Microconversion between murine H-2 genes integrated into yeast

Patchwork homology observed between divergent members of polymorphic multigene families is thought to reflect evolution by short-tract gene conversion (nonreciprocal recombination), although this mechanism cannot usually be confirmed in higher organisms. In contrast to meiotic conversions observed in laboratory yeast strains, apparent conversions between polymorphic sequences, such as the class I loci of the major histocompatibility complex (MHC), are short and do not seem to be associated with reciprocal recombination (crossover, exchanges). We have now integrated two nonallelic murine class I genes into yeast to characterize their meiotic recombination. We found no crossovers between the MHC genes, but short-tract 'microconversions' of 1-215 base-pairs were observed in about 6% of all meioses. Strikingly, one of these events was accompanied by a single base-pair mutation. These results underscore both the importance of meiotic gene conversion and sequence heterology in determining conversion patterns between divergent genes.     

Fine-scale recombination rate differences between sexes, populations and individuals

Meiotic recombinations contribute to genetic diversity by yielding new combinations of alleles. Recently, high-resolution recombination maps were inferred from high-density single-nucleotide polymorphism (SNP) data using linkage disequilibrium (LD) patterns that capture historical recombination events. The use of these maps has been demonstrated by the identification of recombination hotspots and associated motifs, and the discovery that the PRDM9 gene affects the proportion of recombinations occurring at hotspots. However, these maps provide no information about individual or sex differences. Moreover, locus-specific demographic factors like natural selection can bias LD-based estimates of recombination rate. Existing genetic maps based on family data avoid these shortcomings, but their resolution is limited by relatively few meioses and a low density of markers. Here we used genome-wide SNP data from 15,257 parent-offspring pairs to construct the first recombination maps based on directly observed recombinations with a resolution that is effective down to 10 kilobases (kb). Comparing male and female maps reveals that about 15% of hotspots in one sex are specific to that sex. Although male recombinations result in more shuffling of exons within genes, female recombinations generate more new combinations of nearby genes. We discover novel associations between recombination characteristics of individuals and variants in the PRDM9 gene and we identify new recombination hotspots. Comparisons of our maps with two LD-based maps inferred from data of HapMap populations of Utah residents with ancestry from northern and western Europe (CEU) and Yoruba in Ibadan, Nigeria (YRI) reveal population differences previously masked by noise and map differences at regions previously described as targets of natural selection.     

Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome

Positive correlation between recombination rate and nucleoUde diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombination rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleoUde diversity was found to be significantly correlated with the recombination rate （r=0.27, P〈0.0005）. Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleoUde diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution.     

Comparison of human genetic and sequence-based physical maps

Recombination is the exchange of information between two homologous chromosomes during meiosis. The rate of recombination per nucleotide, which profoundly affects the evolution of chromosomal segments, is calculated by comparing genetic and physical maps. Human physical maps have been constructed using cytogenetics, overlapping DNA clones and radiation hybrids; but the ultimate and by far the most accurate physical map is the actual nucleotide sequence. The completion of the draft human genomic sequence provides us with the best opportunity yet to compare the genetic and physical maps. Here we describe our estimates of female, male and sex-average recombination rates for about 60% of the genome. Recombination rates varied greatly along each chromosome, from 0 to at least 9 centiMorgans per megabase (cM Mb(-1)). Among several sequence and marker parameters tested, only relative marker position along the metacentric chromosomes in males correlated strongly with recombination rate. We identified several chromosomal regions up to 6 Mb in length with particularly low (deserts) or high (jungles) recombination rates. Linkage disequilibrium was much more common and extended for greater distances in the deserts than in the jungles.     

Mapping determinants of human gene expression by regional and genome-wide association

To study the genetic basis of natural variation in gene expression, we previously carried out genome-wide linkage analysis and mapped the determinants of approximately 1,000 expression phenotypes. In the present study, we carried out association analysis with dense sets of single-nucleotide polymorphism (SNP) markers from the International HapMap Project. For 374 phenotypes, the association study was performed with markers only from regions with strong linkage evidence; these regions all mapped close to the expressed gene. For a subset of 27 phenotypes, analysis of genome-wide association was performed with >770,000 markers. The association analysis with markers under the linkage peaks confirmed the linkage results and narrowed the candidate regulatory regions for many phenotypes with strong linkage evidence. The genome-wide association analysis yielded highly significant results that point to the same locations as the genome scans for about 50% of the phenotypes. For one candidate determinant, we carried out functional analyses and confirmed the variation in cis-acting regulatory activity. Our findings suggest that association studies with dense SNP maps will identify susceptibility loci or other determinants for some complex traits or diseases.     

