title: Lagging-strand replication shapes the mutational landscape of the genome.
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.
authors.affiliation: MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, UK.
authors.forename: Martin A M
authors.initials: MAM
authors.lastname: Reijns
authors.affiliation: MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, UK.
authors.forename: Harriet
authors.initials: H
authors.lastname: Kemp
authors.affiliation: MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, UK.
authors.forename: James
authors.initials: J
authors.lastname: Ding
authors.affiliation: MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, UK.
authors.forename: Sophie Marion
authors.initials: SM
authors.lastname: de Procé
authors.affiliation: MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, UK.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Jackson
authors.affiliation: MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, UK.
authors.forename: Martin S
authors.initials: MS
authors.lastname: Taylor
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D017124:Conserved Sequence / Q000235:genetics; D004247:DNA / Q000096:biosynthesis* / Q000235:genetics*; D004256:DNA Polymerase I / Q000378:metabolism; D004258:DNA Polymerase III / Q000378:metabolism; D004261:DNA Replication / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000378:metabolism; D019143:Evolution, Molecular; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008954:Models, Biological; D016296:Mutagenesis / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; C022262:Okazaki fragments; D014157:Transcription Factors; D004247:DNA; D004256:DNA Polymerase I; D004258:DNA Polymerase III