Searching journal content for articles similar to Kim et al. 35 (5): 1108.

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  1. Method: Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals
    • M. Jordan Rowley,
    • Axel Poulet,
    • Michael H. Nichols,
    • Brianna J. Bixler,
    • Adrian L. Sanborn,
    • Elizabeth A. Brouhard,
    • Karen Hermetz,
    • Hannah Linsenbaum,
    • Gyorgyi Csankovszki,
    • Erez Lieberman Aiden,
    • and Victor G. Corces
    Genome Res. March 2020 30: 447-458; Published in Advance March 3, 2020, doi:10.1101/gr.257832.119
    ...contact maps in Kc167 cells contain a few hundred loops that lack CTCF, and their formation does not depend on cohesin (Rowley et al. 2019). Many nonvertebrate organisms, including Caenorhabditis elegans, lack a CTCF homolog (Heger et al. 2012). It is possible that proteins distinct from CTCF are able...
  2. Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    • Olga M. Sigalova,
    • Mattia Forneris,
    • Frosina Stojanovska,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Adam Rabinowitz,
    • Fayrouz Hammal,
    • Benoît Ballester,
    • Judith B. Zaugg,
    • and Eileen E.M. Furlong
    Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
    ..., such as enhancers and promoters (Wray 2007; Fairfax et al. 2012; Chen et al. 2016; Cannavò et al. 2017; Abramov et al. 2021; Floc'hlay et al. 2021). However, establishing a mechanistic link between DNA sequence variation and TF binding remains challenging (Deplancke et al. 2016). Sequence variation that disrupts...
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  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
    ...the complexity of chromatin organization and the nuanced differences in how genomic elements interact within the nucleus (Hyle et al. 2019; Szczepińska et al. 2021; Chakraborty et al. 2023; Spracklin et al. 2023).CTCF/cohesin loopsIn addition to compartments, advancements in -wide chromatin contact mapping have...
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  4. Review: The structure, function, and evolution of plant centromeres
    • Matthew Naish and
    • Ian R. Henderson
    Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
    ...satellite sequences (green), and Chromosome 1 BAC sequences (yellow) (Naish et al. 2021). Scale bar, 10 μm. (C) Arabidopsis male meiocyte at pachytene stage immunostained for the SMC3 cohesin (red) and stained for DNA (DAPI; blue) (Lambing et al. 2020). FISH was performed against the CEN178 satellite...
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  5. Resource: Multiparameter functional diversity of human C2H2 zinc finger proteins
    • Frank W. Schmitges,
    • Ernest Radovani,
    • Hamed S. Najafabadi,
    • Marjan Barazandeh,
    • Laura F. Campitelli,
    • Yimeng Yin,
    • Arttu Jolma,
    • Guoqing Zhong,
    • Hongbo Guo,
    • Tharsan Kanagalingam,
    • Wei F. Dai,
    • Jussi Taipale,
    • Andrew Emili,
    • Jack F. Greenblatt,
    • and Timothy R. Hughes
    Genome Res. December 2016 26: 1742-1752; Published in Advance November 16, 2016, doi:10.1101/gr.209643.116
    ...can be driven by alteration of DNA sequence specificity, protein–protein interactions (PPIs), and the expression pattern of the TF-encoding gene. All three parameters contribute to divergence within the Caenorhabditis elegans bHLH TF family (Grove et al. 2009), but it is largely unknown whether...
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  6. 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
    ...-characterized epigenetic inheritance paradigms, this review will focus on epigenomic insights into the folding of the and thus will not cover DNA modifications or RNAs. Below, we introduce the general methodologies for epigenomic analysis. Then, we discuss the structural organization of the eukaryotic , starting with 3C...
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