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Lagging-strand replication shapes the mutational landscape of the genome.

Reijns MA, Kemp H, Ding J, de Procé SM, Jackson AP, Taylor MS - Nature (2015)

Bottom Line: The origin of mutations is central to understanding evolution and of key relevance to health.Here we report that the 5' ends of Okazaki fragments have significantly increased levels of nucleotide substitution, indicating a replicative origin for such mutations.Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo, comprising approximately 1.5% of the mature genome.

View Article: PubMed Central - PubMed

Affiliation: Medical and Developmental Genetics, MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.

ABSTRACT
The origin of mutations is central to understanding evolution and of key relevance to health. Variation occurs non-randomly across the genome, and mechanisms for this remain to be defined. Here we report that the 5' ends of Okazaki fragments have significantly increased levels of nucleotide substitution, indicating a replicative origin for such mutations. Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo, comprising approximately 1.5% of the mature genome. We propose that DNA-binding proteins that rapidly re-associate post-replication act as partial barriers to Pol-δ-mediated displacement of Pol-α-synthesized DNA, resulting in incorporation of such Pol-α tracts and increased mutation rates at specific sites. We observe a mutational cost to chromatin and regulatory protein binding, resulting in mutation hotspots at regulatory elements, with signatures of this process detectable in both yeast and humans.

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Elevated substitution rates at OJsa, b, Nucleotide substitution rates (red) closely correlate with elevated OJ site frequency (blue) at (a) nucleosome and (b) Reb1 binding sites. S. cerevisiae polymorphism rates per nucleotide computed using sequences from nucleosome and Reb1 binding sites. Individual data points, open circles. Solid curves, best fit splines. Mean, dashed grey line; ±10% dotted grey lines.
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Figure 1: Elevated substitution rates at OJsa, b, Nucleotide substitution rates (red) closely correlate with elevated OJ site frequency (blue) at (a) nucleosome and (b) Reb1 binding sites. S. cerevisiae polymorphism rates per nucleotide computed using sequences from nucleosome and Reb1 binding sites. Individual data points, open circles. Solid curves, best fit splines. Mean, dashed grey line; ±10% dotted grey lines.

Mentions: We were struck by the similarity of the distribution of S. cerevisiae OJ sites at nucleosomes17 to that previously reported for nucleotide substitutions7,8,10-12, and set out to investigate the potential reasons for this. We established that nucleotide substitution and OJ distributions are highly correlated (Pearson’s correlation coefficient = 0.76, p = 2.2·10−16) and essentially identical in pattern (Fig. 1a). Furthermore, differences in OJ distribution by nucleosome type (genic vs non-genic), spacing or consistency of binding were mirrored by the substitution rate distribution (Extended data Fig. 1a-f). We found similar strong correlation in the regions directly surrounding TF binding sites of Reb1 (Fig. 1b; Pearson’s cor = 0.57, p = 5.6·10−15), and Rap1 (Extended data Fig. 1g), providing further evidence for a direct association. At the sequence-specific binding sites themselves, substitution rates were depressed relative to the OJ, resulting from strong selection pressure to maintain TF binding, and obscuring any mutational signal at these nucleotides.


Lagging-strand replication shapes the mutational landscape of the genome.

Reijns MA, Kemp H, Ding J, de Procé SM, Jackson AP, Taylor MS - Nature (2015)

Elevated substitution rates at OJsa, b, Nucleotide substitution rates (red) closely correlate with elevated OJ site frequency (blue) at (a) nucleosome and (b) Reb1 binding sites. S. cerevisiae polymorphism rates per nucleotide computed using sequences from nucleosome and Reb1 binding sites. Individual data points, open circles. Solid curves, best fit splines. Mean, dashed grey line; ±10% dotted grey lines.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4374164&req=5

Figure 1: Elevated substitution rates at OJsa, b, Nucleotide substitution rates (red) closely correlate with elevated OJ site frequency (blue) at (a) nucleosome and (b) Reb1 binding sites. S. cerevisiae polymorphism rates per nucleotide computed using sequences from nucleosome and Reb1 binding sites. Individual data points, open circles. Solid curves, best fit splines. Mean, dashed grey line; ±10% dotted grey lines.
Mentions: We were struck by the similarity of the distribution of S. cerevisiae OJ sites at nucleosomes17 to that previously reported for nucleotide substitutions7,8,10-12, and set out to investigate the potential reasons for this. We established that nucleotide substitution and OJ distributions are highly correlated (Pearson’s correlation coefficient = 0.76, p = 2.2·10−16) and essentially identical in pattern (Fig. 1a). Furthermore, differences in OJ distribution by nucleosome type (genic vs non-genic), spacing or consistency of binding were mirrored by the substitution rate distribution (Extended data Fig. 1a-f). We found similar strong correlation in the regions directly surrounding TF binding sites of Reb1 (Fig. 1b; Pearson’s cor = 0.57, p = 5.6·10−15), and Rap1 (Extended data Fig. 1g), providing further evidence for a direct association. At the sequence-specific binding sites themselves, substitution rates were depressed relative to the OJ, resulting from strong selection pressure to maintain TF binding, and obscuring any mutational signal at these nucleotides.

Bottom Line: The origin of mutations is central to understanding evolution and of key relevance to health.Here we report that the 5' ends of Okazaki fragments have significantly increased levels of nucleotide substitution, indicating a replicative origin for such mutations.Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo, comprising approximately 1.5% of the mature genome.

View Article: PubMed Central - PubMed

Affiliation: Medical and Developmental Genetics, MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.

ABSTRACT
The origin of mutations is central to understanding evolution and of key relevance to health. Variation occurs non-randomly across the genome, and mechanisms for this remain to be defined. Here we report that the 5' ends of Okazaki fragments have significantly increased levels of nucleotide substitution, indicating a replicative origin for such mutations. Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo, comprising approximately 1.5% of the mature genome. We propose that DNA-binding proteins that rapidly re-associate post-replication act as partial barriers to Pol-δ-mediated displacement of Pol-α-synthesized DNA, resulting in incorporation of such Pol-α tracts and increased mutation rates at specific sites. We observe a mutational cost to chromatin and regulatory protein binding, resulting in mutation hotspots at regulatory elements, with signatures of this process detectable in both yeast and humans.

Show MeSH
Related in: MedlinePlus