Dissertations, Theses, and Capstone Projects

Date of Degree

6-2026

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy

Program

Biochemistry

Advisor

Sharon M. Loverde

Committee Members

Sebastien Poget

Angelo Bongiorno

Mariana Torrente

Guillaume Lamoureux

Subject Categories

Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Biological and Chemical Physics | Computational Chemistry | Computer-Aided Engineering and Design | Dynamical Systems | Dynamics and Dynamical Systems | Molecular Genetics | Nucleic Acids, Nucleotides, and Nucleosides | Oncology | Statistical Models | Theory and Algorithms

Keywords

Nucleosome Dynamics, Chromatin regulation, Epigenetics, Free energy, Markov State Model, Molecular Dynamics Simulations

Abstract

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access DNA within the tightly packaged chromatin structure during gene regulation, it is essential to employ epigenetic mechanisms, including DNA methylation, post-translational modifications (PTMs), and histone variants. We used long-time-scale all-atom molecular dynamics (MD) simulations to investigate the structure and dynamics of the nucleosome system under epigenetic changes. Epigenetic modifications of histone N-terminal tails play a critical role in regulating chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Acetylation neutralizes the positive charge of the lysine residues by adding an acetyl group. Epigenetic modifications are ubiquitous in the development of diseases such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome and principal component analysis (PCA) to demonstrate that acetylation of the histone tails alters their conformational space and their interactions with DNA. The conformational changes in acetylated tails aid in the binding and docking of regulatory molecules, and the tails' flexibility serves as an epigenetic mark for regulatory proteins to recognize.

To understand the dynamics of histone tails, we utilized the Markov State Model (MSM), a powerful computational framework that relies on the future state depending on the current conformation, rather than the past, to model slow processes by building a transition probability matrix. We used all-atom MD simulations at microseconds timescales to analyze the kinetics of histone tails. The histone tails H3, H4, H2A, and H2B showed distinct kinetics, with acetylation showing more flexibility changes between the tail states and a higher mean first passage time (MFPT), pointing towards faster kinetics when acetylated. As we observed, H2B acetylation yields a faster MFPT; this can facilitate a rapid transition from inter- to intra-nucleosome interactions in regulating higher-order chromatin structure. The faster transition between states can also facilitate a rapid search for new binding proteins, as the tail reduces its interactions with nucleosomal DNA.

Epigenetic regulation of chromatin structure is strongly influenced by not only post-translational modifications (PTMs) but also by histone variants. The conserved histone variant H2A.Z has been functionally linked to the pioneer factors Sox2 and Oct4, which open chromatin and activate cell fate-specific transcriptional programs. However, the molecular basis of this interaction remains poorly understood. Here, we combine molecular dynamics (MD) simulations with experiments to investigate how H2A.Z nucleosome dynamics influence pioneer factor binding. We find that H2A.Z enhances the association of Sox2 and Oct4 at distinct positions within nucleosomes, correlating with increased DNA accessibility and altering dynamics of the H3 N-terminal tail. MD simulations reveal that H2A.Z promotes DNA unwrapping and inter-gyre gapping, and induces more flexible H3 tail conformations, while reducing contacts with DNA and the H2A.Z C-terminal tail. Taken together, PTMs and variants provide remarkable insights into nucleosome dynamics, including histone tail conformations and DNA unwrapping, thereby increasing DNA accessibility to other regulatory proteins and influencing chromatin structure and epigenetic regulation.

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