Searching journal content for articles similar to Stavreva et al. 25 (6): 845.

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  1. Research: SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
    • A. Rasim Barutcu,
    • Bryan R. Lajoie,
    • Andrew J. Fritz,
    • Rachel P. McCord,
    • Jeffrey A. Nickerson,
    • Andre J. van Wijnen,
    • Jane B. Lian,
    • Janet L. Stein,
    • Job Dekker,
    • Gary S. Stein,
    • and Anthony N. Imbalzano
    Genome Res. September 2016 26: 1188-1201; Published in Advance July 19, 2016, doi:10.1101/gr.201624.115
    ...with many different protein partners, SMARCA4 is involved in nuclear structure and inmediating specific long-range chromatin interactions (Trotter and Archer 2008; Euskirchen et al. 2011; Imbalzano et al. 2013a). The organization of chromatin occurs in a hierarchical manner. Chromosomes are positioned...
  2. Research: TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
    • Morgan A. Sammons,
    • Jiajun Zhu,
    • Adam M. Drake,
    • and Shelley L. Berger
    Genome Res. February 2015 25: 179-188; Published in Advance November 12, 2014, doi:10.1101/gr.181883.114
    ...reports suggest that TP53-regulated genes are controlled in part by long-range chromatin interactions (Link et al. 2013; Melo et al. 2013). Hence, it is striking that TP53 binding sites adjacent to activated genes comprise the smallest overall proportion of sites and have lower correspondence to consensus...
  3. Article: Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
    • Timothy E. Reddy,
    • Florencia Pauli,
    • Rebekka O. Sprouse,
    • Norma F. Neff,
    • Kimberly M. Newberry,
    • Michael J. Garabedian,
    • and Richard M. Myers
    Genome Res. December 2009 19: 2163-2171; Published in Advance October 2, 2009, doi:10.1101/gr.097022.109
    ...with measurements of gene expression response showed that the majority of down-regulation occurs independently of proximal GR–DNA interactions. Furthermore, kinetic evaluation shows that repression occurs more slowly than activation. One explanation is that GR-mediated repression involves long-range cis-interactions...
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  4. Method: Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication
    • Zihao Wang,
    • Zhenquan Zhang,
    • Songhao Luo,
    • Tianshou Zhou,
    • and Jiajun Zhang
    Genome Res. January 2024 34: 106-118; Published in Advance January 3, 2024, doi:10.1101/gr.278631.123
    ...because structures are stochastic at the organization level and are suggestively linked to gene transcription. To address this challenge, we develop a generic theoretical framework that integrates chromatin dynamics, enhancer–promoter (E-P) communication, and gene-state switching to study transcriptional...
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  5. Perspective: Epigenomics and the structure of the living genome
    • Nir Friedman and
    • Oliver J. Rando
    Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
    ...of structures we review above, from long-range chromosomal interactions to nucleosome chemical modifications. Understanding the function of the structures observed will ultimately require knowing the relevant time-scales for the structures in question. Insights into dynamics can be gained using live...
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