Proofreading and Secondary Structure Processing Determine the Orientation Dependence of CAG·CTG Trinucleotide Repeat Instability in<i>Escherichia coli</i>

Zahra, Rabaab; Blackwood, John K.; Sales, Jill; Leach, David R. F.

doi:10.1534/genetics.106.069724

Cited by 19 publications

(27 citation statements)

References 69 publications

(82 reference statements)

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“…The more stable folded conformations could serve as substrates for DNA repair and might therefore be excised (Wojciechowska et al 2006;Mirkin 2007). Alternatively, these structures could be bypassed by the DNA replication complex (Iyer et al 2000;Wells et al 2005;Mirkin 2007;Zahra et al 2007). Hence, those sequences that adopted the more stable non-B DNA conformations would tend to be lost over evolutionary time and consequently display reduced length distributions.…”

Section: Resultsmentioning

confidence: 99%

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Bacolla¹,

Larson²,

Collins³

et al. 2008

Genome Res.

105

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Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra-and trinucleotide repeats revealed an inverse correlation between the stability of folded-back hairpin and quadruplex structures and the sequence representation for repeats Ն30 bp in length in nine vertebrate genomes. Alternatively, the predicted energies of base-stacking interactions correlated directly with the longest length distributions in vertebrate genomes. Genome-wide analyses indicated that unstable sequences, such as CAG:CTG and CCG:CGG, were over-represented in coding regions and that micro/minisatellites were recruited in genes involved in transcription and signaling pathways, particularly in the nervous system. Microsatellite instability (MSI) is a hallmark of cancer, and length polymorphism within genes can confer susceptibility to inherited disease. Sequences that manifest the highest MSI values also displayed the strongest base-stacking interactions; analyses of 62 tri-and tetranucleotide repeat-containing genes associated with human genetic disease revealed enrichments similar to those noted for micro/minisatellite-containing genes. We conclude that DNA structure and base-stacking determined the number and length distributions of microsatellite repeats in vertebrate genomes over evolutionary time and that micro/minisatellites have been recruited to participate in both gene and protein function.

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Section: Resultsmentioning

confidence: 99%

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Bacolla¹,

Larson²,

Collins³

et al. 2008

Genome Res.

105

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show abstract

“…The observed rate of recombination increased as a function of the length of the repeat tract. Although CAG TNRs (CAG on the leading-strand template) were also shown to stimulate zeocin recombination slightly, their length dependency could not be tested as the CAG repeats are highly prone to deletions (16), preventing the construction of an array longer than CAG 84 .…”

Section: Resultsmentioning

confidence: 99%

“…CAG·CTG TNR instability assays were carried out by GeneMapper analysis following capillary electrophoresis as previously described (16). Twelve cultures derived from independent single colonies were plated on LB plates to generate single colonies.…”

Section: Methodsmentioning

confidence: 99%

DNA tandem repeat instability in the Escherichia coli chromosome is stimulated by mismatch repair at an adjacent CAG·CTG trinucleotide repeat

Blackwood

Okely²,

Zahra³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Approximately half the human genome is composed of repetitive DNA sequences classified into microsatellites, minisatellites, tandem repeats, and dispersed repeats. These repetitive sequences have coevolved within the genome but little is known about their potential interactions. Trinucleotide repeats (TNRs) are a subclass of microsatellites that are implicated in human disease. Expansion of CAG·CTG TNRs is responsible for Huntington disease, myotonic dystrophy, and a number of spinocerebellar ataxias. In yeast DNA double-strand break (DSB) formation has been proposed to be associated with instability and chromosome fragility at these sites and replication fork reversal (RFR) to be involved either in promoting or in preventing instability. However, the molecular basis for chromosome fragility of repetitive DNA remains poorly understood. Here we show that a CAG·CTG TNR array stimulates instability at a 275-bp tandem repeat located 6.3 kb away on the Escherichia coli chromosome. Remarkably, this stimulation is independent of both DNA double-strand break repair (DSBR) and RFR but is dependent on a functional mismatch repair (MMR) system. Our results provide a demonstration, in a simple model system, that MMR at one type of repetitive DNA has the potential to influence the stability of another. Furthermore, the mechanism of this stimulation places a limit on the universality of DSBR or RFR models of instability and chromosome fragility at CAG·CTG TNR sequences. Instead, our data suggest that explanations of chromosome fragility should encompass the possibility of chromosome gaps formed during MMR.DNA repair | DNA replication | fragile site

