Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories

Publication date: 31 January 2017
Source:Cell Reports, Volume 18, Issue 5
Author(s): Assaf Amitai, Andrew Seeber, Susan M. Gasser, David Holcman
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.

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Teaser

Amitai et al. present a robust analytical workflow for the analysis of single-particle trajectories. The extracted biophysical parameters allow accurate modeling of chromatin dynamics. The authors predict and show that, at double-strand breaks, chromatin decompacts and induces break relocation, while nuclear oscillation arises from cytoskeleton forces.


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