The structure and dynamics of the nucleosome at a single molecule level
Open Access
- Author:
- Huynh, Mai
- Graduate Program:
- Chemistry
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- March 15, 2023
- Committee Members:
- Mark Hedglin, Major Field Member
Lu Bai, Outside Unit & Field Member
Tae-Hee Lee, Chair & Dissertation Advisor
Philip Bevilacqua, Program Head/Chair
Ruobo Zhou, Major Field Member - Keywords:
- transcription
nucleosome
histone post-translational modifications
histone acetylation
histone methylation
histone ubiquitylation - Abstract:
- The basic unit of packaging for a eukaryotic genome is the nucleosome. The kinetics of numerous DNA-templated processes, including transcription elongation by RNA Polymerase II (Pol II), are controlled by dynamic interactions between DNA and histones in the nucleosome. The global and local stability of the nucleosome can be regulated by a number of elements, such as histone modifications and histone chaperones. By utilizing single-molecule FRET measurements with chemically modified histones, we investigated the effects of histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) on the structure of the nucleosome and the interactions between two nucleosomes as well as the potential effects of histone H3 acetylation at K56 (H3K56ac), histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3K79 trimethylation (H3K79me3) on the kinetics of transcription elongation by Pol II. We found that whereas H2BK120 ubiquitylation has no effect on the nucleosome structure or internucleosomal contacts, H2BK34 ubiquitylation expands the DNA gyre gap in the nucleosome and stabilizes long- and short-range interactions. We also observed that H3K56 acetylation and H2B ubiquitylation suppress pauses and decrease pause durations close to the nucleosome entry, while H3K79me3 shortens pause durations and speeds up RNA elongation close to the nucleosome center. Additionally, we discovered that H2BK34ub promotes partial nucleosome rewrapping upon Pol II passage. All these results imply that H3K56ac and H3K79me3 promote Pol II progression perhaps by disrupting the local nucleosome structure, while H2B ubiquitylations promote transcription elongation and aid in maintaining the chromatin structure by inducing and stabilizing nucleosome intermediates. Overall, our findings outline the processes by which these changes, when joined by a network of regulatory proteins, enable transcription in various nucleosome areas and assist in maintaining the structure of the chromatin during active transcription.