True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin
Márton Gelléri,
Shih-Ya Chen,
Barbara Hübner,
Jan Neumann,
Ole Kröger,
Filip Sadlo,
Jorg Imhoff,
Michael J. Hendzel,
Marion Cremer,
Thomas Cremer,
Hilmar Strickfaden,
Christoph Cremer
Affiliations
Márton Gelléri
Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Corresponding author
Shih-Ya Chen
Institute of Molecular Biology (IMB), 55128 Mainz, Germany
Barbara Hübner
Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
Jan Neumann
Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany
Ole Kröger
Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
Filip Sadlo
Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
Jorg Imhoff
Neuroconsult GmbH, 69120 Heidelberg, Germany
Michael J. Hendzel
Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
Marion Cremer
Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
Thomas Cremer
Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
Hilmar Strickfaden
Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada; Corresponding author
Christoph Cremer
Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany; Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University Heidelberg, 69120 Heidelberg, Germany; Corresponding author
Summary: Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2–10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from 300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
