Searching journal content for articles similar to Chang et al. 11 (7): 1145.

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  1. 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...
  2. 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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  3. LETTER: Microsatellites in Different Eukaryotic Genomes: Survey and Analysis
    • Gábor Tóth,
    • Zoltán Gáspári,
    • and Jerzy Jurka
    Genome Res. July 1, 2000 10: 967-981; doi:10.1101/gr.10.7.967
    ...to be controlled at multiple steps in vivo. An active role of the DNA mismatch repair system to stabilize simple sequence repeats has been revealed in Escherichia coli , yeast, and humans (for review, see Sia et al. 1997 ). Although a number of experimental results argue in favor of the above model, homologous...
  4. Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
    • Wilfried M. Guiblet,
    • Marzia A. Cremona,
    • Monika Cechova,
    • Robert S. Harris,
    • Iva Kejnovská,
    • Eduard Kejnovsky,
    • Kristin Eckert,
    • Francesca Chiaromonte,
    • and Kateryna D. Makova
    Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
    ...polymerases and enzymes from numerous DNA repair pathways (Sweasy et al. 2006). Furthermore, mutation occurrence is influenced by additional factors (e.g., chromatin, etc.) (Makova and Hardison 2015). Notwithstanding all these caveats, our results, together with published results of Du and colleagues (Du et...
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  5. LETTER: Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties
    • Albino Bacolla,
    • Jacquelynn E. Larson,
    • Jack R. Collins,
    • Jian Li,
    • Aleksandar Milosavljevic,
    • Peter D. Stenson,
    • David N. Cooper,
    • and Robert D. Wells
    Genome Res. October 2008 18: 1545-1553; Published in Advance August 7, 2008, doi:10.1101/gr.078303.108
    ...or incisions at the 3-/4-way junctions by the Holliday junction resolvase may initiate DNA repair and exonucleolytic cleavage, followed by single-strand annealing ( Al-Minawi et al. 2008 ) or nonhomologous end-joining ( Inagaki et al. 2007 ), respectively. Second, cleaved hairpins may impose a mutational...
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  6. Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    ...repair (Cmya5 and Zcchc9), but it is unclear how those would contribute to an STR mutator phenotype.Msh3 is well known to be involved in regulating STR stability. Msh3 is one of multiple homologs of the Escherichia coli MutS MMR protein, which recognizes mismatched bases in DNA that arise during DNA...
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  7. 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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  8. Research: Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency
    • Linghua Wang,
    • Shuichi Tsutsumi,
    • Tokuichi Kawaguchi,
    • Koichi Nagasaki,
    • Kenji Tatsuno,
    • Shogo Yamamoto,
    • Fei Sang,
    • Kohtaro Sonoda,
    • Minoru Sugawara,
    • Akio Saiura,
    • Seiko Hirono,
    • Hiroki Yamaue,
    • Yoshio Miki,
    • Minoru Isomura,
    • Yasushi Totoki,
    • Genta Nagae,
    • Takayuki Isagawa,
    • Hiroki Ueda,
    • Satsuki Murayama-Hosokawa,
    • Tatsuhiro Shibata,
    • Hiromi Sakamoto,
    • Yae Kanai,
    • Atsushi Kaneda,
    • Tetsuo Noda,
    • and Hiroyuki Aburatani
    Genome Res. February 2012 22: 208-219; Published in Advance December 7, 2011, doi:10.1101/gr.123109.111
    ...). Its molecular basis iswell understood inhereditary cancers, inwhich it has been linked to mutations in DNA mismatch repair (MMR) genes. One of the best-documented examples is the hereditary nonpolyposis colon cancer (HNPCC). In general, MMR defects are the result of a germline mutation in one...
  9. LETTER: Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)
    • Marzena Gajecka,
    • Andrew J. Gentles,
    • Albert Tsai,
    • David Chitayat,
    • Katherine L. Mackay,
    • Caron D. Glotzbach,
    • Michael R. Lieber,
    • and Lisa G. Shaffer
    Genome Res. November 2008 18: 1733-1742; Published in Advance September 2, 2008, doi:10.1101/gr.077453.108
    ...of chromosome 22, and the microhomology is extended by polymerase μ or λ, which accidently polymerizes a G–T mismatch during the process. The mismatch is aberrantly repaired, resulting in a one-base mutation. The remaining 3′ overhang end of chromosome 1 has some microhomology in the 5′ overhang end...
  10. Research: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
    • Mariana Villalba de la Peña,
    • Pauliina A.M. Summanen,
    • Martta Liukkonen,
    • and Ilkka Kronholm
    Genome Res. April 2023 33: 599-611; Published in Advance March 15, 2023, doi:10.1101/gr.276992.122
    ...why heterochromatic regions have a higher mutation rate. In yeast, actively transcribed regions contain acetylation at H3K56, which suppresses spontaneous mutations (Kadyrova et al. 2013). Moreover, analyses based on human tumors suggest that DNA mismatch repair works more efficiently in euchromatin...
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