

Somatic diversification of immunoglobulin heavy chain VDJ genes: evidence for somatic gene conversion in rabbits.

Rabbits preferentially utilize only one of their multiple functional germline immunoglobulin VH genes. This preferential usage of one gene, VH1, raises the question of how rabbits generate antibody diversity. VDJ diversification was analyzed by cloning and sequencing VH1 gene rearrangements. Comparison of these sequences with that of germline VH1 identified clusters of nucleotide changes, including codon insertions and deletions. To investigate whether gene conversion was involved in this somatic diversification, we searched a data base of rabbit germline VH gene sequences for donor VH genes; potential donors were identified for five diversified regions. We conclude that somatic gene conversion has a major role in generating antibody diversity in rabbits. These studies provide clear evidence for somatic gene conversion of mammalian VDJ genes.

Animals↗
PubMed1983

Evolution of a large population under gene conversion.

The dynamics of allelic frequencies at a single multiallelic locus under gene conversion is studied. Generations are discrete and nonoverlapping; the diploid monoecious population mates at random; selection, mutation, and random drift are negligible. Analytical and numerical investigation indicates the following. (i) If gene conversion is biased within at least one pair of alleles, then the frequency of at least one allele must become arbitrarily small. (ii) If conversion is biased within every pair of alleles, then the frequency of at most one allele can fail to become arbitrarily small. Although allelic frequencies may become repeatedly small instead of remaining small, the biological ubiquity of small random perturbations (due, e.g., to random genetic drift) guarantees the ultimate loss of at least one allele in case i and of all alleles but one in case ii. The decay of genetic variability is often sufficiently rapid to imply that biased gene conversion can be an important mechanism for the genetic divergence of isolated populations.

Alleles↗
PubMed2005

Recovering haplotype structure through recombination and gene conversion.

MOTIVATION: Understanding haplotype evolution subject to mutation, recombination and gene conversion is fundamental to understand genetic specificities of human populations and hereditary bases of complex disorders. The goal of this project is to develop new algorithmic tools assisting the reconstruction of historical relationships between haplotypes and the inference of haplotypes from genotypes. RESULTS: We present two new algorithms. The first one finds an optimal pathway of mutations, recombinations and gene conversions leading to a given haplotype of size m from a population of h haplotypes. It runs in time O(mhs(2)), where s is the maximum number of contiguous sites that can be exchanged in a single gene conversion. The second one finds an optimal pathway of mutations and recombinations leading to a given genotype, and runs in time O(mh(2)). Both algorithms are based on a penalty score model and use a dynamic programming approach. We apply the second one to the problem of inferring haplotypes from genotypes, and show how it can be used as an independent tool, or to improve the performance of existing methods. AVAILABILITY: The algorithms have been implemented in JAVA and are available on request.

Algorithms↗
PubMed1990

Null alleles of human complement C4. Evidence for pseudogenes at the C4A locus and for gene conversion at the C4B locus.

The two genes for the C4A and C4B isotypes of the fourth component of human complement are located in the MHC class III region. Previous studies have demonstrated the unusual expression of C4 genes in the form of aberrant or duplicated haplotypes. Null alleles of C4A or C4B (AQ0 or BQ0) have been defined by the absence of gene products and occur at frequencies of 0.1-0.3. However, only some C4 null alleles are due to gene deletions, the remainder were thought to be nonexpressed genes. We have analyzed the C4 gene structure of 26 individuals lacking either C4A or C4B protein. The DNA of individuals with apparently nonexpressed C4 genes was tested for the presence of C4A- and C4B-specific sequences using restriction fragment analysis and isotype-specific oligonucleotide hybridization of DNA amplified by polymerase chain reaction. All nondeleted AQ0 allels had C4A-specific sequences and may thus be described as pseudogenes, whereas the nondeleted BQ0 alleles had C4A-instead of C4B-specific sequences. Gene conversion is the probable mechanism by which a C4A gene is found at the second C4 locus normally occupied by C4B genes.

Alleles↗
PubMed2004

Immunoglobulin gene conversion in chicken DT40 cells largely proceeds through an abasic site intermediate generated by excision of the uracil produced by AID-mediated deoxycytidine deamination.

Diversification of the primary antibody repertoire in chickens is achieved by a gene conversion process that uses a set of immunoglobulin variable (IgV) pseudogenes as templates. Studies usingthe chicken DT40 B lymphoma cell line have shown that this gene conversion is dependent on activation-induced deaminase, which deaminates deoxycytidine to deoxyuridine in the IgV gene. The mechanism by which the resultant deoxyuridine/deoxyguanosine (dU/dG) mismatch acts to initiate the gene conversion process is unknown but likely involves either (i) recognition of the dU/dG pair by the mismatch repair complex or (ii) recognition of the dU itself by uracil-DNA glycosylase. To discriminate these possibilities, we have investigated the effects on IgV gene conversion of inhibiting uracil-DNA glycosylase. We find that such inhibition diminishes gene conversion, biasing instead towards point mutations. These results demonstrate that IgV gene conversion in DT40 cells is substantially dependent on uracil excision and implies that it proceeds by a pathway involving an abasic site, which could be acted upon by an apyrimidinic endonuclease to generate a DNA strand break facilitating the conversion process.

Animals↗
PubMed1994

Analysis of sequence transfers resembling gene conversion in a mouse antibody transgene.

The role of gene conversion in murine immunoglobulin gene diversification is unclear. An antibody gene construct designed to provide the homologous donor and acceptor sequences required for conversion mechanisms was produced and used to generate transgenic mice. When these transgenic mice were immunized, DNA sequence transfers between tandem transgene VDJ regions were detectable and resembled gene conversion events. There is a strong link between these conversion-like sequence transfers and transgene somatic hypermutation, suggesting that both processes might occur at the same stage of B cell differentiation.

Animals↗