The landscape of recombination in African Americans

Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P?value 相似文献   

Construction of AFLP-based genetic linkage maps for the Chinese shrimp Fenneropaeneus chinensis

Fenneropaeneus chinensis is an important species in marine fishery resources and aquaculture in China. A genetic linkage map is essential for improving the efficiency of its breeding by marker-as- sisted selection and identifying commercially important genes. Linkage maps of F. chinensis were constructed with an F2 mapping population (110 progenies) using amplified fragment length polymor- phic (AFLP) marker in this study. Fifty-five AFLP primer combinations produced 532 AFLP markers fitting for map strategy in mapping family. The markers with 3:1 segregating ratios were analyzed using F2 intercross model for the common linkage map, while the markers with 1:1 ratio were analyzed using the pseudo-testcross strategy. The maps of male, female and common were constructed. The female map included 103 markers that formed 28 linkage groups, covering a total length of 1090 cM. All mark- ers were linked with the linkage groups. Segregation distortion was observed for 6 of 103 markers in the female map. The average distance between markers was 14.53 cM and ranged from 4.4 to 24.8 cM. The male map included 144 markers that formed 35 linkage groups. Ten markers remained unlinked in male map. Segregation distortion was observed for 7 of 144 markers in the male map. The total dis- tance of male map covered 1617 cM. The average distance between markers was 16.36 cM. The male map was 32.6% longer than the female map, which may reflect sex-specific recombination rates in Chinese shrimp. The common map was composed of 216 markers, including in 44 linkage groups covering a total distance of 1772.1 cM. Two markers remained unlinked. No distorted markers of 216 markers were shown in the common map. The distance between markers was 10.42 cM. An average estimated genome size for the Chinese shrimp was 2420 cM, which was consistent with the relative size of the Penaeid genome. The distribution of AFLP markers was relatively even in chromosomes of Chi- nese shrimp maps. The linkage analysis presented in this work provided some insight into the level of polymorphism and genetic variation of Chinese shrimp.     

RecA介导的特异性DNA片段捕获

外显子捕获联合高通量测序技术在检测新的致病基因,特别是罕见的基因变异时,表现出很高的检测效率.但在具体使用过程中,探针易出现非特异性杂交,设计探针时需考虑Tm值均一性、所需初始样品量较大等问题.RecA是原核生物同源重组的中心分子,参与DNA损伤的重组修复.通过在体外模拟RecA蛋白在原核生物体内重组寻找同源序列的途径,用以捕获目标DNA分子,以期提高外显子捕获过程中的探针杂交效率和特异性.根据RecA在体内同源重组中的作用模式,先将基因组染色质片段化,再纯化DNA,设计生物素标记的特异性探针,在RecA蛋白的介导下以捕获基因组中的目的同源片段.结果显示:设计的和目标片段互补的探针高效而特异地捕获了目标DNA片段,ATP和水能够破坏RecA介导形成的三链复合体的稳定性,可以作为很好的杂交后洗脱试剂,而且水直接作为洗脱试剂可以提高洗脱目的 DNA片段的效率和纯度.     

Double-strand breaks at an initiation site for meiotic gene conversion

It has been proposed that the initiation of meiotic recombination involves either single-strand or double-strand breaks in DNA. It is difficult to distinguish between these on the basis of genetic evidence because they give rise to similar predictions. All models invoke initiation at specific sites to explain polarity, which is a gradient in gene conversion frequency from one end of a gene to the other. In the accompanying paper we describe the localization of an initiation site for gene conversion to the promoter region of the ARG4 gene of the yeast Saccharomyces cerevisiae. Here, we show that a double-strand break appears at the ARG4 recombination initiation site at the time of recombination, and that the broken DNA molecules end in long single-stranded tails.     

