Replication slippage involves DNA polymerase pausing and dissociation

Genome rearrangements can take place by a process known as replication slippage or copy‐choice recombination. The slippage occurs between repeated sequences in both prokaryotes and eukaryotes, and is invoked to explain microsatellite instability, which is related to several human diseases. We analysed the molecular mechanism of slippage between short direct repeats, using in vitro replication of a single‐stranded DNA template that mimics the lagging strand synthesis. We show that slippage involves DNA polymerase pausing, which must take place within the direct repeat, and that the pausing polymerase dissociates from the DNA. We also present evidence that, upon polymerase dissociation, only the terminal portion of the newly synthesized strand separates from the template and anneals to another direct repeat. Resumption of DNA replication then completes the slippage process.

[1]  B. Michel,et al.  Mechanisms of illegitimate recombination. , 1993, Gene.

[2]  R. Wells.  Molecular Basis of Genetic Instability of Triplet Repeats (*) , 1996, The Journal of Biological Chemistry.

[3]  Samuel H. Wilson,et al.  Error-prone polymerization by HIV-1 reverse transcriptase. Contribution of template-primer misalignment, miscoding, and termination probability to mutational hot spots. , 1993, The Journal of biological chemistry.

[4]  T. Petes,et al.  Triplet repeats form secondary structures that escape DNA repair in yeast. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[5]  R. Fuchs,et al.  Lesions in DNA: hurdles for polymerases. , 2000, Trends in biochemical sciences.

[6]  Base Stacking and Even/Odd Behavior of Hairpin Loops in DNA Triplet Repeat Sequences Undergoing Slippage and Expansion with DNA Polymerase , 2000 .

[7]  R. Sinden,et al.  DNA‐Directed Mutations: Leading and Lagging Strand Specificity , 1999, Annals of the New York Academy of Sciences.

[8]  R. Wells,et al.  Pausing of DNA Synthesis in Vitro at Specific Loci in CTG and CGG Triplet Repeats from Human Hereditary Disease Genes (*) , 1995, The Journal of Biological Chemistry.

[9]  D. Tautz,et al.  Simple sequences. , 1994, Current opinion in genetics & development.

[10]  B. Alberts,et al.  The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairpin helix. A model for polymerase release following the termination of each Okazaki fragment. , 1994, The Journal of biological chemistry.

[11]  B. Michel,et al.  Deletions at stalled replication forks occur by two different pathways , 1997, The EMBO journal.

[12]  E. Friedberg,et al.  The many faces of DNA polymerases: strategies for mutagenesis and for mutational avoidance. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Robert I. Richards,et al.  Simple repeat DNA is not replicated simply , 1994, Nature Genetics.

[14]  R. Bambara,et al.  Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III. , 1983, Biochemistry.

[15]  D. Leach,et al.  Evidence for two preferred hairpin folding patterns in d(CGG).d(CCG) repeat tracts in vivo. , 1998, Journal of Molecular Biology.

[16]  B. Michel.  Replication fork arrest and DNA recombination. , 2000, Trends in biochemical sciences.

[17]  Z. Debyser,et al.  Coordination of leading and lagging strand DNA synthesis at the replication fork of bacteriophage T7 , 1994, Cell.

[18]  Karen N. Allen,et al.  On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo. , 1991, Genetics.

[19]  P. Djian,et al.  Evolution of Simple Repeats in DNA and Their Relation to Human Disease , 1998, Cell.

[20]  M. O’Donnell,et al.  Dynamics of β and Proliferating Cell Nuclear Antigen Sliding Clamps in Traversing DNA Secondary Structure* , 2000, The Journal of Biological Chemistry.

[21]  B. Alberts,et al.  Sequence-specific pausing during in vitro DNA replication on double-stranded DNA templates. , 1989, The Journal of biological chemistry.

[22]  M. Mitas,et al.  Trinucleotide repeats associated with human disease. , 1997, Nucleic acids research.

[23]  S. Ehrlich,et al.  Copy-choice recombination mediated by DNA polymerase III holoenzyme from Escherichia coli. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[24]  S. Mirkin,et al.  Trinucleotide repeats affect DNA replication in vivo , 1997, Nature Genetics.

