Searching journal content for articles similar to Rowley et al. 30 (3): 447.

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  1. Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
    • Jun Kim,
    • Haoyu Wang,
    • and Sevinç Ercan
    Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
    ...at sites bound by the C. elegans ortholog of NIPBL and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains...
  2. Research: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
    • Marielle L. Bond,
    • Eric S. Davis,
    • Ivana Y. Quiroga,
    • Anubha Dey,
    • Manjari Kiran,
    • Michael I. Love,
    • Hyejung Won,
    • and Douglas H. Phanstiel
    Genome Res. August 2023 33: 1258-1268; Published in Advance September 12, 2023, doi:10.1101/gr.277397.122
    ...://github.com/moshe-olshansky/EigenVector), topologically associating domains (TADs) using arrowhead (Rao et al. 2014), and chromatin loops using SIP (Supplemental Fig. S1C; Rowley et al. 2020). Replicates showed high similarity as measured by principal component analysis (PCA) (Supplemental Fig. S1D). We identified a total of 33,914 loops merged across...
  3. Mini-Review: The chromatin tapestry as a framework for neurodevelopment
    • Ben Nolan,
    • Timothy E. Reznicek,
    • Christopher T. Cummings,
    • and M. Jordan Rowley
    Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
    ...methods to identify different aspects of chromatin architecture. 3D organization—Digestion and ligation of 3D proximal loci are often used to identify long-range chromatin interactions -wide. Typical implementations include Hi-C (restriction enzyme digestion) and Micro-C (micrococcal nuclease [MNase...
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  4. Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
    • Brian S. Roberts,
    • Ashlyn G. Anderson,
    • E. Christopher Partridge,
    • Gregory M. Cooper,
    • and Richard M. Myers
    Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
    ..., the time elapsed from the perturbation does not appear to affect the types of ENCODE cCREs involved in DegCre associations.Comparison of DegCre associations to Hi-C loopsWe sought to compare DegCre associations to Hi-C-derived loop calls from Reed et al. (2022), generated using Sip (Rowley et al. 2020...
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