中国人群β珠蛋白基因簇RFLP连锁不平衡及其在产前诊断中的意义

根据中国人群β珠蛋白基因簇上八个RFLP所构成的单倍型的分布频率,应用群体遗传学方法和统计学方法,分析了各种组合的RFLP之间的连锁不平衡情况,发现中国人群β~A和β~T珠蛋白基因簇上RFLP都存在不均一的连锁不平衡,把整个β蛋白基因簇分成5′—基因簇和3′—基因簇两部分。根据连锁不平衡对遗传标记的诊断意义的影响规律,结合可诊断率的研究结果,我们认为,在产前诊断β地中海贫血时,选择3′—基因簇的RFLP较选择5′—基因簇内的RFLP为佳,但在排除基因重组的情况下,则同时选择两个基因簇的RFLP可大大提高可以进行准确产前诊断的β地中海贫血家庭。     

Genome-wide phenotype analysis in ES cells by regulated disruption of Bloom's syndrome gene

The chief limitation of phenotype-based genetic screening in mammalian systems is the diploid nature of the genome. Cells deficient in the Bloom's syndrome gene (Blm) show an increased rate of loss of heterozygosity. Here we have used a tetracycline-regulated Blm allele (Blm(tet)) to introduce bi-allelic mutations across the genome in mouse embryonic stem (ES) cells. Transient loss of Blm expression induces homologous recombination not only between sister chromatids but also between homologous chromosomes. We considered that the phenotype of ES cells bearing bi-allelic mutations would be maintained after withdrawal of the tetracycline analogue doxycycline. Indeed, a combination of N-ethyl-N-nitrosourea mutagenesis and transient loss of Blm expression enabled us to generate an ES cell library with genome-wide bi-allelic mutations. The library was evaluated by screening for mutants of glycosylphosphatidylinositol-anchor biosynthesis, which involves at least 23 genes distributed throughout the genome. Mutants derived from 12 different genes were obtained and two unknown mutants were simultaneously isolated. Our results indicate that phenotype-based genetic screening with Blm(tet) is very efficient and raises possibilities for identifying gene functions in ES cells.     

A first-generation linkage disequilibrium map of human chromosome 22

DNA sequence variants in specific genes or regions of the human genome are responsible for a variety of phenotypes such as disease risk or variable drug response. These variants can be investigated directly, or through their non-random associations with neighbouring markers (called linkage disequilibrium (LD)). Here we report measurement of LD along the complete sequence of human chromosome 22. Duplicate genotyping and analysis of 1,504 markers in Centre d'Etude du Polymorphisme Humain (CEPH) reference families at a median spacing of 15 kilobases (kb) reveals a highly variable pattern of LD along the chromosome, in which extensive regions of nearly complete LD up to 804 kb in length are interspersed with regions of little or no detectable LD. The LD patterns are replicated in a panel of unrelated UK Caucasians. There is a strong correlation between high LD and low recombination frequency in the extant genetic map, suggesting that historical and contemporary recombination rates are similar. This study demonstrates the feasibility of developing genome-wide maps of LD.     

A haplotype map of the human genome

Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.     

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster.

Two genomic regions with unusually low recombination rates in Drosophila melanogaster have normal levels of divergence but greatly reduced nucleotide diversity, apparently resulting from the fixation of advantageous mutations and the associated hitch-hiking effect. Here we show that for 20 gene regions from across the genome, the amount of nucleotide diversity in natural populations of D. melanogaster is positively correlated with the regional rate of recombination. This cannot be explained by variation in mutation rates and/or functional constraint, because we observe no correlation between recombination rates and DNA sequence divergence between D. melanogaster and its sibling species, D. simulans. We suggest that the correlation may result from genetic hitch-hiking associated with the fixation of advantageous mutants. Hitch-hiking thus seems to occur over a large fraction of the Drosophila genome and may constitute a major constraint on levels of genetic variation in nature.     

