Searching journal content for articles similar to Zhan et al. 27 (3): 479.

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  1. Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
    • Yangyang Liu,
    • Bingqiang Liu,
    • and Juntao Liu
    Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
    ...2016; Norton et al. 2018; Chang et al. 2020). Taken together, precise and robust identification of TADs, hierarchical TADs, and partially overlapping TADs using Hi-C data are essential for a deeper understanding of 3D-folding mechanisms and their epigenetic and gene regulatory functions.In recent years...
  2. Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
    • Dachang Dang,
    • Shao-Wu Zhang,
    • Ran Duan,
    • and Shihua Zhang
    Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
    ..., Hangzhou 310024, China Corresponding author: zhangsw@nwpu.edu.cn, zsh@amss.ac.cnAbstractTopologically associating domains (TADs) have emerged as basic structural and functional units of organization and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained...
  3. Research: Hormone-control regions mediate steroid receptor–dependent genome organization
    • François Le Dily,
    • Enrique Vidal,
    • Yasmina Cuartero,
    • Javier Quilez,
    • A. Silvina Nacht,
    • Guillermo P. Vicent,
    • José Carbonell-Caballero,
    • Priyanka Sharma,
    • José Luis Villanueva-Cañas,
    • Roberto Ferrari,
    • Lara Isabel De Llobet,
    • Gaetano Verde,
    • Roni H.G. Wright,
    • and Miguel Beato
    Genome Res. January 2019 29: 29-39; Published in Advance December 14, 2018, doi:10.1101/gr.243824.118
    ...in controlling gene expression (Fig. 2D). For example, such interactions were observed between the promoter of PGR gene and the HCRs detected in its TAD (Fig. 2E). We also used the in situ Hi-C data to measure the frequency of contacts between HCRs located >2 Mb apart within the same chromosome. We observed...
  4. Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
    • Federico Comoglio,
    • Hyun Jung Park,
    • Stefan Schoenfelder,
    • Iros Barozzi,
    • Daniel Bode,
    • Peter Fraser,
    • and Anthony R. Green
    Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
    ...that A/B compartments and TADs are not hierarchically organized but represent independent structural (and possibly functional) units of 3D organization (Nora et al. 2017; Rao et al. 2017; Schwarzer et al. 2017; Wutz et al. 2017).Enhancer–promoter communication preferentially occurs within TADs (Zhan et...
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