Genome Architecture meets Systems Biology

Methods Mol Biol
Sven Sewitz, Karen Lipkow
Systems Biology Approaches for Understanding Genome Architecture (2016)

Abstract
The linear and three-dimensional arrangement and composition of chromatin in eukaryotic genomes underlies the mechanisms directing gene regulation. Understanding this organization requires the integration of many data types and experimental results. Here we describe the approach of integrating genome-wide protein-DNA binding data to determine chromatin states. To investigate spatial aspects of genome organization, we present a detailed description of how to run stochastic simulations of protein movements within a simulated nucleus in 3D. This systems level approach enables the development of novel questions aimed at understanding the basic mechanisms that regulate genome dynamics.

Keywords: Chromatin states; Genome organization; Hidden Markov models; Stochastic spatial simulations; Systems biology.