Searching journal content for articles similar to Sun et al. 25 (11): 1703.

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  1. Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
    • Marina Veil,
    • Lev Y. Yampolsky,
    • Björn Grüning,
    • and Daria Onichtchouk
    Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
    ..., transcription after ZGA depends on a small number of maternal enhancer-binding transcription factors (TFs). Zygotic activators include Zelda in Drosophila (Liang et al. 2008), as well as three homologs of pluripotency TFs, Pou5f3, Nanog, and Sox19b in zebrafish (Lee et al. 2013; Leichsenring et al. 2013...
  2. Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
    • Nina Koenecke,
    • Jeff Johnston,
    • Qiye He,
    • Samuel Meier,
    • and Julia Zeitlinger
    Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
    ...factor. A potential pioneer transcription factor is Zelda (Zld), which is present ubiquitously in theDrosophila early embryo and primes enhancers even before DV patterning begins (Liang et al. 2008; Harrison et al. 2011; Nien et al. 2011).While Zld is required tomake someDV enhancers accessible (Yanez...
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  3. Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
    • Aaron C. Daugherty,
    • Robin W. Yeo,
    • Jason D. Buenrostro,
    • William J. Greenleaf,
    • Anshul Kundaje,
    • and Anne Brunet
    Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
    ...a dimeric version of the canonical GAGA motif bound by Trl/GAGA-Associated Factor (GAF) in Drosophila. GAF is a multifaceted transcription factor that can associate with heterochromatin (Raff et al. 1994), remodel chromatin in concert with nucleosome remodelers (Okada and Hirose 1998), and act...
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  4. Resource: Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
    • Jamie C. Kwasnieski,
    • Terry L. Orr-Weaver,
    • and David P. Bartel
    Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
    .... 2007; Ali-Murthy et al. 2013; Heyn et al. 2014).Zelda is a major regulator of ZGA in Drosophila and activates the expression of hundreds of genes (Liang et al. 2008; Harrison et al. 2011; Nien et al. 2011). To evaluate if Zelda might also be activating expression of these very-early-transcribed genes...
  5. Research: ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
    • Marta Bozek,
    • Roberto Cortini,
    • Andrea Ennio Storti,
    • Ulrich Unnerstall,
    • Ulrike Gaul,
    • and Nicolas Gompel
    Genome Res. May 2019 29: 771-783; Published in Advance April 8, 2019, doi:10.1101/gr.242362.118
    ...chromatin structure and reduced nucleosome occupancy prior to zygotic activation (Li et al. 2014; Blythe and Wieschaus 2016). This early opening of enhancers is mediated by a maternally deposited TF, Zelda, a pioneer TF that actively destabilizes nucleosomes or prevents their deposition after the initial...
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  6. Research: Evolution of transcription factor binding through sequence variations and turnover of binding sites
    • Gat Krieger,
    • Offir Lupo,
    • Patricia Wittkopp,
    • and Naama Barkai
    Genome Res. June 2022 32: 1099-1111; Published in Advance May 26, 2022, doi:10.1101/gr.276715.122
    ...evolution were modeled for Drosophila enhancers (He et al. 2011a), but not for yeast promoters (Mustonen et al. 2008). The flexibility and high rate of binding site evolution suggests that in many cases binding site loss or addition is not deleterious. Overall, we find that TF binding evolves through gains...
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