Recombination directionality factors (RDFs), or excisionases, are essential players of prophage excisive recombination. Despite the essentially catalytic role of the integrase in both integrative and excisive recombination, RDFs are required to direct the reaction towards excision and to prevent re-integration of the prophage genome when entering a lytic cycle. KplE1, HK620 and numerous (pro)phages that integrate at the same site in enterobacteria genomes (such as the argW tRNA gene) all share a highly conserved recombination module. This module comprises the attL and attR recombination sites and the RDF and integrase genes. The KplE1 RDF was named TorI after its initial identification as a negative regulator of the tor operon. However, it was characterized as an essential factor of excisive recombination. In this study, we designed an extensive random mutagenesis protocol of the torI gene and identified key residues involved in both functions of the TorI protein. We show that, in addition to TorI-TorR
Meiosis is a cell division process that produces haploid gametes from diploid cells. Several important meiotic events take place during prophase of meiosis I, most important being homologous chromosome pairing, meiotic recombination and formation of the synaptonemal complex (SC). These processes assure proper segregation of the homologous chromosomes into the haploid germ cells. Improper segregation of the homologos can cause chromosomal abnormality (aneuploidy), which causes various human disorders, notably mental retardation and pregnancy loss.. This thesis focuses on the relationship between recombination and the formation of SCs, aggregates of SC-related materials (polycomplexes) and recombination enzymes during meiosis. We have investigated SC formation in the absence of recombination, nature of polycomplexes and recombination enzymes in relation to the SCs structures and recombination nodules (RNs) in yeast Saccharomyces cerevisiae.. Studies on yeast mutants suggest that the formation of ...
60125DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 1rkycwgcttt yktrtacnaa stsgb 25225DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 2agccwgcttt yktrtacnaa ctsgb 25325DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 3gttcagcttt cktrtacnaa ctsgb 25425DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 4agccwgcttt cktrtacnaa gtsgb 25525DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 5gttcagcttt yktrtacnaa gtsgb 25625DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 6agcctgcttt tttgtacaaa cttgt 25725DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 7agcctgcttt cttgtacaaa cttgt 25825DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence 8acccagcttt cttgtacaaa gtggt 25925DNAUnknownDescription of Unknown Recombination products oligonucleotide sequence ...
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 ...
Author Summary Homologous recombination is an indispensable feature of the mammalian meiotic program and an important mechanism for creating genetic diversity. Despite its central significance, recombination rates vary markedly between species and among individuals. Although recent studies have begun to unravel the genetic basis of recombination rate variation within populations, the genetic mechanisms of species divergence in recombination rate remain poorly characterized. In this study, we show that two closely related house mouse subspecies differ in their genomic recombination rates by ∼30%, providing an excellent model system for studying evolutionary divergence in this trait. Using quantitative genetic methods, we identify eight genomic regions that contribute to divergence in global recombination rate between these subspecies, including large effect loci and multiple loci on the X-chromosome. Our study uncovers novel genomic loci contributing to species divergence in global recombination rate
In Saccharomyces cerevisiae, Rad59 is required for multiple homologous recombination mechanisms and viability in DNA replication-defective rad27 mutant cells. Recently, four rad59 missense alleles were found to have distinct effects on homologous recombination that are consistent with separation-of-function mutations. The rad59-K166A allele alters an amino acid in a conserved α-helical domain, and, like the rad59 null allele diminishes association of Rad52 with double-strand breaks. The rad59-K174A and rad59-F180A alleles alter amino acids in the same domain and have genetically similar effects on homologous recombination. The rad59-Y92A allele alters a conserved amino acid in a separate domain, has genetically distinct effects on homologous recombination, and does not diminish association of Rad52 with double-strand breaks. In this study, rad59 mutant strains were crossed with a rad27 null mutant to examine the effects of the rad59 alleles on the link between viability, growth and the stimulation of
View Notes - Bacterial Recombination from MCB 2000 at University of Florida. BACTERIAL RECOMBINATION Purposes A. Vaccine production (subunit type) B. Production of proteins (growth hormone) C.
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To create this landmark map, Comeron and colleagues generated recombinant advanced intercross lines (RAIL), derived from eight crosses among twelve wild-derived lines. To accurately identify crossover and noncrossover events, haplotype rather than genotype data are required, and Comeron and colleagues use a clever technique to recover haplotypes. RAIL females were individually crossed to D. simulans, and the genomes of single hybrid progeny were sequenced with Illumina technology. Reads mapping to D. simulans were removed bioinformatically to reveal a haploid, meiotically produced D. melanogaster genome. In all, over 100,000 recombination events were localized with kilobase-level precision.. Certainly, this genome-wide recombination map will empower population genetic and molecular evolutionary studies in Drosophila for years to come. However, the sheer number of events catalogued combined with the resolution at which breakpoints could be mapped facilitates a great deal more than quantifying ...
Recombination increases dramatically during meiosis to promote genetic exchange and generate recombinant progeny. Interestingly, meiotic recombination is unevenly distributed throughout genomes, and, as a consequence, genetic and physical map distances do not have a simple linear relationship. Recombination hotspots and coldspots have been described in many organisms and often reflect global features of chromosome structure. In particular, recombination frequencies are often distorted within or outside sex-determining regions of the genome. Here, we report that recombination is elevated adjacent to the mating-type locus (MAT) in the pathogenic basidiomycete Cryptococcus neoformans. Among fungi, C. neoformans has an unusually large MAT locus, and recombination is suppressed between the two |100-kilobase mating-type specific alleles. When genetic markers were introduced at defined physical distances from MAT, we found the meiotic recombination frequency to be ~20% between MAT and a flanking marker at 5,
Recombination hotspots are regions in a genome that exhibit elevated rates of recombination relative to a neutral expectation. The recombination rate within hotspots can be hundreds of times that of the surrounding region. Recombination hotspots result from higher DNA break formation in these regions, and apply to both mitotic and meiotic cells. This appellation can refer to recombination events resulting from the uneven distribution of programmed meiotic double-strand breaks. Meiotic recombination through crossing over is thought to be a mechanism by which a cell promotes correct segregation of homologous chromosomes and repair of DNA damages. Crossing over requires a DNA double-stranded break followed by strand invasion of the homolog and subsequent repair. Initiation sites for recombination are usually identified by mapping crossing over events through pedigree analysis or through analysis of linkage disequilibrium. Linkage disequilibrium has identified more than 30,000 hotspots within the ...
Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. Based on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant
Accessory replicative helicases aid the primary replicative helicase in duplicating protein-bound DNA, especially transcribed DNA. Recombination enzymes also aid genome duplication by facilitating the repair of DNA lesions via strand exchange and also processing of blocked fork DNA to generate structures onto which the replisome can be reloaded. There is significant interplay between accessory helicases and recombination enzymes in both bacteria and lower eukaryotes but how these replication repair systems interact to ensure efficient genome duplication remains unclear. Here, we demonstrate that the DNA content defects of Escherichia coli cells lacking the strand exchange protein RecA are driven primarily by conflicts between replication and transcription, as is the case in cells lacking the accessory helicase Rep. However, in contrast to Rep, neither RecA nor RecBCD, the helicase/exonuclease that loads RecA onto dsDNA ends, is important for maintaining rapid chromosome duplication. Furthermore, RecA
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We have characterized homologous recombination between linear DNA and the bacterial chromosome that depends on λ recombination functions, involves very short homologies, and is very efficient. We examined several parameters to establish a maximal efficiency for phage-mediated recombination with short homologies. Maximal recombination levels are achieved with induction times from 7.5-17.5 min at 42°C, and a homology segment of 40-50 bp. Recombination saturates at a linear DNA substrate concentration of about 300 molecules per cell.. The fact that 30- to 50-bp homologies are able to recombine in vivo opens a vast array of new possibilities for generating recombinant DNA. Several steps normally involved in generating recombinant DNA molecules are eliminated. Restriction enzyme digests are not required to generate DNA fragments, and DNA ligase reactions are not required to join different DNA fragments at novel junctions. PCR amplification followed by electroporation of the linear DNA into cells is ...
October 3, 2004. October 3, 2004 - In a paper published today in the online edition of Nature Genetics, a deCODE-led team of scientists present the results of a large-scale population study linking recombination rate with maternal age and fertility. In the paper, entitled "Recombination rate and reproductive success in humans," the deCODE team establish a novel and significant correlation between recombination - the shuffling of chromosomal material that takes place in the formation of eggs and sperm - and maternal age and fertility. Specifically, the average number of recombinations in eggs that go on to become successful live births tends to increase with the mothers age, and mothers with a higher recombination rate in general also tend to have more children than do those with a lower recombination rate. The authors conclude that the most likely explanation for this phenomenon is that recombination, which is one of the most important mechanisms for generating genetic diversity in ...
Rates of intragenic recombination are suppressed in the vicinity of Ds and Mu1 insertions (23, 34, 40). In addition, Ds insertions are thought to alter the distribution of recombination breakpoints in the otherwise uniformly recombinogenic bz1 locus to create allele-specific hot and cold spots (34). In contrast, a preliminary analysis did not provide any evidence that a Mu1 insertion in the a1 gene alters the distribution of recombination event (23).. In this previous study, the positions of 15 recombination events isolated from the a1-mum2/a1∷rdt heterozygote were physically mapped within the 1.2-kb interval of the a1 gene that is defined by the Mu1 and rdt transposon insertions. All but one of these recombination events resolved within a 377-bp recombination hot spot. Xu et al. (23) compared this distribution of recombination events to those isolated from a directly comparable heterozygote that does not contain the Mu1 insertion in the a1 gene (A1-LC/a1∷rdt). This comparison is appropriate ...
RECOMBINATION plays a crucial role in the molecular evolution of many bacteria, in spite of the clonal nature of bacterial reproduction. Indeed, for a large number of species surveyed in recent studies (Vos and Didelot 2009; Fearnhead et al. 2015), homologous recombination was found to account for a similar or greater number of nucleotide changes than point mutation.. However, many traditional phylogenetic methods (Huelsenbeck and Ronquist 2001; Drummond et al. 2002; Guindon and Gascuel 2003) do not account for recombination. This is regrettable for several reasons. First, ignoring recombination is known to bias phylogenetic analyses in various ways such as by overestimating the number of mutations along branches, artificially degrading the molecular clock hypothesis, and introducing apparent exponential population growth (Schierup and Hein 2000). Second, much of modern computational phylogenetics extends beyond the inference of phylogenetic relationships and instead focuses on the parametric ...
In viruses, recombination may allow foreign genes to be acquired or may create a composite genome through recombination between different virus variants. The ability to identify a recombinant virus and the positions where recombination occurred is only as certain as the identification of the component parental viral genomes from which it was generated. Recombination detection thus shares many elements and is ultimately dependent on evolutionary reconstructions and, most importantly, on methods for the delineation of separate phylogenetic groups. The structure of the 5 untranslated region (5 UTR) of picornaviruses provides a further example of modular exchange through recombination during the evolution of separate genera within the picornavirus family. Members of the same picornavirus genus show conserved gene order and content, and over the much shorter evolutionary time scale in which species and serotypes developed, gene exchange is best documented as homologous recombination events. One of the
Meiotic recombination hotspots control the frequency and distribution of Spo11 (Rec12)-initiated recombination in the genome. Recombination occurs within and is regulated in part by chromatin structure, but relatively few of the many chromatin remodeling factors and histone posttranslational modifications (PTMs) have been interrogated for a role in the process. We developed a chromatin affinity purification and mass spectrometry-based approach to identify proteins and histone PTMs that regulate recombination hotspots. Small (4.2 kbp) minichromosomes (MiniCs) bearing the fission yeast ade6-M26 hotspot or a basal recombination control were purified approximately 100,000-fold under native conditions from meiosis; then, associated proteins and histone PTMs were identified by mass spectrometry. Proteins and PTMs enriched at the hotspot included known regulators (Atf1, Pcr1, Mst2, Snf22, H3K14ac), validating the approach. The abundance of individual histones varied dynamically during meiotic progression in
Genetic recombination is the production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be passed on from the parents to the offspring. Most recombination is naturally occurring. During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes. This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed) (see SDSA pathway in Figure); or by the breaking and rejoining of DNA strands, which forms new molecules of DNA (see DHJ pathway in Figure). Recombination may also occur during mitosis in eukaryotes where it ordinarily involves the two sister chromosomes formed after chromosomal replication. In this case, new combinations of ...
In yeast meiosis, ascosporal colonies are sometimes sectored for a marker--i.e., half the colony has one allele and half has the other. This is interpreted as replicative resolution of heteroduplex DNA (hDNA) formed as a recombination intermediate. We have looked for similar evidence of hDNA formation during mitotic recombination between two repeated sequences on the same chromosome. The two repeats, an ochre suppressor and a wild-type tRNA gene, are separated by plasmid DNA and the URA3 marker. Recombination between the repeats excises the URA3 gene and one copy of the repeat, leaving either the wild-type tRNA or the suppressor on the chromosome. A red/white color assay is used to distinguish between the two. We find that some colonies that have lost the URA3 gene are sectored for the suppressor. This suggests that hDNA is formed across the anticodon during the recombination event and then resolved by replication. The disruption of either of two genes involved in recombination and repair, RAD1 and
[email protected] research • lab members • publications. My lab is active in three somewhat related research areas: 1) the mechanism of mitotic recombination, 2) the genetic regulation of genome stability, and 3) genetic instability associated with interstitial telomeric sequences. Almost all of our studies are done using the yeast Saccharomyces cerevisiae.. Mechanism of mitotic recombination. Mitotic recombination, an important mechanism for the repair of DNA damage, is less well characterized than meiotic recombination. One difficulty is that mitotic recombination events are 104-fold less frequent than meiotic recombination events. We developed a greatly improved system for identifying and mapping mitotic crossovers at 1-kb resolution throughout the genome. This system uses DNA microarrays to detect loss of heterozygosity (LOH) resulting from mitotic crossovers. We identified motifs associated with high levels of spontaneous mitotic recombination. In particular, we demonstrated that a ...
