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Corrigendum: Corrigendum: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
- Bettina Meier,
- Nadezda V. Volkova,
- Ye Hong,
- Pieta Schofield,
- Peter J. Campbell,
- Moritz Gerstung,
- and Anton Gartner
Genome Res. September 2019 29: 1566_2; doi:10.1101/gr.255596.119
...: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers Bettina Meier , Nadezda V. Volkova , Ye Hong , Pieta Schofield , Peter J. Campbell , Moritz Gerstung and Anton Gartner Genome Research 28: 666–675 (2018) The authors would like to correct an error in the link...
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Research: C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
- Bettina Meier,
- Susanna L. Cooke,
- Joerg Weiss,
- Aymeric P. Bailly,
- Ludmil B. Alexandrov,
- John Marshall,
- Keiran Raine,
- Mark Maddison,
- Elizabeth Anderson,
- Michael R. Stratton,
- Anton Gartner,
- and Peter J. Campbell
Genome Res. October 2014 24: 1624-1636; Published in Advance July 16, 2014, doi:10.1101/gr.175547.114
..., can cause genotoxic damage inmice (Langevin et al. 2011) and are associated with esophageal cancer (Brooks et al. 2009). Discussion We have used C. elegans as an experimental system to study the effects of carcinogens and DNA repair deficiencies on mutational signatures, and their interactions...
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Research: Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
- Scott A. Lujan,
- Anders R. Clausen,
- Alan B. Clark,
- Heather K. MacAlpine,
- David M. MacAlpine,
- Ewa P. Malc,
- Piotr A. Mieczkowski,
- Adam B. Burkholder,
- David C. Fargo,
- Dmitry A. Gordenin,
- and Thomas A. Kunkel
Genome Res. November 2014 24: 1751-1764; Published in Advance September 12, 2014, doi:10.1101/gr.178335.114
...state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic...
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Research: Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans
- Moein Rajaei,
- Ayush Shekhar Saxena,
- Lindsay M. Johnson,
- Michael C. Snyder,
- Timothy A. Crombie,
- Robyn E. Tanny,
- Erik C. Andersen,
- Joanna Joyner-Matos,
- and Charles F. Baer
Genome Res. September 2021 31: 1602-1613; Published in Advance August 17, 2021, doi:10.1101/gr.275372.121
...:C → T:A transversions are often interpreted as a signature of oxidative damage to DNA (Krašovec et al. 2017; Suzuki and Kamiya 2017; Poetsch et al. 2018). Although much of the early work linking ROS with 8-oxodG and mutation was conducted in somatic cells (Dollé et al. 2000; Busuttil et al. 2003...
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Research: Polymerase theta-mediated end joining of replication-associated DNA breaks in C. elegans
- Sophie F. Roerink,
- Robin van Schendel,
- and Marcel Tijsterman
Genome Res. June 2014 24: 954-962; Published in Advance March 10, 2014, doi:10.1101/gr.170431.113
...that exhibits genetic interactionwith Atm. Mol Cell Biol 24: 10381–10389. Tijsterman M, Pothof J, Plasterk RHA. 2002. Frequent germline mutations and somatic repeat instability in DNA mismatch-repair-deficient Caenorhabditis elegans. Genetics 161: 651–660. Ye K, SchulzMH, LongQ, Apweiler R, Ning Z. 2009. Pindel...
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Method: Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq
- Pete H. Taylor,
- Amanda Cinquin,
- and Olivier Cinquin
Genome Res. November 2016 26: 1600-1611; Published in Advance October 19, 2016, doi:10.1101/gr.200501.115
...be dominated by sequencer errors but may also receive a contribution from in vitro replication errors occurring during the later cycles of PCR and from reference errors. Finally, the mutation spectrum is determined by the combination of DNA damage and repair events. We found that raw mismatches are mostly T...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...to repair attempts and bypass of the checkpoint arrest through the adaptation to DNA damage process (Blasco et al. 1997; Lee et al. 1998; Chin et al. 1999; Artandi et al. 2000; Hackett et al. 2001; Hackett and Greider 2003; Maciejowski et al. 2015; Coutelier et al. 2018; Henninger and Teixeira 2020...
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Research: Mechanisms of precise genome editing using oligonucleotide donors
- Yinan Kan,
- Brian Ruis,
- Taylor Takasugi,
- and Eric A. Hendrickson
Genome Res. July 2017 27: 1099-1111; Published in Advance March 29, 2017, doi:10.1101/gr.214775.116
...strand nicks via SDSA. (B) Repair of nicks on the same strand via ssDI. Schematic elements are labeled as follows: (Top) genomic DNA, black; genomic lesions and DNA ends, hatched orange lines; ODNs, red; knock-in mutations, green; resection nucleases, yellow PAC-MAN; base-pairing, purple vertical lines...
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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...systems of overall rising temperature and regional climatic instability remain poorly understood. One major unknown is the effect of global warming on mutation, the raw fuel of biological evolution. Mutations can arise due to faulty repair of DNA replication errors or from oxidative stress- or irradiation...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...Harbor, New York 11724, USA ↵3 These authors contributed equally to this work. Corresponding author: martiens@cshl.eduAbstractIn Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated si...

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