Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions

Assaf Amitai, Mathias Toulouze, Karine Dubrana and David Holcman

PLOS Computational Biology, 2015, vol. 11, issue 8, 1-16

Abstract: 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.

Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1004433

DOI: 10.1371/journal.pcbi.1004433

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