The emergence of novel pathogenic organisms due to the acquisition of virulence determinants from bacteriophages has generated significant interest in the pathways responsible for genomic rearrangements. Phageλ encodes its own recombination system, the Red system, comprising Exo, β and γ proteins. In addition,λ encodes another recombinase, Orf, which participates in the initial stages of genetic exchange and supplies a frmction equivalent to that of the Escherichia coli RecFOR proteins. This thesis focuses on determining the function of Orf in phage and bacterial recombination pathways by analysing its impact on recombinases encoded by λ and E. coli. Experiments revealed that Orf interacts with bacterial and phage recombination proteins in the initial exchange step of recombination, modulating the activities of both Exo and RecA. Orf, along with β, attenuates the 5-3 exonuclease activity of Exo, a feature that depends largely on the ability of Orf to bind DNA. Orf also facilitates ...
Parasites and hosts are involved in a continuous coevolutionary process leading to genetic changes in both counterparts. To understand this process, it is necessary to track host responses, one of which could be an increase in sex and recombination, such as is proposed by the Red Queen hypothesis. In this theoretical framework, the inducible recombination hypothesis states that B-chromosomes (genome parasites that prosper in natural populations of many living beings) elicit an increase in host chiasma frequency that is favoured by natural selection because it increases the proportion of recombinant progeny, some of which could be resistant to both B-chromosome effects and B-accumulation in the germline. We have found a clear parallelism between host recombination and the evolutionary status of the B-chromosome polymorphism, which provides explicit evidence for inducible recombination and strong support for the Red Queen hypothesis.. ...
Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genom …
Although DNA is surprisingly fluid, there are enzymes that mediate recombination--by initiating DNA binding, strand invasion, and stabilizing ssDNA intermediates. Also, of important note, is that organisms have varying degrees of recombination levels. A classical example occurs within the Mycobacteria. Mycobacterium smegmatis has relatively low levels of illegitimate recombination (IR), while M. tuberculosis is notorious for high levels of IR compared to homologous recombination. This raises a question that can be phrased in a few ways. "What enzymes are responsible for IR?" or perhaps, "What enzymes for homologous recombination are lacking ...
Lien vers Pubmed [PMID] - 15218022. J. Biol. Chem. 2004 Aug;279(35):36625-32. By frequently rearranging large regions of the genome, genetic recombination is a major determinant in the plasticity of the human immunodeficiency virus type I (HIV-1) population. In retroviruses, recombination mostly occurs by template switching during reverse transcription. The generation of retroviral vectors provides a means to study this process after a single cycle of infection of cells in culture. Using HIV-1-derived vectors, we present here the first characterization and estimate of the strength of a recombination hot spot in HIV-1 in vivo. In the hot spot region, located within the C2 portion of the gp120 envelope gene, the rate of recombination is up to ten times higher than in the surrounding regions. The hot region corresponds to a previously identified RNA hairpin structure. Although recombination breakpoints in vivo cluster in the top portion of the hairpin, the bias for template switching in this same ...
Meiotic recombination is initiated by DNA double-strand breaks (DSBs) created by the topoisomerase-like protein Spo11. During DSB formation, Spo11 becomes covalently attached to the 5 DSB ends. Removal of Spo11 is essential to repair the DSB by homologous recombination. Spo11 is removed endonucleolytically creating short-lived Spo11-oligonucleotide products. Here I demonstrate that: 1. Spo11-oligonucleotide products are not detected in recombination mutants believed to be defective in meiotic DSB formation. 2. When DSB repair is delayed, Spo11-oligonucleotides persist for longer. 3. Processing of Spo11-DSB ends to create Spo11-oligonucleotides is largely dependent on Mec1 and Tel1 activity. In the process of investigating Spo11-oligonucleotide degradation, it was observed that a mutant defective in both the meiotic recombination checkpoint and in DSB repair failed to accumulate the expected level of DSBs. Work described here leads to the proposal of a DSB feedback mechanism that functions ...
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Recombination raises during meiosis to market genetic exchange and generate recombinant progeny dramatically. hereditary markers were released at described physical ranges from we discovered the meiotic recombination rate of recurrence to become ~20% between and a flanking marker at 5, 10, 50, or 100 kilobases from the proper border. As a total result, the physical/hereditary map percentage in the areas adjacent to can be distorted ~10- to 50-collapse set alongside the genome-wide normal. Moreover, recombination frequently occurred on both family member edges of and bad disturbance between crossovers was observed. heterozygosity had not been required for improved recombination, implying that process CALNA2 isnt because of a physical distortion from both non-paired alleles and may also happen during same-sex mating. Series analysis exposed a 68550-75-4 supplier relationship between high G + C content material and these hotspot areas. We hypothesize that the current presence of recombinational ...
I have posted a few times before about a new group bionet.molbio.recombination that I will be proposing soon.... Here is the rough proposal... if you have any comments please send them!!!! Start----------- Proposal to establish RECOMBINATION/bionet.molbio.recombination Proposed USENET name: bionet.molbio.recombination (unmoderated) Proposed mailing list name: RECOMBINATION Proposed e-mail addresses: recom at net.bio.net recom at daresbury.ac.uk Discussion leaders: Graham Dellaire, e-mail: popa0206 at po-box.mcgill.ca (b2xe at musicb.mcgill.ca) Department of Medicine (Div. of Exp. Medicine), McGill Univeristy, Montreal, Quebec, Canada George Szatmari, e-mail: szat at ere.umontreal.ca Tentatively Denis Cournoyer (Mcgill Experimental Medicine) (gene therapy) Terry Chow (McGill): e-mail MDTY at Musica.mcgill.ca (mammalian genetics) Charter: The purpose of the RECOMBINATION newsgroup is to provide a proper forum for the discussion of issues pertaining and involving recombination of DNA or RNA, in its ...
