Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories.
Chromatin moves with subdiffusive and spatially constrained dynamics within the cell nucleus. Here, we use single-locus tracking by time-lapse fluorescence microscopy to uncover information regarding the forces that influence chromatin movement following the induction of a persistent DNA double-strand break (DSB). Using improved time-lapse imaging regimens, we monitor trajectories of tagged DNA loci at a high temporal resolution, which allows us to extract biophysical parameters through robust statistical analysis. Polymer modeling based on these parameters predicts chromatin domain expansion near a DSB and damage extrusion from the domain. Both phenomena are confirmed by live imaging in budding yeast. Calculation of the anomalous exponent of locus movement allows us to differentiate forces imposed on the nucleus through the actin cytoskeleton from those that arise from INO80 remodeler-dependent changes in nucleosome organization. Our analytical approach can be applied to high-density single-locus trajectories obtained in any cell type.
Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Assaf
A
Amitai
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland.
Andrew
A
Seeber
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland. Electronic address: susan.gasser@fmi.ch.
Susan M
SM
Gasser
Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France; Department of Applied Mathematics and Theoretical Physics, University of Cambridge and Churchill College, Cambridge CB30DS, UK. Electronic address: david.holcman@ens.fr.
David
D
Holcman
D018797:Cell Cycle Proteins / Q000378:metabolism; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly / Q000502:physiology; D053903:DNA Breaks, Double-Stranded; D004249:DNA Damage / Q000502:physiology*; D004260:DNA Repair / Q000502:physiology; D011108:Polymers / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D004718:Saccharomycetales / Q000378:metabolism; D059008:Time-Lapse Imaging / Q000379:methods
D018797:Cell Cycle Proteins; D002843:Chromatin; D011108:Polymers; D029701:Saccharomyces cerevisiae Proteins
DNA damage; DNA mobility; actin cytoskeleton; chromatin dynamics; double-strand break; microtubules; nucleosome compaction; numerical stimulations; polymer model; time-lapse imaging