Chromatin Configuration Simulations and Inferred Contact Maps

April 2, 2022

Adam Lamson’s simulated chromatin configurations serve as both material and as a conceptual framework for Sticky Settings.

Chromatin is a complex of DNA and protein found in eukaryotic cells.

Chromatin packages long DNA molecules into more compact, denser structures in order to prevent strands of DNA from becoming tangled, prevent damage to DNA during cell division, and regulate gene expression in DNA replication. Chromatin configurations change over time, which in turn changes the expression of genes. Simulations of chromatin configurations can be run with biophysical models composed of hard spheres  (“beads”) connected by springs in a viscous fluid. Parameters can be adjusted to tune the simulation. Contact maps are used by scientists to reveal changing structural features of chromatin over time such as interactions between DNA wound around the nucleosomes (“beads”) in the chromatin. They can reveal how a genome is organized and show how likely two parts of the genome are to be close to one another. Adam Lamson generates simulated contact maps (representing different points in time or an ensemble average) from his biophysical models. The contact maps show how the genomes of the simulated models are organized.

Image Credits: Adam Lamson / Laura Splan

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