Whereas the core homologous-recombination machinery is conserved between yeast and humans, it is now clear that additional important homologous-recombination proteins, such as BRCA1 and BRCA2, are present only in mammalian cells. Germline mutations in the BRCA1 and BRCA2 genes were first identified because they predispose carriers to breast cancer [17]. Early on, associations between both BRCA proteins and human Rad51 were demonstrated, suggesting a link between homologous recombination and the BRCA proteins [17]. The involvement of the BRCA proteins in homologous recombination has now been firmly established by recent experiments from a number of laboratories.. The involvement of mouse Brca1 in homologous recombination was established by the Jasin [18] and Koller [19] laboratories. They used homologous gene-targeting assays to measure the efficiency of homologous recombination. They found that gene targeting in Brca1-deficient mouse embryonic stem cells was reduced by more than 20-fold compared ...
Molecular models of meiotic recombination have evolved over the years as relevant evidence accumulated. A major incentive for developing a fundamental understanding of the mechanism of meiotic recombination is that such understanding is crucial for solving the problem of the adaptive function of sex, a major unresolved issue in biology. A recent model that reflects current understanding was presented by Anderson and Sekelsky,[7] and is outlined in the first figure in this article. The figure shows that two of the four chromatids present early in meiosis (prophase I) are paired with each other and able to interact. Recombination, in this version of the model, is initiated by a double-strand break (or gap) shown in the DNA molecule (chromatid) at the top of the first figure in this article. However, other types of DNA damage may also initiate recombination. For instance, an inter-strand cross-link (caused by exposure to a cross-linking agent such as mitomycin C) can be repaired by HRR. As ...
Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits, such as the emergence of pathogenicity. Here, we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species and found all species have hot regions with elevated rates relative to the genome average. We examined the size, gene content, and chromosomal features associated with these regions and the correlations between closely related species. The recombination landscape is variable and evolves rapidly. For example in Salmonella, only short regions of around 1 kb in length are hot whereas in the closely related species Escherichia coli, some hot regions exceed 100 kb, spanning many genes. Only Streptococcus pyogenes shows evidence for the positive correlation between GC content and recombination that has been reported for several
Homologous recombination is a process that occurs within the chromosome and which allows one piece of DNA to be exchanged for another piece. It is a cellular mechanism that is probably part of the normal process cells use to repair breaks in their chromosomes. Homologous recombination A modified version of the target gene replaces it in the chromosome. The target gene is removed and degraded. In this example, the gene is modified by insertion of an antibiotic resistance gene, which both inactivates the gene and allows efficient selection of transformed cells. requires that the pieces of DNA undergoing recombination be almost identical (homologous) in sequence. In addition, sequences on either side of the target should be identical, to promote more efficient targeting and recombination.. By constructing a sequence that is homologous to a target sequence (such as a gene), laboratory researchers can replace one of the cells own copies of a particular gene with a copy that has been altered in some ...
Methods for evolving recombinase protein homologues and RecA/VirE2 fusion proteins which complement VirE2 deficient Agrobacterium are provided. The use of recombinase protein homologues and RecA/VirE2 fusion proteins in the context of Agrobacterium mediated transformation are provided. Methods for producing transgenic organisms by homologous recombination using evolved recombinase proteins and Agrobacterium strains which express recombinase protein homologues or RecA/VirE2 fusion proteins are provided. Transgenic cells and organisms which have integrated an exogenous DNA sequence into a predetermined site in their genome are provided.
Eukaryotic organisms maintain stable genomes despite the presence of repeated DNA sequences and efficient homologous recombination. The absence of frequent deletions and translocations due to exchange between repeats, particularly in meiosis where recombination is elevated, suggests the existence of mechanisms to suppress such recombination. Indeed, the amount of meiotic recombination per unit length DNA falls dramatically as the size and repetitive DNA content of eukaryotic genomes increases. For example, although human cells contain ∼150 times more DNA per haploid genome than yeast, both species exhibit similar numbers of reciprocal exchanges per meiosis (Lewin, 1990). The basis for this decline in recombination frequencies is not well understood, but may be explained by such diverse mechanisms as changes in chromosome compaction and altered distribution and/or reduced frequency of recombination initiation sites in the genome.. Our laboratory has investigated the pathways of recombination in ...
BACKGROUND: Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. RESULTS: Recombination rate is negatively correlated with genome size, which is likely caused by the ...
Mechanism and Control of Meiotic Recombination. We study homologous recombination and chromosome structural changes that occur during meiosis, using budding yeast as a model system. Recombination, and in particular the crossover products of recombination, are essential for proper chromosome segregation during meiosis. Chromosome mis-segregation caused by defects in meiotic recombination leads to chromosome imbalance in gametes, and these chromosome imbalances are a leading cause of infertility and birth defects in modern human populations. We aim to describe the molecular steps of meiotic recombination, and how they are regulated in parallel with changes in chromosome structure and with cell cycle transitions that occur during meiosis. Because meiosis is an excellent model system to study homologous recombination, our findings also have provided insight into mechanisms by which DNA damage is repaired and genome integrity is maintained during the mitotic cell cycle.. Meiotic recombination ...
Mph1 is a member of the conserved FANCM family of DNA motor proteins that play key roles in genome maintenance processes underlying Fanconi anemia, a cancer predisposition syndrome in humans. Here, we identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. In vitro, Mte1 (Mph1-associated telomere maintenance protein 1) binds directly to DNA with a preference for branched molecules such as D loops and fork structures. In addition, Mte1 stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Deletion of MTE1 reduces crossover recombination and suppresses the sensitivity of mph1Δ mutant cells to replication stress. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres, and MTE1 deletion results in elongated telomeres. Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication ...
A molecular clone containing the complete sequence of a mitochondrial circular plasmid-like DNA (the R plasmid) isolated from the date-palm variety V3DP was used as a probe in Southern analyses of mitochondrial DNA prepared from other varieties. Another circular structure (the S plasmid) was detected in some of these varieties, and sequenced from variety V2DP. It appears that the R plasmid could have arisen from the S plasmid by an intermolecular recombination event at a set of 26-bp imperfect short direct repeats.
