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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-[alpha] (Pol-[alpha]) 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-[delta]-mediated displacement of Pol-[alpha]-synthesized DNA, resulting in incorporation of such Pol-[alpha] 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. The emRiboSeq sequencing method is used to track polymerase activity genome-wide in vivo; despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-[alpha] (Pol-[alpha]) is retained in vivo and comprises ~1.5% of the genome, establishing Pol-[alpha] as an important source of genomic variability and providing a mechanism for site-specific variation in nucleotide substitution rates. Replication-linked genome variation The mechanisms that underpin non-random distribution of mutations across the genome remain to be defined. Here Andrew Jackson and colleagues report that the 5' ends of Okazaki fragments -- short fragments of DNA synthesized on the lagging strand of DNA during replication -- have increased levels of nucleotide substitution. With the help of a newly developed method tracking polymerase activity known as emRiboSeq, they show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-[alpha] (Pol-[alpha]) is retained in vivo, and comprises about 1.5% of the genome. These findings establish establishing Pol-[alpha] as an important source of genomic variability, and provide a mechanism for site-specific variation in nucleotide substitution rates. Mutation hotspots at regulatory elements are therefore a mutational cost of chromatin and regulatory protein binding., Author(s): Martin A. M. Reijns [sup.1] , Harriet Kemp [sup.2] , James Ding [sup.1] , Sophie Marion de Procé [sup.2] , Andrew P. Jackson [sup.1] , Martin S. Taylor [sup.2] [...]

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., Mutations occur despite the exquisite fidelity of DNA replication, efficient proofreading and mismatch repair (1), resulting in heritable disease and providing the raw material for evolution. Genome variation is non-uniform [...]

Medulloblastomas are the most common malignant brain tumours in children (1). Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, [...]

Author(s): Victor Serebrov [1]; Anna Marie Pyle (corresponding author) [1, 2] The NS3 helicase is essential for cytoplasmic RNA replication by the hepatitis C virus [1, 2, 3, 4], and [...]

Author(s): Giovanni Maga (corresponding author) [1, 4]; Giuseppe Villani [2]; Emmanuele Crespan [1]; Ursula Wimmer [4]; Elena Ferrari [4]; Barbara Bertocci [3]; Ulrich Hübscher [4] Specialized DNA polymerases (DNA pols) [...]

Author(s): Courtney Prochnow [1, 2]; Ronda Bransteitter [1, 2]; Michael G. Klein [1]; Myron F. Goodman [1]; Xiaojiang S. Chen (corresponding author) [1] APOBEC-2 (APO2) belongs to the family of [...]

During the first half of the twentieth century, biochemists pondered the identity of genetic material with great wonderment. How can biological material replicate itself? This question was answered, in principle, [...]