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Showing 1–18 of 18 results
Advanced filters: Author: Geoffrey Fudenberg Clear advanced filters

  • During meiotic prophase chromosomes organise into a series of chromatin loops, but the mechanisms of assembly remain unclear. Here the authors use Saccharomyces cerevisiae to elucidate how this elaborate three-dimensional chromosome organisation is linked to genomic sequence, and demonstrate an essential role for cohesin during this process.

    • Stephanie A. Schalbetter
    • Geoffrey Fudenberg
    • Matthew J. Neale
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-12

  • The boundaries of topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. Here the authors find that CTCF positions cohesin through its N-terminus but does not control its overall binding dynamics on chromatin, and show how the orientation of CTCF binding sites translates into genome folding patterns.

    • Elphège P. Nora
    • Laura Caccianini
    • Benoit G. Bruneau
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-13

  • Schalbetter et al. show by Hi-C and modelling that mitotic chromosome compaction in budding yeast occurs by cis-looping of chromatin, and reveal distinct roles for cohesin and condensin depending on chromatin context.

    • Stephanie Andrea Schalbetter
    • Anton Goloborodko
    • Jonathan Baxter
    Research
    Nature Cell Biology
    Volume: 19, P: 1071-1080

  • Homologs are paired in Drosophila somatic cells from embryogenesis to adulthood. Using a computational approach for haplotype-resolved Hi-C, the authors reveal highly structured homolog pairing in Drosophila embryos during zygotic genome activation and demonstrate its application to mammalian embryos.

    • Jelena Erceg
    • Jumana AlHaj Abed
    • C.-ting Wu
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-13

  • Trans-homolog interactions, such as homolog pairing, are highly structured and associated with gene function in Drosophila cells. Here, the authors use haplotype-resolved Hi-C to identify genome-wide trans-homolog interactions in a Drosophila hybrid cell line and investigate their patterns and functional roles.

    • Jumana AlHaj Abed
    • Jelena Erceg
    • C.-ting Wu
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-14

  • Depletion of chromosome-associated cohesin leads to loss of topologically associating domains in interphase chromosomes, without affecting segregation into compartments, and instead, it unmasks a finer compartment structure that reflects local chromatin and transcriptional activity.

    • Wibke Schwarzer
    • Nezar Abdennur
    • Francois Spitz
    Research
    Nature
    Volume: 551, P: 51-56

  • Genome-wide chromatin conformation capture (Hi-C) is used to investigate three-dimensional genome organization in Schizosaccharomyces pombe; small domains of chromatin interact locally on chromosome arms to form globules, which depend on cohesin but not heterochromatin for formation, and heterochromatin at centromeres and telomeres provides crucial structural constraints to shape genome architecture.

    • Takeshi Mizuguchi
    • Geoffrey Fudenberg
    • Shiv I. S. Grewal
    Research
    Nature
    Volume: 516, P: 432-435

  • Attractions between heterochromatic regions are essential for phase separation of the active and inactive genome in inverted and conventional nuclei, whereas chromatin–lamina interactions are necessary to build the conventional genomic architecture from these segregated phases.

    • Martin Falk
    • Yana Feodorova
    • Leonid A. Mirny
    Research
    Nature
    Volume: 570, P: 395-399

  • This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.

    • Geoffrey Fudenberg
    • Maxim Imakaev
    Research
    Nature Methods
    Volume: 14, P: 673-678

  • CTCF is a conserved DNA- and RNA-binding protein with roles in genome folding and transcriptional regulation. Two recent studies investigated how CTCF knockout perturbs genome biology and derails embryogenesis in zebrafish and Drosophila melanogaster, revealing contrasting effects across species.

    • Geoffrey Fudenberg
    • Elphège P. Nora
    News & Views
    Nature Structural & Molecular Biology
    Volume: 28, P: 774-776

  • Using super-resolution imaging to directly observe the three-dimensional organization of Drosophila chromatin at a scale spanning sizes from individual genes to entire gene regulatory domains, the authors find that transcriptionally active, inactive and Polycomb-repressed chromatin states each have a distinct spatial organisation.

    • Alistair N. Boettiger
    • Bogdan Bintu
    • Xiaowei Zhuang
    Research
    Nature
    Volume: 529, P: 418-422