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The tyrosine family of recombinases produces two smaller DNA circles when acting on circular DNA harboring two recombination sites in head-to-tail orientation. If the substrate is supercoiled, these circles can be unlinked or form multiply linked catenanes. The topological complexity of the products varies strongly even for similar recombination systems. This dependence has been solved here. Our computer simulation of the synapsis showed that the bend angles, phi, created in isolated recombination sites by protein binding before assembly of the full complex, determine the product topology. To verify the validity of this theoretical finding we measured the values of phi for Cre/loxP and Flp/FRT systems. The measurement was based on cyclization of the protein-bound short DNA fragments in solution. Despite the striking similarity of the synapses for these recombinases, action of Cre on head-to-tail target sites produces mainly unlinked circles, while that of Flp yields multiply linked catenanes. In full
Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In
This paper proposes a model for the evolution of recombination. The model is based on the notion that when a species (say species 1) interacts with other antagonistic species, species 1 will act as a selective force on them, favouring antagonists best able to destroy its most frequent phenotypes. Only if the progeny of these phenotypes are different from their parents are they able to escape the full force of selected antagonists. A deterministic haploid genetic model with two linked loci and a third unlinked recombination-modifying locus is constructed, using frequency-dependent selection with time delay, to describe the effects of antagonists. Analysis of the model shows that a modifier mutant causing recombination usually starts to spread into a population without recombination, and under certain conditions can spread even if there is already some recombination in the population. The relevance of these results to observations of recombination in the natural world is discussed. ...
Meiosis is a special division during which a cell undergoes two sequential rounds of chromosome segregation with no intervening DNA replication, to generate gamete cells with half the original chromosomal complement. During the first meiotic division (meiosis I), recombination among homologous chromosomes generates novel genetic combinations that play an important role in evolution and breeding. Crossovers persist as cytologically visible chiasmata until homologues segregate in metaphase I and are important for ensuring balanced segregation of homologues [1]. Thus the evolutionarily important effects of recombination and allele shuffling are intimately tied to the physical workings of meiotic chromosome segregation and the maintenance of genome integrity over generations.. Meiotic recombination is an elaborate process, involving numerous steps that take place over the course of many hours (e.g. [2]). Recombination is essentially a DNA repair process that relies on initial programmed double ...
The biochemical processes of DNA repair, replication and recombination compete for the same substrate, the DNA molecule. This competition is natural, as each process requires the same template. In order to resolve possible conflicts between these processes, when they take place on a particular stretch of DNA, certain crosstalk is expected. The complexity is additionally increased by the existence of another DNA dependent process, which occurs in all phases of the cell cycle: transcription.. This thesis aims to investigate the link between transcription inhibition and homologous recombination, especially in the context of UV-induced DNA damage. The results show that the transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) induces homologous recombination. The DNA damage caused by UVC irradiation is repaired mainly via nucleotide excision repair, however, it is also known to trigger recombinational repair. In the presence of UV-induced damage, transcription inhibition by ...
Homologous recombination utilizing hosts own recombination machinery is widely used for genome engineering. More specifically, a plasmid that carries homologous arms to the upstream and downstream areas of target gene(s), is introduced into the host. In order to select for a double crossover event (gene deletion), a positive selection (such as antibiotic resistance cassettes) or combination with a negative selection (such as mazF [84] or pyrE [85]) is used. Other variant methods that rely on homologous recombination also include Allele-Coupled Exchange (ACE) [86], Triple crossover [87] and scar-less, marker-less knockout or knock-in using two negative selection markers (C. thermocellum), detailed information has recently been reviewed [88]. In some instances, specific DNA sequences which can be recognized by site-specific recombinases, flanking the antibiotic resistance cassettes were introduced into the chromosome at the same time during the double crossover event. The antibiotic resistance ...
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Recombination frequency is a measure of genetic linkage and is used in the creation of a genetic linkage map. Recombination frequency (θ) is the frequency with which a single chromosomal crossover will take place between two genes during meiosis. A centimorgan (cM) is a unit that describes a recombination frequency of 1%. In this way we can measure the genetic distance between two loci, based upon their recombination frequency. This is a good estimate of the real distance. Double crossovers would turn into no recombination. In this case we cannot tell if crossovers took place. If the loci were analysing are very close (less than 7 cM) a double crossover is very unlikely. When distances become higher, the likelihood of a double crossover increases. As the likelihood of a double crossover increases we systematically underestimate the genetic distance between two loci. During meiosis, chromosomes assort randomly into gametes, such that the segregation of alleles of one gene is independent of ...
Resumen en: The wing Somatic Mutation and Recombination Test (SMART) in Drosophila melanoguster has been used to analyse five different promutagens for genotoxicity...
We have asked here how the remarkable variation in maize haplotype structure affects recombination. We compared recombination across a genetic interval of 9S in 2 highly dissimilar heterozygotes that shared 1 parent. The genetic interval in the common haplotype is approximately 100 kb long and contains 6 genes interspersed with gene-fragment-bearing Helitrons and retrotransposons that, together, comprise 70% of its length. In one heterozygote, most intergenic insertions are homozygous, although polymorphic, enabling us to determine whether any recombination junctions fall within them. In the other, most intergenic insertions are hemizygous and, thus, incapable of homologous recombination. Our analysis of the frequency and distribution of recombination in the interval revealed that: (i) Most junctions were circumscribed to the gene space, where they showed a highly nonuniform distribution. In both heterozygotes, more than half of the junctions fell in the stc1 gene, making it a clear ...
Although the prevailing view among geneticists suggests that recombination hotspots exist ubiquitously across the human genome, there is only limited experimental evidence from a few genomic regions to support the generality of this claim. A small number of true recombination hotspots are well suppo …
Homologous recombination is the exchange of pieces of DNA during the formation of eggs and sperm. Recombination allows the chromosomes to shuffle their genetic material, increasing the potential of genetic diversity. Homologous recombination is also known as crossing over. ...
InferRho is a MCMC based program for jointly estimating the crossing-over and gene-conversion parameters from population genomic datasets under a Bayesian framework. It uses a full-likelihood method to infer the posterior distribution of recombination rates along the sequence under a variable recombination rate model assuming that the ratio of gene- conversion to crossing-over rate ( f ) is uniform along the sequence. The program assumes a prior distribution for background recombination rates and hotspots. The starts, ends and intensities of hotspots are also output by the program in the posterior distribution generated by the MCMC chain. ...
RecBCD is the key enzyme of double strand (ds) breaks repair and recombination in Escherichia coli[1-3]. RecBCD enzyme is a large heterotrimer (330 kDa) comprising RecB, RecC and RecD polypeptides [4, 5], and has dsDNA and single strand (ss)DNA exonuclease, ssDNA endonuclease, helicase, DNA-dependent ATPase and RecA loading activities [1-3, 6]. This multifunctionality enables the enzyme to initiate homologous recombination. RecBCD carries out the presynaptic step of recombination to produce a 3 single-strand overhang. The E. coli hotspot Chi (5 GCTGGTGG 3) stimulates recombination near to and distant from its 3 end, so it facilitates the enzymes task [6, 7].. Genetic and physical assays show that recombinational DNA repair in E. coli occurs as follows: if there is a ds break in the chromosome, RecBCD specifically binds to the blunt or near-blunt dsDNA ends [8, 9]. Unlike other helicases, RecBCD has two independent helicase subunits, RecB and RecD, so the enzyme is a processive helicase (,30 ...
