UCSF

The nucleosome is a highly dynamic macromolecular complex that is at the center of regulating access to genetic information in eukaryotes. The structural dynamics of nucleosomes are an ensemble of the dynamics of its component parts: the globular histone octamer core, the wrapped DNA, and the flexible histone tails. The coordination of these dynamics presents modes of regulation of nucleosome function. Although nucleosomes have long been considered exceptionally static and stable complexes, it has become clear that this is not the case. This thesis builds upon past work highlighting the central importance of understanding both the nature of nucleosome dynamics and the ways in which they are regulated. This thesis first addresses how nucleosome conformational dynamics are regulated by a class of nuclear proteins termed architectural proteins. Nuclear architectural proteins globally alter nucleosome structure and dynamics to induce effects on chromatin genome wide. The two most abundant nuclear architectural proteins, the linker histone H1 and HMGB1 (high mobility group box 1), compete with one another in this respect. We present a molecular model for how HMGB1 and H1 compete at many scales. We find that HMGB1 and H1 co-occupy nucleosomes and chromatin and modulate one another’s effect on DNA accessibility and mesoscale chromatin dynamics. This leads to a model wherein the dynamics of nucleosomes and chromatin can be precisely tuned by influencing the competition between these two proteins. This model also highlights the effect of altering atomic-scale nucleosome conformational dynamics on the mesoscale function of chromatin and uncovers a global role for nucleosome conformational dynamics in chromatin regulation. In addition to the work on nuclear architectural proteins, we design a proteomics-based screening platform to identify novel regulators of nucleosome conformational dynamics. Initial results from this platform implicate a number of interesting chromatin proteins and complexes as potentially having an effect on the conformational dynamics of nucleosomes. These results also imply that nucleosome conformational dynamics can be a point of regulation in a wide variety of chromatin processes. Finally, this screening platform is highly adaptable. Future iterations of this screen could target specific subsets of chromatin, focus on the activities of chromatin modifying enzymes, and shed light on potential allosteric pathways of the nucleosome itself. Overall, this thesis explores the nature and the role of nucleosome conformational dynamics in regulating a wide variety of chromatin processes.