Title: Network analyses of 4D genome datasets automate detection of community-scale gene structure and plasticity,
Abstract: Chromosome conformation capture and Hi-C technologies provide gene-gene
proximity datasets of stationary cells, revealing chromosome territories,
topologically associating domains, and chromosome topology. Imaging of tagged
DNA sequences in live cells through the lac operator reporter system provides
dynamic datasets of chromosomal loci. Chromosome modeling explores the
mechanisms underlying 3D genome structure and dynamics. Here, we automate 4D
genome dataset analysis with network-based tools as an alternative to gene-gene
proximity statistics and visual structure determination. Temporal network
models and community detection algorithms are applied to 4D modeling of G1 in
budding yeast with transient crosslinking of $5 kb$ domains in the nucleolus,
analyzing datasets from four decades of transient binding timescales. Network
tools detect and track transient gene communities (clusters) within the
nucleolus, their size, number, persistence time, and frequency of gene
exchanges. An optimal, weak binding affinity is revealed that maximizes
community-scale plasticity whereby large communities persist, frequently
exchanging genes.