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Ganji, M. (author), Kim, S.H. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
DNA supercoiling crucially affects cellular processes such as DNA replication, gene expression, and chromatin organization. However, mechanistic understanding of DNA supercoiling and the related DNA-processing enzymes has remained limited, mainly due to the lack of convenient experimental tools to probe these phenomena. Here, we report a...
journal article 2016
document
Nechemia-Arbely, Yael (author), Fachinetti, Daniele (author), Miga, Karen H. (author), Sekulic, Nikolina (author), Soni, G.V. (author), Kim, Dong Hyun (author), Wong, Adeline K. (author), Lee, Ah Young (author), Nguyen, Kristen (author), Dekker, C. (author), Ren, Bing (author), Black, Ben E. (author), Cleveland, Don W. (author)
Chromatin assembled with centromere protein A (CENP-A) is the epigenetic mark of centromere identity. Using new reference models, we now identify sites of CENP-A and histone H3.1 binding within the megabase, α-satellite repeat-containing centromeres of 23 human chromosomes. The overwhelming majority (97%) of α-satellite DNA is found to be...
journal article 2017
document
Kim, S.H. (author), Vlijm, R. (author), van der Torre, J. (author), Dalal, Y. (author), Dekker, C. (author)
Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test...
journal article 2016
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Kim, S.H. (author), Ganji, M. (author), Kim, E. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes ...
journal article 2018
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Vlijm, R. (author), Kim, S.H. (author), De Zwart, P. L. (author), Dalal, Y. (author), Dekker, C. (author)
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness...
journal article 2017
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Elbatsh, Ahmed M.O. (author), Kim, E. (author), Eeftens, J.M. (author), Raaijmakers, Jonne A. (author), van der Weide, Robin H. (author), García-Nieto, Alberto (author), Bravo, Sol (author), Ganji, M. (author), Dekker, C. (author)
Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster...
journal article 2019
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