Nonequilibrium Active Loop Extrusion Model of Chromatin Organization in Interphase

Abstract

Double stranded DNA and proteins form a complex known as chromatin in eukaryotic cells. The mechanisms that regulate the spatial conformations and dynamics of chromatin in the nucleus are not well understood. Chromatin organization is important to understand because gene transcription can be affected by spatial contacts between genomic sequences located hundreds of kilo-base pairs away. Experiments suggest that chromatin adopts a compact conformation on genomic length scales between tens and hundreds of kilo-base pairs, corresponding to the typical length of topologically associated domains (TADs). Gene regulation by enhancers and silencers frequently acts within these domains, but not across the domain boundaries. One mechanism thought to contribute to maintenance of TADs is loop extrusion, which describes the cohesin protein complex threading chromatin into dynamic loops. This dissertation describes a model of how nonequilibrium active loop extrusion regulates chromatin organization during interphase. Computer simulations of the model support its predictions for chromatin conformation and dynamics. Furthermore, comparisons between the model and experimental data validate the results.This work specifically considers a version of loop extrusion in which the cohesin protein complex consumes energy in the form of ATP to translocate and organize chromatin. The model predicts that the probability of forming certain types of chromatin loops by extrusion is a non-monotonic function of the loop length, consistent with experimental observations. This is because loop formation is a competition between the average number of extruding proteins bound within a genomic section which grows linearly with genomic length, and an exponential distribution of loop lengths extruded by a single cohesin. The model also describes the probability of contact between specific genomic loci within TADs. The nonequilibrium nature of active loop extrusion is critical for chromatin compaction within TADs. Compaction occurs because chromatin sections above a certain length scale cannot fully relax while they are actively extruded. The compaction causes a decrease in spatial overlaps between neighboring TADs, which contributes to effective transcriptional regulation within TADs and insulation across TADs. Additionally, active loop extrusion causes anomalous dynamics of both individual chromatin loci and also chromatin-bound cohesins. This dissertation presents a theoretical model linking nonequilibrium, active loop extrusion kinetics to the spatiotemporal organization of chromatin during interphase. This model may help inform future experimental strategies to modulate gene expression by engineering chromatin contacts.