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  1. Research: The organization of genome duplication is a critical determinant of the landscape of genome maintenance
    • Blanca Gómez-Escoda and
    • Pei-Yun Jenny Wu
    Genome Res. August 2018 28: 1179-1192; Published in Advance June 22, 2018, doi:10.1101/gr.224527.117
    ...eukaryotic organisms, their biological importance for cellular physiology remains largely unexplored. We address this fundamental question in the context of maintenance, taking advantage of the inappropriate origin firing that occurs when fission yeast cells lacking the Rad3/ATR checkpoint kinase...
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  2. Research: Orc4 spatiotemporally stabilizes centromeric chromatin
    • Lakshmi Sreekumar,
    • Kiran Kumari,
    • Krishnendu Guin,
    • Asif Bakshi,
    • Neha Varshney,
    • Bhagya C. Thimmappa,
    • Leelavati Narlikar,
    • Ranjith Padinhateeri,
    • Rahul Siddharthan,
    • and Kaustuv Sanyal
    Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
    ...of centromere DNA is its replication timing. Whereas metazoan cells replicate centromeres during late S phase (Ten Hagen et al. 1990), centromeres replicate at early S phase in fungi (Pohl et al. 2012). This temporal distinction in the centromere DNA replication in two major eukaryotic kingdoms can...
  3. Method: Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase
    • Jared M. Peace,
    • Sandra K. Villwock,
    • John L. Zeytounian,
    • Yan Gan,
    • and Oscar M. Aparicio
    Genome Res. March 2016 26: 365-375; Published in Advance January 4, 2016, doi:10.1101/gr.196857.115
    ...levels of origin firing observed in early S phase. Total DNA content in HU was little changed due to Fkh1-OE or Fkh2-OE, suggesting little if any change in dNTP pool levels (Supplemental Fig. S5A). In contrast, overexpression of ribonucleotide reductase (RNR3), which has been shown to increase d...
  4. Research: Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
    • Vishnu Dileep,
    • Ferhat Ay,
    • Jiao Sima,
    • Daniel L. Vera,
    • William S. Noble,
    • and David M. Gilbert
    Genome Res. August 2015 25: 1104-1113; Published in Advance May 20, 2015, doi:10.1101/gr.183699.114
    ...: 2149–2158. ↵Hayano M, Kanoh Y, Matsumoto S, Renard-Guillet C, Shirahige K, Masai H. 2012. Rif1 is a global regulator of timing of replication origin firing in fission yeast. Genes Dev 26: 137–150. ↵Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang C-W, Lyou Y, Townes TM, Schübeler D, Gilbert DM...
  5. Methods: Predictable dynamic program of timing of DNA replication in human cells
    • Romain Desprat,
    • Danielle Thierry-Mieg,
    • Nathalie Lailler,
    • Julien Lajugie,
    • Carl Schildkraut,
    • Jean Thierry-Mieg,
    • and Eric E. Bouhassira
    Genome Res. December 2009 19: 2288-2299; Published in Advance September 18, 2009, doi:10.1101/gr.094060.109
    ...is true -wide. Temporal transition regions Analysis of the TimEX profiles suggests that the spatial distribution and the timing of the firing origins of replication in the are very uneven. In parts of the , large regions replicate in a coordinated manner early or late in S phase, suggesting...
  6. Research: Random replication of the inactive X chromosome
    • Amnon Koren and
    • Steven A. McCarroll
    Genome Res. January 2014 24: 64-69; Published in Advance September 24, 2013, doi:10.1101/gr.161828.113
    ...). The gradual loss of replication structure as S phase progresses (Fig. 3) is consistent with elevated origin initiation rates at later times during S phase, as observed in single-molecule analyses in frogs (Herrick et al. 2000), human cells (Guilbaud et al. 2011), and fission yeast (Patel et al. 2006...
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