[25]  C. McHenry.  DNA polymerase III holoenzyme. Components, structure, and mechanism of a true replicative complex. , 1991, The Journal of biological chemistry.

[26]  Robert I. Richards,et al.  Dynamic mutations: A new class of mutations causing human disease , 1992, Cell.

[27]  B. Michel,et al.  The replication termination signal terB of the Escherichia coli chromosome is a deletion hot spot. , 1991, The EMBO journal.

[28]  M. DePamphilis,et al.  The role of palindromic and non-palindromic sequences in arresting DNA synthesis in vitro and in vivo. , 1984, Journal of molecular biology.

[29]  R. Sinden,et al.  Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA. , 1998, Current opinion in structural biology.

[30]  P. V. von Hippel,et al.  Processive proofreading is intrinsic to T4 DNA polymerase. , 1992, The Journal of biological chemistry.

[31]  I. Haworth,et al.  The trinucleotide repeat sequence d(CGG)15 forms a heat-stable hairpin containing Gsyn. Ganti base pairs. , 1995, Biochemistry.

[32]  D. Leach.  Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair , 1994, BioEssays : news and reviews in molecular, cellular and developmental biology.

[33]  M. O’Donnell,et al.  Accessory proteins bind a primed template and mediate rapid cycling of DNA polymerase III holoenzyme from Escherichia coli. , 1987, The Journal of biological chemistry.

[34]  B. Michel,et al.  Copy‐choice illegitimate DNA recombination revisited. , 1994, The EMBO journal.

[35]  J. Jurka,et al.  Microsatellites in different eukaryotic genomes: survey and analysis. , 2000, Genome research.

[36]  John M. Hancock,et al.  Trinucleotide Expansion Diseases in the Context of Micro‐ and Minisatellite Evolution Hammersmith Hospital, April 1–3, 1998 , 1998, The EMBO journal.

[37]  H. Maki,et al.  Strand Asymmetry of +1 Frameshift Mutagenesis at a Homopolymeric Run by DNA Polymerase III Holoenzyme of Escherichia coli * , 1999, The Journal of Biological Chemistry.

[38]  S. Ehrlich,et al.  Replication Slippage of Different DNA Polymerases Is Inversely Related to Their Strand Displacement Efficiency* , 1999, The Journal of Biological Chemistry.

[39]  B. Michel,et al.  Isolation of a dnaE mutation which enhances RecA‐independent homologous recombination in the Escherichia coli chromosome , 1997, Molecular microbiology.

[40]  Alex van Belkum,et al.  Short-Sequence DNA Repeats in Prokaryotic Genomes , 1998, Microbiology and Molecular Biology Reviews.

[41]  M. Dixon,et al.  Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. , 1999, Molecular cell.

[42]  R. Wells,et al.  Hairpin Formation during DNA Synthesis Primer Realignmentin Vitro in Triplet Repeat Sequences from Human Hereditary Disease Genes* , 1997, The Journal of Biological Chemistry.

[43]  C. Millar,et al.  Palindromes as substrates for multiple pathways of recombination in Escherichia coli. , 2000, Genetics.

[44]  M. O’Donnell,et al.  Total reconstitution of DNA polymerase III holoenzyme reveals dual accessory protein clamps. , 1990, The Journal of biological chemistry.

[45]  D. Leach,et al.  Replication strand preference for deletions associated with DNA palindromes , 1998, Molecular microbiology.

[46]  B. Michel,et al.  When replication forks stop , 1994, Molecular microbiology.

[47]  M. Goodman,et al.  Base Stacking and Even/Odd Behavior of Hairpin Loops in DNA Triplet Repeat Slippage and Expansion with DNA Polymerase* , 2000, The Journal of Biological Chemistry.

[48]  M. DePamphilis,et al.  Specific sequences in native DNA that arrest synthesis by DNA polymerase alpha. , 1982, The Journal of biological chemistry.

[49]  J. Wagner,et al.  All three SOS‐inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis , 2000, The EMBO journal.

[50]  S. Lovett,et al.  A sister-strand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherichia coli. , 1993, Genetics.

[51]  M. Goodman,et al.  Analysis of Strand Slippage in DNA Polymerase Expansions of CAG/CTG Triplet Repeats Associated with Neurodegenerative Disease* , 1998, The Journal of Biological Chemistry.