Searching journal content for articles similar to Chen et al. 24 (7): 1138.

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  1. Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
    • Michelle Kudron,
    • Louis Gevirtzman,
    • Alec Victorsen,
    • Bridget C. Lear,
    • Jiahao Gao,
    • Jinrui Xu,
    • Swapna Samanta,
    • Emily Frink,
    • Adri Tran-Pearson,
    • Chau Huynh,
    • Dionne Vafeados,
    • Ann Hammonds,
    • William Fisher,
    • Martha Wall,
    • Greg Wesseling,
    • Vanessa Hernandez,
    • Zhichun Lin,
    • Mary Kasparian,
    • Kevin White,
    • Ravi Allada,
    • Mark Gerstein,
    • LaDeana Hillier,
    • Susan E. Celniker,
    • Valerie Reinke,
    • and Robert H. Waterston
    Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
    ...contain more than 250 peaks in the worm, suggesting regions of extremely dense TF binding. High occupied target (HOT) sites were recognized in early modENCODE papers (Moorman et al. 2006; Gerstein et al. 2010) and have been defined subsequently in various ways (Chen et al. 2014; Wreczycka et al. 2019...
  2. Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
    • Tess E. Jeffers and
    • Jason D. Lieb
    Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
    ...JE, Phillips D, Skidmore CJ, Walker IO. 1978. The interaction of core histones withDNA: equilibrium binding studies. Nucleic Acids Res 5: 3643–3664. Chen RAJ, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J. 2014. Extreme HOT regions are CpG-dense promoters in C. elegans and humans. Genome Res 24...
  3. Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
    • Belle A. Moyers,
    • E. Christopher Partridge,
    • Mark Mackiewicz,
    • Michael J. Betti,
    • Roshan Darji,
    • Sarah K. Meadows,
    • Kimberly M. Newberry,
    • Laurel A. Brandsmeier,
    • Barbara J. Wold,
    • Eric M. Mendenhall,
    • and Richard M. Myers
    Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
    ...promoter elements (Supplemental Figs. 22, 23; see P-values in Supplemental Table 16).Analysis of HOT sites shows that ABC score increases with DAP occupancyHOT sites are regions of the with a high number of associated DAPs (Yip et al. 2012), and their biological meaning is an area of ongoing interest...
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  4. Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
    • Jungkyun Seo,
    • D. Dewran Koçak,
    • Luke C. Bartelt,
    • Courtney A. Williams,
    • Alejandro Barrera,
    • Charles A. Gersbach,
    • and Timothy E. Reddy
    Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
    ...regions (Gerstein et al. 2010). In addition, HOT regions were discovered across multiple cell types and species with disparate functions, consistent with our findings of AP-1 hotspots observed in different cell types of mouse and human (MacArthur et al. 2009; Gerstein et al. 2010; Araya et al. 2014; Chen...
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