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Nanoscale Imaging pp 297–323Cite as

Probing Chromatin Structure with Magnetic Tweezers

Part of the Methods in Molecular Biology book series (MIMB,volume 1814)

Abstract

Magnetic tweezers form a unique tool to study the topology and mechanical properties of chromatin fibers. Chromatin is a complex of DNA and proteins that folds the DNA in such a way that meter-long stretches of DNA fit into the micron-sized cell nucleus. Moreover, it regulates accessibility of the genome to the cellular replication, transcription, and repair machinery. However, the structure and mechanisms that govern chromatin folding remain poorly understood, despite recent spectacular improvements in high-resolution imaging techniques. Single-molecule force spectroscopy techniques can directly measure both the extension of individual chromatin fragments with nanometer accuracy and the forces involved in the (un)folding of single chromatin fibers. Here, we report detailed methods that allow one to successfully prepare in vitro reconstituted chromatin fibers for use in magnetic tweezers-based force spectroscopy. The higher-order structure of different chromatin fibers can be inferred from fitting a statistical mechanics model to the force-extension data. These methods for quantifying chromatin folding can be extended to study many other processes involving chromatin, such as the epigenetic regulation of transcription.

Key words

  • Magnetic tweezers
  • Force spectroscopy
  • Single molecule
  • Chromatin
  • Nucleosome

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Acknowledgments

We are grateful to Nicolaas Hermans, He Meng, Kurt Andresen, Orkide Ordu, and Ineke de Boer for the help in establishing these methods. This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program, by the NWO-VICI research program, project 680-47-616.

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Authors and Affiliations

  1. Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands

    Artur Kaczmarczyk, Thomas B. Brouwer, Chi Pham & John van Noort

  2. Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands

    Artur Kaczmarczyk & Nynke H. Dekker

Authors
  1. Artur Kaczmarczyk
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  2. Thomas B. Brouwer
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  3. Chi Pham
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  4. Nynke H. Dekker
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  5. John van Noort
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Corresponding author

Correspondence to John van Noort .

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Editors and Affiliations

  1. Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA

    Dr. Yuri L. Lyubchenko

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Kaczmarczyk, A., Brouwer, T.B., Pham, C., Dekker, N.H., van Noort, J. (2018). Probing Chromatin Structure with Magnetic Tweezers. In: Lyubchenko, Y. (eds) Nanoscale Imaging. Methods in Molecular Biology, vol 1814. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8591-3_18

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  • DOI: https://doi.org/10.1007/978-1-4939-8591-3_18

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  • Publisher Name: Humana Press, New York, NY

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