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

PLoS Computational Biology
A AmitaiDavid Holcman

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.

References

Jun 28, 2003·Biophysical Journal·Gerhard Hummer, Attila Szabo
Jun 18, 2010·Cold Spring Harbor Perspectives in Biology·Angela TaddeiSusan M Gasser
Nov 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Gerhard Hummer, Attila Szabo
Mar 9, 2011·The Journal of Cell Biology·Christophe Zimmer, Emmanuelle Fabre
Apr 10, 2012·Nature Cell Biology·Judith Miné-Hattab, Rodney Rothstein
Aug 30, 2012·Nature Methods·Caroline A SchneiderKevin W Eliceiri

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Citations

Mar 31, 2016·Biophysical Journal·Guido TianaLuca Giorgetti
Sep 13, 2018·Annual Review of Genetics·Andrew SeeberSusan M Gasser
Dec 23, 2017·Nucleus·Emmanuelle Fabre, Christophe Zimmer
Mar 16, 2018·Physical Review Letters·K E PolovnikovM V Tamm
Dec 30, 2017·Genes & Development·Michael H Hauer, Susan M Gasser
May 20, 2018·Physical Review. E·A Amitai, D Holcman
Apr 19, 2020·Current Opinion in Genetics & Development·Maxime Mc TortoraDaniel Jost
Dec 11, 2019·Biophysical Journal·Jonah A Eaton, Alexandra Zidovska

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Methods Mentioned

BETA
PCR

Software Mentioned

Metamorph
ImageJ
Matlab

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