Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics

Trends in Genetics : TIG
Ofir ShukronD Holcman

Abstract

Chromatin organization remains complex and far from understood. In this article, we review recent statistical methods of extracting biophysical parameters from in vivo single-particle trajectories of loci to reconstruct chromatin reorganization in response to cellular stress such as DNA damage. We look at methods for analyzing both single locus and multiple loci tracked simultaneously and explain how to quantify and describe chromatin motion using a combination of extractable parameters. These parameters can be converted into information about chromatin dynamics and function. Furthermore, we discuss how the timescale of recurrent encounter between loci can be extracted and interpreted. We also discuss the effect of sampling rate on the estimated parameters. Finally, we review a polymer method to reconstruct chromatin structure using crosslinkers between chromatin sites. We list and refer to some software packages that are now publicly available to simulate polymer motion. To conclude, chromatin organization and dynamics can be reconstructed from locus trajectories and predicted based on polymer models.

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Citations

Mar 4, 2020·Nucleic Acids Research·Haitham A Shaban, Andrew Seeber
Apr 22, 2020·Genome Biology·Haitham A ShabanKerstin Bystricky
Dec 17, 2020·PLoS Computational Biology·Samuel P IngramMichael J Merchant
Jan 11, 2021·Current Opinion in Genetics & Development·Timothée Lionnet, Carl Wu
May 19, 2021·Cold Spring Harbor Perspectives in Biology·Feiyue Lu, Timothée Lionnet
Dec 3, 2021·The Journal of Cell Biology·Satoshi UchinoHiroshi Kimura

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