Inverted DNA repeats: a source of eukaryotic genomic instability.

While inverted DNA repeats are generally acknowledged to be an important source of genetic instability in prokaryotes, relatively little is known about their effects in eukaryotes. Using bacterial transposon Tn5 and its derivatives, we demonstrate that long inverted repeats also cause genetic instability leading to deletion in the yeast Saccharomyces cerevisiae. Furthermore, they induce homologous recombination. Replication plays a major role in the deletion formation. Deletions are stimulated by a mutation in the DNA polymerase delta gene (pol3). The majority of deletions result from imprecise excision between small (4- to 6-bp) repeats in a polar fashion, and they often generate quasipalindrome structures that subsequently may be highly unstable. Breakpoints are clustered near the ends of the long inverted repeats (< 150 bp). The repeats have both intra- and interchromosomal effects in that they also create hot spots for mitotic interchromosomal recombination. Intragenic recombination is 4 to 18 times more frequent for heteroalleles in which one of the two mutations is due to the insertion of a long inverted repeat, compared with other pairs of heteroalleles in which neither mutation has a long repeat. We propose that both deletion and recombination are the result of altered replication at the basal part of the stem formed by the inverted repeats.

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Factors Affecting Inverted Repeat Stimulation of Recombination and Deletion in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/148.4.1507 ◽

1998 ◽

Vol 148 (4) ◽

pp. 1507-1524 ◽

Cited By ~ 9

Author(s):

Kirill S Lobachev ◽

Boris M Shor ◽

Hiep T Tran ◽

Wendy Taylor ◽

J Dianne Keen ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Secondary Structure ◽

Genetic Instability ◽

Inverted Repeats ◽

Dna Repeats ◽

Origin Of Replication ◽

Adjacent Region ◽

Factors Affecting ◽

Stimulation Of

AbstractInverted DNA repeats are an at-risk motif for genetic instability that can induce both deletions and recombination in yeast. We investigated the role of the length of inverted repeats and size of the DNA separating the repeats for deletion and recombination. Stimulation of both deletion and recombination was directly related to the size of inverted repeats and inversely related to the size of intervening spacers. A perfect palindrome, formed by two 1.0-kb URA3-inverted repeats, increased intra- and interchromosomal recombination in the adjacent region 2,400-fold and 17,000-fold, respectively. The presence of a strong origin of replication in the spacer reduced both rates of deletion and recombination. These results support a model in which the stimulation of deletion and recombination by inverted repeats is initiated by a secondary structure formed between single-stranded DNA of inverted repeats during replication.

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Abstract 2732: Short inverted repeats are hot spots for genetic instability in mammalian cells

10.1158/1538-7445.am2011-2732 ◽

2011 ◽

Author(s):

Steve Lu ◽

Guliang Wang ◽

Karen M. Vasquez

Keyword(s):

Hot Spots ◽

Genetic Instability ◽

Mammalian Cells ◽

Inverted Repeats

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A PRODUCT OF THE TN5 TRANSPOSASE GENE INHIBITS TRANSPOSITION

Genetics ◽

10.1093/genetics/103.4.605 ◽

1983 ◽

Vol 103 (4) ◽

pp. 605-615

Author(s):

John B Lowe ◽

Douglas E Berg

Keyword(s):

Regulatory Mechanism ◽

Inverted Repeats ◽

Multicopy Plasmid ◽

Transposon Tn5 ◽

Transposase Gene ◽

A Cell ◽

Gene Data ◽

Tn5 Transposase ◽

Derivatives Of ◽

Bacterial Transposon

ABSTRACT The bacterial transposon Tn5 possesses a regulatory mechanism that allows it to move with higher efficiency when it is first introduced into a cell than after it is established. Tn5 is a composite transposable element containing inverted repeats of two nearly identical elements, IS50R, which encodes the transposase protein necessary for Tn5 movement, and IS50L which contains an ochre mutant allele of the transposase gene. Data presented here show that Tn5 transposition is inhibited about 50-fold in cells of Escherichia coli which already carry IS50R in the multicopy plasmid pBR322. If the cells contain a plasmid carrying either IS50L instead of IS50R, or derivatives of IS50R in which the transposase gene has been mutated, little if any inhibition of Tn5 transposition is found. Although inhibition had previously been hypothesized to require interaction between the products of IS50L and IS50R, our results show that IS50R alone is sufficient to mediate inhibition and suggest that the inhibitor is a product of the transposase gene itself.

