Search

The time for a DNA sequence to find its homologous depends on a long random search process inside the cell nucleus. Using polymer models, we model and compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined by potential wells. We find that reducing the potential (tethering) forces results in a local polymer decondensation near the loci and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude that the acceleration of the search process after local chromatin decondensation can be used to analyze the local search step during homology search., 3 figures

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.

Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in vivo? Chromatin fragments interact with many partners such as the nuclear membrane, other chromosomes or nuclear bodies, but the resulting forces cannot be directly measured in vivo. However, they impact chromatin dynamics and should be reflected in particular in the motion of a single locus. We present here a method based on polymer models and statistics of single trajectories to extract the force characteristics and in particular when they are generated by the gradient of a quadratic potential well. Using numerical simulations of a Rouse polymer and live cell imaging of the MAT-locus located on the yeast Saccharomyces cerevisiae chromosome III, we recover the amplitude and the distance between the observed and the interacting monomer. To conclude, the confined trajectories we observed in vivo reflect local interaction on chromatin., Author Summary Is it possible to recover the local environment, the external and internal forces acting on a polymer from a single locus trajectories? To study this question, we resolve this reverse cell biology problem by developing a method that uses in vivo live single locus trajectories to extract physical forces applied on chromatin. We applied the method to the statistics of the S. cerevisiae MAT-locus motion and recover tethering forces acting on the chromatin. The local confinement of a chromatin locus can either be due to crowding or to local interactions with partners such as the surface of the nuclear membrane, other chromosomes or nuclear bodies that cannot be directly measured. We conclude here that confined trajectories of a single chromatin locus can be generated by local tethering interactions. This approach is applicable to cells under various conditions, such as during double-stranded DNA break repair.