Nucleosome Structure and Dynamics Investigated with Single-Molecule Methods
Open Access
- Author:
- Lee, JaeHyoun
- Graduate Program:
- Chemistry
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- March 28, 2016
- Committee Members:
- Tae-Hee Lee, Dissertation Advisor/Co-Advisor
Tae-Hee Lee, Committee Chair/Co-Chair
David D Boehr, Committee Member
Squire J Booker, Committee Member
Song Tan, Outside Member - Keywords:
- nucleosome
single-molecule
FRET - Abstract:
- Nucleosomes are the repeating units that comprise chromatin, the DNA-histone complex that holds the genetic information in eukaryotic cell nuclei. Eukaryotic DNA wraps around a histone octamer protein core forming a superhelical structure, thereby being packaged into the nucleosome. The nucleosome imposes a physical barrier to nuclear transactions that require access to DNA including transcription, DNA replication, and DNA repair. Therefore, nucleosomes must at least in part disassemble during these transactions. It is widely accepted that nucleosomes undergo dynamic changes in order to allow for regulated access to genes. These changes include structural changes that lead to regulated nucleosome disassembly or exchanges of histones with histone variants that trigger cascading biochemical events on the nucleosome. These changes are often strongly coupled to post- translational modifications of histones and DNA methylation. Histone chaperones and nucleosome remodelers can facilitate these nucleosome dynamics by depositing or evicting histones in and out of the nucleosome. Understanding the nature of these dynamical changes in the nucleosome and how they are coupled to chemical modifications to the nucleosome are crucial to understanding eukaryotic gene regulation mechanisms. In this dissertation, I present my PhD research on the structure and the dynamics of nucleosomes based on single-molecule fluorescence resonance energy transfer (FRET) measurements. In Chapter 1, following the introduction of the nucleosome and chromatin structure, the processes that alter the structure and dynamics of nucleosomes and the theory of FRET are reviewed. In Chapter 2, experimental methods and materials used for the research is reviewed. In Chapter 3, the mechanism of the nucleosome structure transition upon the incorporation of a histone variant CENP-A is presented. In Chapter 4, the dynamics of nucleosome disassembly mediated by the histone chaperone Nap1 and the effects of histone acetylation on the dynamics are detailed. In Chapter 5, nucleosome disassembly during transcription elongation and the effects of Nap1 on elongation kinetics are discussed. Finally in Chapter 6, brief concluding remarks and future directions of the transcription elongation research are discussed.