Results from a recent study in human and chimpanzee genetics have shipwrecked yet another Darwinian hypothesis.1 Genetic recombination is one of the key events that occur during the production of egg and sperm cells, and secular scientists have long thought it to be a major driver of human and ape evolution. When sperm and egg cells are formed in humans and various animals, the process of meiosis generates genetic variation. For example, since humans have two sets of chromosomes, when similar ones (i.e., sister chromatids)-one each from your mother and father-pair up together in the cell, they undergo a controlled exchange of DNA segments (maintaining the same linear order of segments). This is one reason why the offspring of two parents are always genetically unique, except for identical twins where the fertilized egg cell splits into two identical embryos. This process of exchanging DNA segments across sister chromatids is called genetic or homologous recombination and does not occur randomly ...
No, not integrating into the genome, just cloning of an insert into a vector without using restriction enzymes and ligation. I included a paper earlier in this topic. It described using DH5alpha to do recombination b/w a DNA fragment and a plasmid. I followed the protocol and didnt get any result. There are actually many papers describing homologous recombination cloning in E coli DH5 alpha. Even its RecA-, it can still carry out recombination through a process still not well understood ...
Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offsprings sequence based on sequence data of the sire. The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands
Homologous recombination plays a central role in maintaining genomic DNA as well as cellular tolerance to various DNA-damaging agents (1, 2). Specifically, homologous recombination restores stalled replication at damaged template strands by using the intact sister chromatid as a template for DNA synthesis (3-6) and repairs any double-strand breaks (DSB) that may occur in one of the sister chromatids during replication or as a result of chemotherapeutic treatments with camptothecin, cisplatin, and PARP inhibitor. Individual homologous recombination factors contribute in different ways to various types of homologous recombination (7, 8). In homologous recombination-dependent DSB repair, nucleases initiate homologous recombination by processing DSBs to generate 3′ overhangs, followed by the polymerization of RAD51 recombinase on the overhang (9-11). The resulting RAD51 polymer is responsible for homology search and subsequent strand exchange with intact homologous duplex DNA. RAD51 is required ...
Zhu, M.; Yu, J.; Zhou, C.; Fang, H., 2016: Markerless DNA deletion based on Red recombination and in vivo I-Sec I endonuclease cleavage in Escherichia coli chromosome
Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the αβ and γδ TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the αβ TR chains. In this paper, we present the second version of IMGT/GeneInfo
Every genetic event that is consequential to the genetic landscape of a population is captured in a topological structure called the Ancestral Recombinations Graph (ARG) [1]. The converse of this may not hold, that is every genetic event captured in the ARG may not contribute to the observed genetic patterns in the extant population, but nevertheless is a legitimate component of the relevant and common genetic history of the population. In a sense, the ARG is the phylogeny of the individuals of the population. It should be noted that just as in a phylogeny topology, an ARG also does not have any extraneous nodes. Further, it is not unreasonable to assume that there exists a "true" ARG for a collection of samples or a population. Recall that the nodes of the ARG represent genetic events. The topology is not necessarily a tree, due to genetic exchange events such as recombinations, gene duplications and so on. These are represented as nodes with multiple incoming edges in the ARG. The edges are ...
The protein encoded by this gene is essential for meiotic homologous recombination. Genetic recombination in meiosis plays an important role in generating diversity of genetic information. The product of this gene is structurally and evolutionary related to the products of the yeast RAD51 and E. coli RecA genes. Alternative splice variants of this gene have been described but their full-length nature has not been determined.
Background When mismatches in heteroduplex DNA formed during meiotic recombination are left unrepaired, post-meiotic segregation of the two mismatched alleles occurs during the ensuing round of...
Effect of Mutation and Recombination on the Genotype-Phenotype Map: The effect of genetic operators other than selection, such as mutation and recombination, on
Feil and colleagues [4] meticulously address the question of MRSA diversity by applying a population genomics approach to 165 global isolates. Specifically, the authors report variation in recombination rates between phylogeographically distinct subgroups of MRSA clone ST239. The key metric presented is the ratio of SNPs caused by recombination relative to mutation (r/m), and this value is observed to vary significantly across the three subgroups analyzed: South America, Asia, and Turkey. This variation is most apparent when including mobile genetic elements (which are either manually annotated or defined as any sequence more than 1 kb long not present in all isolates), but it is also apparent in the core genome (sequences conserved in all isolates, excluding mobile genetic elements). The authors speculate about genomic characteristics, population characteristics, or transmission dynamics as possible sources, but the true cause of the observed variation remains an intriguing open ...
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Homology boxes mark the sites of bacterial homologous recombination that are used to generate LTVECs from large cloned genomic fragments (Figure 1). Homology boxes are short segments of DNA, generally double-stranded and at least 40 nudeotides in length, that are homologous to regions within the large cloned genomic fragment flanking the "region to be modified". The hornology boxes are appended to the modification cassette, so that following homologous recombination in bacteria, the modification cassette replaces the region to be modified (Figure 1). The technique of creating a targeting vector using bacterial homologous recombination can be performed in a variety of systems (Yang et al., Nat Biotechnol, 15:859-65,1997; Muyrers et al., Nucleic Acids Res, 27:1555-7,1999; Angrand et al., Nucleic Acids Res, 27:el6,1999; Narayanan et al., Gene Ther,. 6:442-7,1999; Yu, et al., Proc Natl Acad Sci U S A, 97:5978-83, 2000). One example of a favored technology currently in use is ET cloning (Zhang et ...
I recently wrote about the winner-takes-all economy, based on what I read in The Second Machine Age by Erik Brynjolfsson and Andrew McAfee. The authors also provided some fascinating insights into how recombinations are driving economic growth. The insights about recombinations is very helpful in understanding the type of start-ups that are most likely to succeed. Effectively,…
A defective hprt gene was corrected by homologous recombination in a lymphocyte cell line deficient in Hypoxanthine-phosphoribosyl-transferase activity (hp
Researchers from the Universitat Autònoma de Barcelona, in collaboration with researchers in the universities of Sussex and Edinburgh, have quantified one of the most important and hard-to-measure phenomena in molecular evolution: the effect of genetic recombination on a species capacity of adaptation.
DNA recombination occurs frequently in many different cell types, and it has important implications for genomic integrity, evolution, and human disease. Although a number of steps in recombination have been well characterized, many other details about this process remain relatively obscure and the subject of intensive research.
Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans-acting factors like PRDM9 is affected ...
