Searching journal content for articles similar to Schulz et al. 25 (11): 1715.

Displaying results 1-10 of 12
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  1. 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
    ...as a transcriptional activator, in part due to its ability to increase chromatin accessibility (Adkins et al. 2006). Like Drosophila GAF, C. elegans EOR-1 is a transcriptional activator in the Ras/ERK signaling pathway that has been suggested to also repress gene expression (Liu et al. 2011a). GAF and EOR-1 are also...
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  2. Research: Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
    • Yujia Sun,
    • Chung-Yi Nien,
    • Kai Chen,
    • Hsiao-Yun Liu,
    • Jeff Johnston,
    • Julia Zeitlinger,
    • and Christine Rushlow
    Genome Res. November 2015 25: 1703-1714; Published in Advance September 2, 2015, doi:10.1101/gr.192542.115
    ...Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation Yujia Sun 1 , 4 , Chung-Yi Nien 1 , 4 , Kai Chen 2 , Hsiao-Yun Liu 1 , Jeff Johnston 2 , Julia Zeitlinger 2 , 3...
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  3. 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
    ...a function of the domain's position along the AP axis.Differential accessibility is a signature of axis patterning enhancersOpen chromatin regions in the Drosophila blastoderm correspond to a range of functional genomic elements, such as transcribed gene bodies, promoters, distal CREs, insulators...
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  4. 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
    ...% of differentially bound sites were associated with variations in known binding sequences. Similarly, studies comparing binding of six TFs between two Drosophila species revealed only modest correlation between interspecific differences in binding and sequence variations in known motifs (Bradley et al. 2010).The...
  5. Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
    • Xiangxiu Wang,
    • Wen Wang,
    • Yiman Wang,
    • Jia Chen,
    • Guifen Liu,
    • and Yong Zhang
    Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
    ....Metazoans undergo a rapid and well-orchestrated process called zygotic activation (ZGA) in which developmental control is transferred from maternal to zygotic genetic material during early embryo development. Dozens of transcription factors (TFs) have been shown to be key activators in this process as indicated...
  6. Research: The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
    • Rahul Satija and
    • Robert K. Bradley
    Genome Res. April 2012 22: 656-665; Published in Advance January 13, 2012, doi:10.1101/gr.130682.111
    ...-specific transcription factors active in the Drosophila embryo, we found that binding of all factors exhibits a dose-dependent relationship with “TAGteam” sequence motifs bound by the zinc finger protein Vielfaltig, also known as Zelda, a recently discovered activator of the zygotic genome. TAGteam motifs are present...
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  7. 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...
  8. 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...
  9. 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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  10. Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
    • J. Omar Yáñez-Cuna,
    • Huy Q. Dinh,
    • Evgeny Z. Kvon,
    • Daria Shlyueva,
    • and Alexander Stark
    Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
    ...specific motif requirements of individual binding sites. We predict that TF binding in the early Drosophila embryo depends on motifs for the early zygotic TFs Vielfaltig (also known as Zelda) and Tramtrack. We validate experimentally that the activity of Twist-bound enhancers and Twist binding itself...
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