scholarly journals Effect of DNA Sequence Divergence on Homologous Recombination as Analyzed by a Random-Walk Model

Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1973-1988 ◽  
Author(s):  
Youhei Fujitani ◽  
Ichizo Kobayashi
Keyword(s):  
Random Walk ◽  
Homologous Recombination ◽  
Mismatch Repair ◽  
Dna Sequence ◽  
Recombination Frequency ◽  
Sequence Divergence ◽  
Random Walk Model ◽  
Homologous Region ◽  
Dna Duplexes ◽  
Rapid Drop

Abstract A point connecting a pair of homologous regions of DNA duplexes moves along the homology in a reaction intermediate of the homologous recombination. Formulating this movement as a random walk, we were previously successful at explaining the dependence of the recombination frequency on the homology length. Recently, the dependence of the recombination frequency on the DNA sequence divergence in the homologous region was investigated experimentally; if the methyl-directed mismatch repair (MMR) system is active, the logarithm of the recombination frequency decreases very rapidly with an increase of the divergence in a low-divergence regime. Beyond this regime, the logarithm decreases slowly and linearly with the divergence. This “very rapid drop-off” is not observed when the MMR system is defective. In this article, we show that our random-walk model can explain these data in a straightforward way. When a connecting point encounters a diverged base pair, it is assumed to be destroyed with a probability that depends on the level of MMR activity.

scholarly journals Intermolecular homologous recombination in plants.

1990 ◽  
Vol 10 (2) ◽  
pp. 492-500 ◽  
Author(s):  
M Baur ◽  
I Potrykus ◽  
J Paszkowski
Keyword(s):  
Homologous Recombination ◽  
Recombination Frequency ◽  
Strand Break ◽  
Kanamycin Resistance ◽  
Homologous Region ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Linear Molecules ◽  
Or Gene

To study DNA topological requirements for homologous recombination in plants, we have constructed pairs of plasmids that contain nonoverlapping deletions in the neomycin phosphotransferase gene [APH(3')II], which, when intact, confers kanamycin resistance to plant cells. Protoplasts isolated from Nicotiana tabacum were cotransformed with complementary pairs of plasmids containing these truncated gene constructs. Homologous recombination or gene conversion within the homologous sequences (6 to 405 base pairs) of the protein-coding region of the truncated genes led to the restoration of the functional APH(3')II gene, rendering these cells resistant to kanamycin. Circular plasmid DNAs recombined very inefficiently, independent of the length of the homologous region. A double-strand break in one molecule only slightly increased the recombination frequency. The most favorable substrates for recombination were linear molecules. In this case, the recombination frequency was positively correlated with the length of the homologous regions. The recombination frequency of plasmids linearized at sites proximal to the deletion-homology junction was significantly higher than when linearization was distal to the homologous region. Vector homology within cotransformed plasmid sequences also increased the recombination frequency.

Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model

Science ◽  
1992 ◽  
Vol 257 (5075) ◽  
pp. 1410-1412 ◽  
Author(s):  
G van den Engh ◽  
R Sachs ◽  
B. Trask
Keyword(s):  
Random Walk ◽  
Dna Sequence ◽  
Random Walk Model ◽  
Genomic Distance ◽  
Cell Nuclei

Intermolecular homologous recombination in plants

1990 ◽  
Vol 10 (2) ◽  
pp. 492-500
Author(s):  
M Baur ◽  
I Potrykus ◽  
J Paszkowski
Keyword(s):  
Homologous Recombination ◽  
Recombination Frequency ◽  
Strand Break ◽  
Kanamycin Resistance ◽  
Homologous Region ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Linear Molecules ◽  
Or Gene

To study DNA topological requirements for homologous recombination in plants, we have constructed pairs of plasmids that contain nonoverlapping deletions in the neomycin phosphotransferase gene [APH(3')II], which, when intact, confers kanamycin resistance to plant cells. Protoplasts isolated from Nicotiana tabacum were cotransformed with complementary pairs of plasmids containing these truncated gene constructs. Homologous recombination or gene conversion within the homologous sequences (6 to 405 base pairs) of the protein-coding region of the truncated genes led to the restoration of the functional APH(3')II gene, rendering these cells resistant to kanamycin. Circular plasmid DNAs recombined very inefficiently, independent of the length of the homologous region. A double-strand break in one molecule only slightly increased the recombination frequency. The most favorable substrates for recombination were linear molecules. In this case, the recombination frequency was positively correlated with the length of the homologous regions. The recombination frequency of plasmids linearized at sites proximal to the deletion-homology junction was significantly higher than when linearization was distal to the homologous region. Vector homology within cotransformed plasmid sequences also increased the recombination frequency.