Once transcribed, the nascent full-length RNA of HIV-1 must travel to the appropriate host cell sites to be translated or to find a partner RNA for copackaging to form newly generated viruses. In this report, we sought to delineate the location where HIV-1 RNA initiates dimerization and the influence of the RNA transport pathway used by the virus on downstream events essential to viral replication. Using a cell-fusion-dependent recombination assay, we demonstrate that the two RNAs destined for copackaging into the same virion select each other mostly within the cytoplasm. Moreover, by manipulating the RNA export element in the viral genome, we show that the export pathway taken is important for the ability of RNA molecules derived from two viruses to interact and be copackaged. These results further illustrate that at the point of dimerization the two main cellular export pathways are partially distinct. Lastly, by providing Gag in trans, we have demonstrated that Gag is able to package RNA from either
Recombination facilitates DNA repair, creates diversity for evolution, and enables the production of antibodies, whereas defects in this process are linked to cancer‐prone conditions. Recombination can be subdivided into homologous recombination (HR; Liu & West, 2004) and non‐homologous end joining (NHEJ), both of which are crucial for genome stability (Shiloh, 2004; Friedberg et al, 2005a).. S.C. West (London, UK) reviewed the mechanisms of double‐strand break (DSB) repair by HR. Mutations in the breast cancer 2 (BRCA2) gene are associated with early‐onset breast cancer and are linked to defects in DSB repair by HR. The C‐terminal BRCA2 region interacts with the essential recombination protein RAD51 and contains a site (S3291) that is phosphorylated by cyclin‐dependent kinases (CDKs). When this residue is phosphorylated, it blocks C‐terminal interactions between BRCA2 and RAD51. Phosphorylation at this site is low in S‐phase when HR is active, but increases as cells progress to ...
TY - JOUR. T1 - The role of band bending in affecting the surface recombination velocities for Si(111) in contact with aqueous acidic electrolytes. AU - Michalak, David J.. AU - Gstrein, Florian. AU - Lewis, Nathan S. PY - 2008/4/17. Y1 - 2008/4/17. N2 - The role of band bending in affecting surface recombination velocity measurements has been evaluated by combining barrier height data with charge-carrier lifetime measurements for Si(111) surfaces in contact with a variety of acidic aqueous electrolytes. Charge-carrier lifetimes and thus surface recombination velocities have been measured by contactless radio frequency photoconductivity decay techniques for long bulk lifetime n-Si(111) samples in contact with 11 M (40% by weight) NH4F(aq), buffered (pH = 5) HF(aq), 27 M (48% by weight) HF(aq), or concentrated 18 M H 2SO4. Regardless of the sample history or surface condition, long charge-carrier lifetimes were observed for n-Si(111) surfaces in contact with 11 M NH4F(aq) or buffered HF(aq). On ...
Genetic recombination occurs when genetic material is exchanged between two different chromosomes or between different regions within the same chromosome. We can observe it in both eukaryotes (like animals and plants) and prokaryotes (like archaea and bacteria).
Linkage refers to the association and co-inheritance of two DNA segments because they reside close together on the same chromosome. Recombination is the process by which they become separated during crossing over, Physical linkage of genes simply means they are on the same chromosome. To be genetically linked, a pair of genes must be close enough that they are unlikely to be separated by crossing over. which occurs during meiosis. The existence of linkage and the frequency of recombination allow chromosomes to be mapped to determine the relative positions and distances of the genes and other DNA sequences on them. Linkage analysis is also a key tool for discovering the location and ultimate identity of genes for inherited diseases.. ...
Genetic recombination, the process by which sexually reproducing organisms shuffle their genetic material when producing germ cells, leads to offspring with a new genetic make-up and influences the course of evolution.
The F+ strain which contains plasmid gene as an episome (i.e. F plasmid becomes integrated into the host cell genome at one of the several possible sites chromosomal gene) induce more than thousand times the number of genetic recombination than seen in F+ and F- cells. Such a donor strain is called a high frequency of recombination (HFr) strain. ...
Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. Methodology/Principal Findings We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying ...
Poly (ADP-ribose) polymerases (PARPs) are an important family of nucleoproteins highly implicated in DNA damage repair. Among the PARP families, the most studied are PARP1, PARP2 and PARP 3. PARP1 is found to be the most abundant nuclear enzyme under the PARP series. These enzymes are primarily involved in base excision repair as one of the major single strand break (SSB) repair mechanisms. Being double stranded, DNA engages itself in reparation of a sub-lethal SSB with the aid of PARP. Moreover, by having a sister chromatid, DNA can also repair double strand breaks with either error-free homologous recombination or error-prone non-homologous end-joining ...
The identification of RECA3 and MSH1 has made possible a much more detailed investigation of the SSS process by permitting its direct induction. The reproducible events that occur in recA3 and msh1 mutants allow us to infer their normal function, and detailed analysis of mitochondrial genomic regions participating in SSS has permitted us to model the process.. Our model links mitochondrial DNA replication, the generation of chimeric genes, and the nonreciprocal recombination between short repeated sequences resulting in altered stoichiometry and expression of the chimeras. We propose that double-strand breaks are central to all these processes. When double-strand breaks occur, they can be repaired in a number of ways (Aguilera, 2001; Bleuyard et al., 2006; Preston et al., 2006). One possibility is nonhomologous end joining (NHEJ), resulting in chimeric genes. For example, orf315 includes fragments from at least three genes, including atp9, orf153b, and two noncontiguous fragments of orf262 ...
Novel circular vectors containing a recplicable DNA sequence and DNA sequences encoding all or part of at least two distinct parental polypeptides are disclosed. Such vectors are used in novel processes utilizing in vivo recombination to produce recombined circular vectors containing said replicable DNA sequences and hybrid DNA sequences comprising: (1) a first DNA sequence encoding the amino-terminal portion of a hybrid polypeptide corresponding to a first part of a first parental polypeptide sequence and (2) a second DNA sequence encoding a carboxy-terminal portion of said hybrid polypeptide corresponding to a first part of a second parental polypeptide sequence. The hybrid DNA sequences of such recombined circular vectors can exprress novel hybrid polypeptides such as hybrid enzymes in general and in particular hybrid amylases and proteases. Various other processes are disclosed to isolate the recombined circular vector containing said hybrid DNA sequences.
Genetic basis of quantitative virulence and the impact of recombination hotspots in Zymoseptoria tritici identified by high-throughput RAD- ...
As shown in Figure, by using recombination frequency to predict genetic distance, the relative order of genes on chromosome 2 could be inferred. The values shown represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent). Therefore, the genes for body color and wing size were 65.5 − 48.5 = 17 cM apart, indicating that the maternal and paternal alleles for these genes recombine in 17 percent of offspring, on average.. To construct a chromosome map, Sturtevant assumed that genes were ordered serially on threadlike chromosomes. He also assumed that the incidence of recombination between two homologous chromosomes could occur with equal likelihood anywhere along the length of the chromosome. Operating under these assumptions, Sturtevant postulated that alleles that were far apart on a chromosome were more likely to dissociate during meiosis simply because there was a larger region over which recombination could occur. Conversely, alleles that were ...
