Searching journal content for articles similar to Mesner et al. 23 (11): 1774.

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  1. Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
    • Joana Sequeira-Mendes,
    • Zaida Vergara,
    • Ramon Peiró,
    • Jordi Morata,
    • Irene Aragüez,
    • Celina Costas,
    • Raul Mendez-Giraldez,
    • Josep M. Casacuberta,
    • Ugo Bastolla,
    • and Crisanto Gutierrez
    Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
    ...replication originsIn this study, we generated a whole-body ORI map of A. thaliana plants at two different developmental stages. ORI activity was assessed quantitatively from the sequencing data by determining a nascent strand score (NSS) that measures the propensity of a certain genomic location to behave...
  2. Method: Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins
    • Michael S. Foulk,
    • John M. Urban,
    • Cinzia Casella,
    • and Susan A. Gerbi
    Genome Res. May 2015 25: 725-735; Published in Advance February 18, 2015, doi:10.1101/gr.183848.114
    .... Moreover, most of our NS-seq peaks are not near G4 motifs, suggesting that G4s are not necessary for specification of all origins. Likewise, <6% of NSCR peaks had an orientation-specific relationship with G4s (Kunnev et al. 2015), and using the orthogonal origin mapping technique of bubble-seq, Mesner et...
  3. Method: Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins
    • Dimiter Kunnev,
    • Amy Freeland,
    • Maochun Qin,
    • Robert W. Leach,
    • Jianmin Wang,
    • Rajani M. Shenoy,
    • and Steven C. Pruitt
    Genome Res. April 2015 25: 558-569; Published in Advance March 11, 2015, doi:10.1101/gr.176099.114
    ...deficiency reduces DNA replication initiation in gene-rich regions of the genome. DNA structural properties are shown to correlate with sequence motifs associated with replication origins and with locations that are preferentially affected by MCM2 deficiency. Reduced nascent strand density correlates...
  4. Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
    • Maude Strobino,
    • Joanna M. Wenda,
    • Laura Padayachy,
    • and Florian A. Steiner
    Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
    ...to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the is replicated from early and late firing origins and is partitioned into domains...
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  5. 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
    ...to a higher enrichment of Orc4 at these sites, hence overrepresenting the “early” data set. Similar to previous studies (Mesner et al. 2011, 2013), early firing, but not late firing, origins appear to have been sequenced to saturation. Our analysis also reveals a higher contact probability between orc...
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