Searching journal content for articles similar to Khil et al. 22 (5): 957.

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  1. Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
    • Benjamin Davies,
    • Gang Zhang,
    • Daniela Moralli,
    • Samy Alghadban,
    • Daniel Biggs,
    • Chris Preece,
    • Peter Donnelly,
    • and Anjali Gupta Hinch
    Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
    ...meiotic recombination. PRDM9 binds DNA at particular sequence motifs (#1), a subset of which become sites of programmed DSBs by SPO11 (#2). Strand resection creates ssDNA overhangs, which are bound by RPA first (#3) and then by DMC1 and RAD51 (#4). Binding occurs to the left of the break on the forward...
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  2. Method: Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method
    • Zhi-Xiong Zhou,
    • Mei-Jun Zhang,
    • Xu Peng,
    • Yuko Takayama,
    • Xing-Ya Xu,
    • Ling-Zhi Huang,
    • and Li-Lin Du
    Genome Res. April 2013 23: 705-715; Published in Advance December 17, 2012, doi:10.1101/gr.146357.112
    ...immunoprecipitation followed by sequencing (SPI-seq) to map genomic hotspots of DNA damage. We demonstrated this method with Rad52, a homologous recombination repair protein, which binds to ssDNA formed at DNA lesions. SPI-seq faithfully detected, in fission yeast, Rad52 enrichment at artificially induced double...
  3. Research: Histone methyltransferase PRDM9 is not essential for meiosis in male mice
    • Ondrej Mihola,
    • Florencia Pratto,
    • Kevin Brick,
    • Eliska Linhartova,
    • Tatyana Kobets,
    • Petr Flachs,
    • Christopher L. Baker,
    • Radislav Sedlacek,
    • Kenneth Paigen,
    • Petko M. Petkov,
    • R. Daniel Camerini-Otero,
    • and Zdenek Trachtulec
    Genome Res. July 2019 29: 1078-1086; Published in Advance June 11, 2019, doi:10.1101/gr.244426.118
    .... Numerical constraints and feedback control of double-strand breaks in mouse meiosis. Genes Dev 27: 873–886. doi:10.1101/gad.213652.113 ↵Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome Res 22...
  4. Research: In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
    • Corinne Grey,
    • Julie A.J. Clément,
    • Jérôme Buard,
    • Benjamin Leblanc,
    • Ivo Gut,
    • Marta Gut,
    • Laurent Duret,
    • and Bernard de Massy
    Genome Res. April 2017 27: 580-590; Published in Advance March 23, 2017, doi:10.1101/gr.217240.116
    ...:T-to-G:C substitutions. This effect has been detected at mouse recombination hotspots, defined by DMC1 ChIP-seq (Clement and Arndt 2013). GC-biased gene conversion can be measured by estimating the GC content at equilibrium, also named GC∗ (see Methods). At class 1 sites, a sharp GC∗ increase was detected at the center...
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  5. Method: A virome-wide clonal integration analysis platform for discovering cancer viral etiology
    • Xun Chen,
    • Jason Kost,
    • Arvis Sulovari,
    • Nathalie Wong,
    • Winnie S. Liang,
    • Jian Cao,
    • and Dawei Li
    Genome Res. May 2019 29: 819-830; Published in Advance March 14, 2019, doi:10.1101/gr.242529.118
    ...taxonomic classes, including dsDNA, ssDNA, dsRNA, ssRNA (−), ssRNA (+), and retroviruses (Fig. 1B). This library incorporates all currently characterized viral s and represents the largest existing viral reference library.View larger version: In this window In a new window Figure 1. Discovering oncovirus...
  6. Research: Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase
    • Ayako Yamanishi,
    • Kosuke Yusa,
    • Kyoji Horie,
    • Masahiro Tokunaga,
    • Kohji Kusano,
    • Chikara Kokubu,
    • and Junji Takeda
    Genome Res. September 2013 23: 1462-1473; Published in Advance August 1, 2013, doi:10.1101/gr.152744.112
    ...interhomolog DSB repair by homologous recombination may be unfavorable. Instead, the 39 ssDNA tail can seek out its annealing partner by taking advantage of the first few nucleotides, which mediate formation of transient secondary structures by ‘‘loopingout’’ or ‘‘snapping-back’’ motions and prime strand...
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