Searching journal content for articles similar to Belfield et al. 28 (1): 66.

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  1. 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...
  2. 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...
  3. Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
    • Kamal Ajit,
    • Adele Alagia,
    • Kaspar Burger,
    • and Monika Gullerova
    Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
    ...induces DNA SSBs, activating repair pathways such as base excision repair (BER), nucleotide excision repair, and mismatch repair, which are different from DSB-induced HR or NHEJ (Rastogi et al. 2010). Therefore, a mechanism for global transcriptional response could be distinct from UV...
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  4. 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
    ...C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency Bettina Meier 1 , 6 , Susanna L. Cooke 2 , 6 , Joerg Weiss 1 , Aymeric P. Bailly 1 , 3 , Ludmil B. Alexandrov...
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  5. Research: CG dinucleotides enhance promoter activity independent of DNA methylation
    • Dominik Hartl,
    • Arnaud R. Krebs,
    • Ralph S. Grand,
    • Tuncay Baubec,
    • Luke Isbel,
    • Christiane Wirbelauer,
    • Lukas Burger,
    • and Dirk Schübeler
    Genome Res. April 2019 29: 554-563; Published in Advance February 1, 2019, doi:10.1101/gr.241653.118
    ...in transcriptional and/or epigenetic regulation. One explanation portrays CGIs as a footprint of evolution due to lower mutation rates of unmethylated CpGs (Bird 1980). In support of this, unmethylated cytosines deaminate to uracil (Barnes and Lindahl 2004), an improper DNA base that is efficiently repaired...
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  6. Research: Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication
    • Eve Shinbrot,
    • Erin E. Henninger,
    • Nils Weinhold,
    • Kyle R. Covington,
    • A. Yasemin Göksenin,
    • Nikolaus Schultz,
    • Hsu Chao,
    • HarshaVardhan Doddapaneni,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Chris Sander,
    • Zachary F. Pursell,
    • and David A. Wheeler
    Genome Res. November 2014 24: 1740-1750; Published in Advance September 16, 2014, doi:10.1101/gr.174789.114
    ..., the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication. [Supplemental material is available for this article.] Damage to cellular DNA repair systems leads to a high frequency of mutations in all species (Kunkel and Erie 2005...
  7. Research: DDX54 regulates transcriptome dynamics during DNA damage response
    • Miha Milek,
    • Koshi Imami,
    • Neelanjan Mukherjee,
    • Francesca De Bortoli,
    • Ulrike Zinnall,
    • Orsalia Hazapis,
    • Christian Trahan,
    • Marlene Oeffinger,
    • Florian Heyd,
    • Uwe Ohler,
    • Matthias Selbach,
    • and Markus Landthaler
    Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
    ...indicates the relevance of many uncharacterized RBPs potentially involved in the DDR. [Supplemental material is available for this article.] The DNA damage response (DDR) is a collective term for signal transduction pathways that sense, signal, and repair different types of DNA lesions in eukaryotic cells...
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  8. Research: APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication
    • Vladimir B. Seplyarskiy,
    • Ruslan A. Soldatov,
    • Konstantin Y. Popadin,
    • Stylianos E. Antonarakis,
    • Georgii A. Bazykin,
    • and Sergey I. Nikolaev
    Genome Res. February 2016 26: 174-182; Published in Advance January 11, 2016, doi:10.1101/gr.197046.115
    ...occur as clusters (“kataegis”) in single-stranded DNA produced during repair of double-stranded breaks (DSBs). However, the properties of the remaining 87% of nonclustered APOBEC-induced mutations, the source and the genomic distribution of the ssDNA where they occur, are largely unknown. By analyzing...
  9. 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
    ...predominantly by misinsertions or slippage events of replicative polymerases that are missed by their proofreading domains and not corrected by mismatch repair (Lynch 2008). Less frequently, but with a potentially much more detrimental effect, mutations can arise when DNA damage obstructs progression of DNA...
  10. Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    • Phillippa C. Taberlay,
    • Aaron L. Statham,
    • Theresa K. Kelly,
    • Susan J. Clark,
    • and Peter A. Jones
    Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
    ...and insulator elements in prostate and breast cancer cells using simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy (NOMe-seq). We find that the genomic location of nucleosome-depleted regions (NDRs) is mostly cell type specific and preferentially found at enhancers in normal cells...
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