HOTSPOTTER 1.2.1 :: DESCRIPTION HOTSPOTTER is a software for identifying recombination hotspots from population SNP data. ::DEVELOPER Matthew Stephens Lab :: SCREENSHOTS N/A :: REQUIREMENTS Linux /
The course covers the molecular details and mechanisms of the following topics: Genome structure, chromatin, and the nucleosome; The replication of DNA; The mutability and repair of DNA; Homologous recombination at the molecular level; Site-specific recombination and transposition of DNA; Mechanism of transcription; RNA splicing; Translation; Genetic code; The origin and early evolution of life; Transcriptional regulation in prokaryotes; Transcriptional regulation in eukaryotes; Regulatory RNAs.. ...
Dissociative recombination reaction has been studied theoretically and experimentally for about four decades. Because of the complexity of this process there is not yet a definite agreement between theory and experiment. In this work, dissociative recombination (DR) of helium molecular ion in thermal plasma was studied using Time of Flight (TOF) spectroscopy. This method allowed the identification of the final atom states products of DR. We found the following final products of the DR of the molecular ion: He(3S; 1s3s), He(1S; 1s3s), He(3P; 1s3p), He(3D; 1s3d), He(1D; 1s3d), He(1P; 1s3p), He(3S; 1s2s), He(1S; 1s2s) and possibly He(1S; 1s2). Results similar to ours were obtained in experiments done using optical methods. The actual theoretical models predicts only n=2 manifold states. Further theoretical modeling for this complex process is required.
We evaluated the biological origin of host-virus (mosquito-DENV) recombination by comparing its rate to that of recombination between genomes (pillbug-DENV) that never were in contact in a cellular context. This control indicated that the DENV genome and the genome of its mosquito host did not recombine in vivo to a detectable extent, hence, that most, if not all, virus-host chimeras were artificially produced.. We also uncovered within-genome chimeras (e.g., DENV-DENV chimeras) in greater numbers. To assess their biological origin, chimeras involving the genomes of species that were not in contact prior to DNA processing (e.g., pillbug-DENV chimeras) cannot be used as a baseline expectation because they necessarily occurred between different molecules, contrary to within genome chimeras, which most frequently occurred within the same molecule (see below). Thus, they are not informative. However, it is notable that the various within-genome chimeras we detected in datasets obtained with the ...
Homologous recombination is a genetic process in which two similar DNA strands exchange material. The main purpose of homologous...
Homologous Recombination is a in in vivo method. This method is used to achieve desired mutations (e.g. deletion or insertion of any gene fragment in bacterial chromosome) in bacterial (chromosomal DNA). As explain schematically above. There are homolog sequences both bacterial ( genomic-chromosomal DNA) and target DNA which is created according to desired mutation. These homolog sequences cross- over by the help of bacterial enzymes. For example, In E.coli, Rec proteins activate this mechanism, There are Rec ABCDE and All of them has a different mission. Also, for this purpose, for crossing over of these homolog sequences there are several method ...
Single strand annealing was also characterized in several other respects. We have measured its homology dependence and showed that the product formation increases with increasing amounts of homology. Product formation plateaus at about 400 bp and the smallest amount of homology that we have tested was 29 bp which recombined at a level of 0.1%. Interestingly, if one repeat is immediately adjacent to the DSB, as little as 10 bp can be used at a very efficient frequency. We have also separated the repeats by as much as 25 kb and still obtain efficient repair by SSA deletion events. This process takes 6 hours during which time the cells arrest their cell cycle until the DSB can be repaired. This experiment suggests that the tails remain relatively stable during this time.. Genetic Requirements.. RAD52. SSA requires several gene products that are also required for other types of recombination assays. Rad52p, for example, is required for most if not all types of recombination processes including SSA. ...
Homologous recombination between DNA sequences residing in the chromosome and newly introduced, cloned DNA sequences (gene targeting) allows the transfer of any modification of the cloned gene into the genome of a living cell. This article discusses the current status of gene targeting with particular emphasis on germ line modification of the mouse genome, and describes the different methods so far employed to identify those rare embryonic stem cells in which the desired targeting event has occurred. ...
and gene which are key homologous recombination elements in other microorganisms. plasticité est probablement associée à lexistence dévènements de recombinaison homologue qui. Il possède les gènes du groupe dépistasie RAD52 con compris les gènes BIBX 1382 et et sont transcrits différemment chez les trophozo?tes lorsque des cassures double-brin de lADN sont induites par le rayonnement ultraviolet C. En outre il con a une surexpression de la recombinase EhRAD51 dans le noyau après thirty minutes. Dans cet content nous continuons notre analyse du mécanisme de recombinaison homologue chez en étudiant lexpression des protéines EhRAD51 EhRAD54 et EhBLM en réponse au dommage de lADN. Les analyses bioinformatiques montrent que EhRAD54 possède les caractéristiques moléculaires des protéines homologues ce qui indique quelle pourrait avoir les mêmes fonctions. Les essais de Traditional western blot montrent que les protéines EhRAD54 EhRAD51 et EhBLM BIBX 1382 sexpriment de ...
TRF2 (telomeric do it again binding aspect 2) can be an essential element of the telomeric cover where it forms and stabilizes the T-loop junctions. influence on nonhomologous overexpression and end-joining of TRF2 inhibited nonhomologous end-joining. We propose predicated on our outcomes and on the power of TRF2 to mediate strand invasion that TRF2 has an essential function in HR by facilitating the forming of early recombination intermediates. assay that methods the repair of the induced chromosomal break. The reporter cassette for recognition of NHEJ previously was defined (13). It includes the GFP gene with an artificially constructed BIX 02189 3-kb intron in the gene (GFP-Pem1) (Fig. 1intron includes adenoviral exon flanked by identification sequences for I-SceI endonuclease in inverted orientation. Digestive function with I-SceI generates DSB with incompatible DNA ends (Fig. 1ORF. Upon induction of DSBs by appearance of I-SceI the adenoviral exon is normally taken out NHEJ reconstitutes ...
InferRho is a MCMC based program for jointly estimating the crossing-over and gene-conversion parameters from population genomic datasets under a Bayesian framework. It uses a full-likelihood method to infer the posterior distribution of recombination rates along the sequence under a variable recombination rate model assuming that the ratio of gene- conversion to crossing-over rate ( f ) is uniform along the sequence. The program assumes a prior distribution for background recombination rates and hotspots. The starts, ends and intensities of hotspots are also output by the program in the posterior distribution generated by the MCMC chain. ...