GSBS Dissertations and Theses
ORCID ID
0000-0002-1857-7399
Publication Date
2019-12-26
Document Type
Doctoral Dissertation
Academic Program
Interdisciplinary Graduate Program
Department
Program in Molecular Medicine
First Thesis Advisor
Craig L. Peterson
Keywords
H3K56, histone acetylation, nucleosome turnover, nucleosome assembly, NET-seq, nascent RNA, INO80C, Break-seq, genome instability
Abstract
Eukaryotic promoters are inherently bidirectional and allow RNA Polymerase II to transcribe both coding and noncoding RNAs. Dynamic disassembly and reassembly is a prominent feature of nucleosomes around eukaryotic promoters. While H3K56 acetylation (H3K56Ac) enhances turnover events of these promoter-proximal nucleosomes, the chromatin remodeler INO80C ensures their proper positioning. In my dissertation, I explore how chromatin dynamics regulate transcriptional homeostasis. In the first part, I investigate the role of H3K56Ac on the nascent transcriptome throughout the eukaryotic cell cycle. I find that H3K56Ac is a global, positive regulator for coding and noncoding transcription by promoting both initiation and elongation/termination. On the contrary, I find that H3K56Ac represses promiscuous transcription following replication fork passage by ensuring efficient nucleosome assembly during S-phase. In addition, I show that there is a stepwise increase in transcription in the S-G2 transition, and this response to gene dosage imbalance does not require H3K56Ac. This study clearly shows that a single histone modification, H3K56Ac can exert both positive and negative effects on transcription at different cell cycle stages. In the second part, I investigate the role of the chromatin remodeler INO80C on the nascent transcription around replication origins. I show that INO80C, together with the transcription factor Mot1, prevents cryptic transcription around yeast replication origins, and the loss of these proteins lead to an increase in DNA double strand breaks. I hypothesize that recruitment of INO80C ensures proper positioning of nucleosomes around origins and the exclusion of RNA Pol II to prevent cryptic initiation. Together these findings indicate that H3K56Ac regulates transcription globally by enhancing nucleosome turnover, and it prevents cryptic transcription and reinforces transcriptional fidelity by promoting efficient nucleosome assembly in the S-phase. In addition, INO80C maintains genome stability by preventing cryptic transcription around the origins.
Repository Citation
Topal S. (2019). Chromatin Dynamics Regulate Transcriptional Homeostasis. GSBS Dissertations and Theses. https://doi.org/10.13028/wga4-d271. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/1062
DOI
10.13028/wga4-d271
Rights and Permissions
Copyright is held by the author, with all rights reserved.