遗传算法交叉算子的分析

交叉算子是遗传算法中最主要的遗传算子，对种群的搜索性能起着重要的作用。作者就维持种群多样性的角度，提出了有效交叉位置距和有效交叉点的概念，并分析了随交叉点位置不同一点交叉、两点交叉和一致交叉之间的关系，对3种交叉算子各自的搜索空间及交叉算子对模式的影响进行了分析，并给出了一些重要结论。通过函数优化验证了新交叉算子的有效性。     

Cryptic simplicity in DNA is a major source of genetic variation

DNA regions which are composed of a single or relatively few short sequence motifs usually in tandem ('pure simple sequences') have been reported in the genomes of diverse species, and have been implicated in a range of functions including gene regulation, signals for gene conversion and recombination, and the replication of telomeres. They are thought to accumulate by DNA slippage and mispairing during replication and recombination or extension of single-strand ends. In order to systematize the range of DNA simplicity and the genetic nature of the regions that are simple, we have undertaken an extensive computer search of the DNA sequence library of the European Molecular Biology Laboratory (EMBL). We show here that nearly all possible simple motifs occur 5-10 times more frequently than equivalent random motifs. Furthermore, a new computer algorithm reveals the widespread occurrence of significantly high levels of a new type of 'cryptic simplicity' in both coding and noncoding DNA. Cryptically simple regions are biased in nucleotide composition and consist of scrambled arrangements of repetitive motifs which differ within and between species. The universal existence of DNA simplicity from monotonous arrays of single motifs to variable permutations of relatively short-lived motifs suggests that ubiquitous slippage-like mechanisms are a major source of genetic variation in all regions of the genome, not predictable by the classical mutation process.     

Inversion in the H-2 complex of t-haplotypes in mice

Mouse t-haplotypes demonstrate strong linkage disequilibrium between t-lethal genes and specific H-2 types, presumably a result of recombination suppression between t and normal chromosomes. The observation of free recombination occurring between two complementary t-haplotypes suggested a chromosomal mismatch between t and normal chromosomes. Recent data showing the H-2 complex to be misplaced relative to two other markers, T and tf, in t-haplotypes suggested that chromosomal rearrangement in t-haplotypes might be the basis for their 'mismatch' with the normal chromosome. Here, to analyse the molecular nature of the rearrangement, we have cloned a polymorphic H-2 class I restriction fragment, which had previously been shown to map centromeric to the serologically defined H-2 complex in t-haplotypes. Genetic mapping studies show that this cloned t-DNA is homologous to the H-2 D region of wild-type chromosomes, and that the E alpha Ia gene maps telomeric to this DNA fragment in t-haplotypes, in contrast to its orientation in wild-type chromosomes. These results give molecular evidence for an inversion of H-2 in t-haplotypes, which may be at least partially responsible for recombination suppression and thus for linkage disequilibrium.     

Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum

Persistent and recurrent infections by Plasmodium falciparum malaria parasites result from the ability of the parasite to undergo antigenic variation and evade host immune attack. P. falciparum parasites generate high levels of variability in gene families that comprise virulence determinants of cytoadherence and antigenic variation, such as the var genes. These genes encode the major variable parasite protein (PfEMP-1), and are expressed in a mutually exclusive manner at the surface of the erythrocyte infected by P. falciparum. Here we identify a mechanism by which var gene sequences undergo recombination at frequencies much higher than those expected from homologous crossover events alone. These recombination events occur between subtelomeric regions of heterologous chromosomes, which associate in clusters near the nuclear periphery in asexual blood-stage parasites or in bouquet-like configurations near one pole of the elongated nuclei in sexual parasite forms. We propose that the alignment of var genes in heterologous chromosomes facilitates gene conversion and promotes the diversity of antigenic and adhesive phenotypes. The association of virulence factors with a specific nuclear subcompartment may also have implications for variation during mitotic recombination in asexual blood stages.     

Resolution of recombination intermediates generated during yeast mating type switching

Interchromosomal gene conversion between alleles has been shown in yeast frequently to be associated with the recombination of flanking genetic markers. Although this also holds true for gene conversion between two alleles of the yeast mating-type (MAT) locus, initiated by the homothallic switching system, we find no evidence that crossing-over ever accompanies gene conversion between the non-allelic HMR and MAT genes when initiated by this same homothallic switching system.