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Structures and stability of simple DNA repeats from bacteria

Biochemical Journal ◽

10.1042/bcj20190703 ◽

2020 ◽

Vol 477 (2) ◽

pp. 325-339 ◽

Cited By ~ 4

Author(s):

Vaclav Brazda ◽

Miroslav Fojta ◽

Richard P. Bowater

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Genetic Instability ◽

Repetitive Sequences ◽

Biological Significance ◽

Human Diseases ◽

Repetitive Dna Sequences ◽

Dna Repeats ◽

Diverse Range ◽

Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

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Direct and Inverted Repeats Elicit Genetic Instability by Both Exploiting and Eluding DNA Double-Strand Break Repair Systems in Mycobacteria

PLoS ONE ◽

10.1371/journal.pone.0051064 ◽

2012 ◽

Vol 7 (12) ◽

pp. e51064 ◽

Cited By ~ 13

Author(s):

Ewelina A. Wojcik ◽

Anna Brzostek ◽

Albino Bacolla ◽

Pawel Mackiewicz ◽

Karen M. Vasquez ◽

...

Keyword(s):

Genetic Instability ◽

Strand Break ◽

Double Strand Break ◽

Double Strand Break Repair ◽

Inverted Repeats ◽

Dna Double Strand Break ◽

Repair Systems ◽

Break Repair

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Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes.

Molecular and Cellular Biology ◽

10.1128/mcb.15.10.5607 ◽

1995 ◽

Vol 15 (10) ◽

pp. 5607-5617 ◽

Cited By ~ 66

Author(s):

H T Tran ◽

N P Degtyareva ◽

N N Koloteva ◽

A Sugino ◽

H Masumoto ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Genome Stability ◽

Genome Instability ◽

Temperature Sensitive ◽

Direct Repeats ◽

Dna Polymerase Delta ◽

Dna Double Strand Breaks ◽

Yeast Saccharomyces Cerevisiae ◽

Replication Slippage ◽

Random Sequences

Small direct repeats, which are frequent in all genomes, are a potential source of genome instability. To study the occurrence and genetic control of repeat-associated deletions, we developed a system in the yeast Saccharomyces cerevisiae that was based on small direct repeats separated by either random sequences or inverted repeats. Deletions were examined in the LYS2 gene, using a set of 31- to 156-bp inserts that included inserts with no apparent potential for secondary structure as well as two quasipalindromes. All inserts were flanked by 6- to 9-bp direct repeats of LYS2 sequence, providing an opportunity for Lys+ reversion via precise excision. Reversions could arise by extended deletions involving either direct repeats or random sequences and by -1-or +2-bp frameshift mutations. The deletion breakpoints were always associated with short (3- to 9-bp) perfect or imperfect direct repeats. Compared with the POL+ strain, deletions between small direct repeats were increased as much as 100-fold, and the spectrum was changed in a temperature-sensitive DNA polymerase delta pol3-t mutant, suggesting a role for replication. The type of deletion depended on orientation relative to the origin of replication. On the basis of these results, we propose (i) that extended deletions between small repeats arise by replication slippage and (ii) that the deletions occur primarily in either the leading or lagging strand. The RAD50 and RAD52 genes, which are required for the recombinational repair of many kinds of DNA double-strand breaks, appeared to be required also for the production of up to 90% of the deletions arising between separated repeats in the pol3-t mutant, suggesting a newly identified role for these genes in genome stability and possibly replication.

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Cloning and characterization of DST2, the gene for DNA strand transfer protein beta from Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2583 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2583-2592 ◽

Cited By ~ 57

Author(s):

C C Dykstra ◽

K Kitada ◽

A B Clark ◽

R K Hamatake ◽

A Sugino

Keyword(s):

Saccharomyces Cerevisiae ◽

Intragenic Recombination ◽

Temperature Sensitive ◽

Strand Transfer ◽

Gene Encoding ◽

Yeast Saccharomyces Cerevisiae ◽

Prolonged Incubation ◽

Transfer Protein ◽

Dna Strand

The gene encoding the 180-kDa DNA strand transfer protein beta from the yeast Saccharomyces cerevisiae was identified and sequenced. This gene, DST2 (DNA strand transferase 2), was located on chromosome VII. dst2 gene disruption mutants exhibited temperature-sensitive sporulation and a 50% longer generation time during vegetative growth than did the wild type. Spontaneous mitotic recombination in the mutants was reduced severalfold for both intrachromosomal recombination and intragenic gene conversion. The mutants also had reduced levels of the intragenic recombination that is induced during meiosis. Meiotic recombinants were, however, somewhat unstable in the mutants, with a decrease in recombinants and survival upon prolonged incubation in sporulation media. spo13 or spo13 rad50 mutations did not relieve the sporulation defect of dst2 mutations. A dst1 dst2 double mutant has the same phenotype as a dst2 single mutant. All phenotypes associated with the dst2 mutations could be complemented by a plasmid containing DST2.

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