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Research: 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. May 2018 28: 666-675; Published in Advance April 10, 2018, doi:10.1101/gr.226845.117
...DNA strand at some distance to the lesion (Kadyrov et al. 2006, 2007). Exonucleolytic activities in part conferred by Exo1 contribute to the removal of the DNA stretch containing the mismatch followed by gap filling via lagging strand DNA synthesis (Goellner et al. 2015). The most prominent Mut...
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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...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...in populations results from a balance between the birth of new variants by the process of de novo mutation (DNM) in the germline, the loss of variants by genetic drift, and selective forces that increase or decrease the frequency of variants in the population. Until recently, the rate of DNM in the germline...
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Research: An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation
- Andrew M. Lerner,
- Austin J. Hepperla,
- Gregory R. Keele,
- Hashem A. Meriesh,
- Hayretin Yumerefendi,
- David Restrepo,
- Seth Zimmerman,
- James E. Bear,
- Brian Kuhlman,
- Ian J. Davis,
- and Brian D. Strahl
Genome Res. November 2020 30: 1605-1617; Published in Advance October 5, 2020, doi:10.1101/gr.264283.120
..._strahl@med.unc.edu, ian_davis@med.unc.eduAbstractHistone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the -wide dynamics of H3K36me deposition and removal are not known. We established...
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Research: Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4
- Kate Liddiard,
- Brian Ruis,
- Taylor Takasugi,
- Adam Harvey,
- Kevin E. Ashelford,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
...evolution. [Supplemental material is available for this article.] Short telomeres inadequately protected by the shelterin complex (de Lange 2005) are recognized as double-stranded DNA breaks (DSBs), activating nonhomologous end-joining (NHEJ) DNA repair that can result in chromosomal fusions (Cowell...
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LETTER: Evolution of base-substitution gradients in primate mitochondrial genomes
- Sameer Z. Raina,
- Jeremiah J. Faith,
- Todd R. Disotell,
- Hervé Seligmann,
- Caro-Beth Stewart,
- and David D. Pollock
Genome Res. May 2005 15: 665-673; doi:10.1101/gr.3128605
...spent being single-stranded during replication, and different types of substitutions respond differently to this gradient. The gradient is controlled by biological factors including the rate of replication and functionality of repair mechanisms; little is known, however, about the consistency...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...crossover could contribute to centromere evolution (Smith 1976). In this influential model, meiotic DNA double-strand breaks (DSBs) are repaired using a nonallelic location on a homolog, with the potential to cause gain and loss of intervening tandem repeats (Smith 1976). However, it is widely documented...
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Method: Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
- Kentaro Kawata,
- Hiroyasu Wakida,
- Toshimichi Yamada,
- Kenzui Taniue,
- Han Han,
- Masahide Seki,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. October 2020 30: 1481-1491; Published in Advance August 25, 2020, doi:10.1101/gr.264408.120
.... The 4sU incorporated into the Alkyl-RNAs paired with guanines instead of adenines during the reverse transcription. The RNA was subsequently removed, and second-strand synthesis was initiated by a random primer, containing Illumina-compatible linker sequences and appropriate in-line barcodes, followed...

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