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

Assaf Amitai,David Holcman,Mathias Toulouze,Karine Dubrana,Alexandre V Morozov

doi:10.1371/journal.pcbi.1004433

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.

Highlights

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
What can we learn about the local environment, the external and internal forces and the chromatin itself from the motion of a chromatin locus? This motion can be driven by local diffusion and/or forces between monomers of the model polymer [1,2,3]

Summary

Introduction

What can we learn about the local environment, the external and internal forces and the chromatin itself from the motion of a chromatin locus? This motion can be driven by local diffusion and/or forces between monomers of the model polymer [1,2,3]. Much of the chromatin dynamics is reflected in the motion of a single chromosomal locus and a locus motion allows probing the chromatin dynamics [11, 12] at tens of nanometers and millisecond scales resolution [13,14,15]. When this motion is described as a free or confined Brownian motion, classical statistical tools such as the mean square displacement (MSD). Other methods have been developed to extract kinetic rates about molecular events from forces imposed in pulling experiments [19, 20] or in the context of atomic force microscopy [21, 22]

Methods

Results

Discussion

Conclusion