Random-walk model of homologous recombination

1995 ◽  
Vol 52 (6) ◽  
pp. 6607-6622 ◽  
Author(s):  
Youhei Fujitani ◽  
Ichizo Kobayashi
Keyword(s):  
Random Walk ◽  
Homologous Recombination ◽  
Random Walk Model

scholarly journals Mismatch repair impedes meiotic crossover interference

2018 ◽  
Author(s):  
Tim J. Cooper ◽  
Margaret R. Crawford ◽  
Laura J. Hunt ◽  
Marie-Claude Marsolier-Kergoat ◽  
Bertrand Llorente ◽  
...  
Keyword(s):  
Mismatch Repair ◽  
Dna Sequence ◽  
Meiotic Recombination ◽  
Molecular Level ◽  
Computational Modelling ◽  
Sequence Divergence ◽  
Global Distribution ◽  
Crossover Interference ◽  
Genome Wide ◽  
Meiotic Crossover

SummarySequence divergence, mediated by the anti-recombinogenic activity of mismatch repair (MMR), forms a potent barrier to meiotic recombination and in turn the formation of viable gametes1–5. However, exactly how MMR jeopardizes meiotic success is unclear. Here we utilize a combination ofS. cerevisiaegenetics, genome-wide mapping of recombination and computational modelling to demonstrate that MMR unexpectedly influences the global distribution of recombination through preferential suppression of interfering crossovers (COs) at regions of greater sequence divergence. As a result, inactivation of MMR not only increases the rate of recombination, as previously observed, but also, paradoxically, the strength of CO interference. Our observations reveal a new mechanism by which MMR spatially sculpts the meiotic landscape—linking CO control to the mechanisms that can reproductively isolate a population, and highlighting how genomes may become meiotically incompatible at the molecular level, dependent upon interactions of the primary DNA sequence.

A Multi-Label Classification Algorithm Based on Random Walk Model

2010 ◽  
Vol 33 (8) ◽  
pp. 1418-1426 ◽  
Author(s):  
Wei ZHENG ◽  
Chao-Kun WANG ◽  
Zhang LIU ◽  
Jian-Min WANG
Keyword(s):  
Random Walk ◽  
Classification Algorithm ◽  
Random Walk Model

The Effect of Mismatch Repair and Heteroduplex Formation on Sexual Isolation in Bacillus

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 13-18 ◽  
Author(s):  
Jacek Majewski ◽  
Frederick M Cohan
Keyword(s):  
Mismatch Repair ◽  
Wild Type Strain ◽  
Resistance Mechanism ◽  
Sequence Divergence ◽  
Sexual Isolation ◽  
Wild Type ◽  
Exponential Relationship ◽  
Dna Strands ◽  
The Relationship ◽  
Heteroduplex Formation

AbstractIn Bacillus transformation, sexual isolation is known to be an exponential function of the sequence divergence between donor and recipient. Here, we have investigated the mechanism under which sequence divergence results in sexual isolation. We tested the effect of mismatch repair by comparing a wild-type strain and an isogenic mismatch-repair mutant for the relationship between sexual isolation and sequence divergence. Mismatch repair was shown to contribute to sexual isolation but was responsible for only a small fraction of the sexual isolation observed. Another possible mechanism of sexual isolation is that more divergent recipient and donor DNA strands have greater difficulty forming a heteroduplex because a region of perfect identity between donor and recipient is required for initiation of the heteroduplex. A mathematical model showed that this heteroduplex-resistance mechanism yields an exponential relationship between sexual isolation and sequence divergence. Moreover, this model yields an estimate of the size of the region of perfect identity that is comparable to independent estimates for Escherichia coli. For these reasons, and because all other mechanisms of sexual isolation may be ruled out, we conclude that resistance to heteroduplex formation is predominantly responsible for the exponential relationship between sexual isolation and sequence divergence in Bacillus transformation.

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