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“…that DNA polymerase proofreading activity (44) and weak strand displacement activity (45) contribute to orientation dependence of 5Ј-CAG/5Ј-CTG TNR instability in E. coli. Overall, these data argue against a model in which the hairpins form ahead of the polymerase and initiate the polymerase impediment.…”

Section: Discussionmentioning

confidence: 98%

Single-stranded DNA-binding Protein in Vitro Eliminates the Orientation-dependent Impediment to Polymerase Passage on CAG/CTG Repeats

Delagoutte

Goellner

Guo

et al. 2008

Journal of Biological Chemistry

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Small insertions and deletions of trinucleotide repeats (TNRs) can occur by polymerase slippage and hairpin formation on either template or newly synthesized strands during replication. Although not predicted by a slippage model, deletions occur preferentially when 5-CTG is in the lagging strand template and are highly favored over insertion events in rapidly replicating cells. The mechanism for the deletion bias and the orientation dependence of TNR instability is poorly understood. We report here that there is an orientation-dependent impediment to polymerase progression on 5-CAG and 5-CTG repeats that can be relieved by the binding of single-stranded DNAbinding protein. The block depends on the primary sequence of the TNR but does not correlate with the thermodynamic stability of hairpins. The orientation-dependent block of polymerase passage is the strongest when 5-CAG is the template. We propose a "template-push" model in which the slow speed of DNA polymerase across the 5-CAG leading strand template creates a threat to helicase-polymerase coupling. To prevent uncoupling, the TNR template is pushed out and by-passed. Hairpins do not cause the block, but appear to occur as a consequence of polymerase pass-over. Expansion of simple trinucleotide repeats (TNRs)4 is the underlying genetic defect of a number of human neurodegenerative diseases. TNR-associated pathophysiology in human diseases strictly depends on the number of trinucleotide repeats (reviewed in Refs. 1-3). Although expansion can occur in germ cells (4) and in somatic cells with age (5, 6), emerging evidence suggests that rapid cell division in the early embryo can reduce the size of the repeats and modulate disease potential (7). TNR deletion during rapid cell division may serve as a natural defense mechanism for keeping the length of the repeats in check at critical times in development. Reducing the length of the repeat tract in disease genes is being explored as a therapeutic strategy. However, the mechanisms by which deletions rather than expansions are favored during replication remain poorly understood.DNA polymerase and strand slippage has been proposed as the primary mechanism for instability of trinucleotide repeats (1-3). During replication, the TNR units can misalign resulting in an extrahelical DNA loop that increases TNR length if it occurs on the daughter strand and decreases TNR length if it occurs on the template strand (1-3). In both prokaryotic and eukaryotic models, it is well established that TNR instability is sensitive to the length of the repeat (8 -12), to its structure forming potential (13-17), and to its proximity to the origin of replication (18). The factors that regulate the probability and frequency of deletion events, however, remain poorly understood. By a polymerase slippage model, a deletion implies that hairpin formation has occurred on the template strand. Theoretically, for an identical sequence located either on the template or daughter strand, slippage and hairpin formation can occur with equivalent frequen...

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Proofreading and Secondary Structure Processing Determine the Orientation Dependence of CAG·CTG Trinucleotide Repeat Instability inEscherichia coli

Cited by 19 publications

References 69 publications

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

DNA tandem repeat instability in the Escherichia coli chromosome is stimulated by mismatch repair at an adjacent CAG·CTG trinucleotide repeat

Single-stranded DNA-binding Protein in Vitro Eliminates the Orientation-dependent Impediment to Polymerase Passage on CAG/CTG Repeats

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