Date of Award

2021

Document Type

Dissertation

Degree Name

Philosophy (Ph.D)

Department

Biological Sciences

First Advisor

Ales Vancura

Second Advisor

Ivana Vancurova

Third Advisor

Yong Yu

Abstract

My dissertation contains two projects. The first project is focused on the mechanism of DNA damage checkpoint (DDC)- mediated repression of histone mRNAs. The second project deals with the role of acetyl-CoA in histone transcription. Proliferating cells coordinate histone and DNA synthesis to maintain correct stoichiometric amounts for chromatin assembly. Histone mRNA levels must be repressed when DNA replication is inhibited to prevent toxicity and genome instability due to free non-chromatinized histone proteins. In the first project we show that, unlike in mammalian cells, DNA replication stress does not trigger decay of histone mRNAs in the yeast Saccharomyces cerevisiae. However, histone mRNAs can be degraded by both 5' to 3' and 3' to 5' pathways as indicated by significantly elevated half-lives of histone mRNAs in strains with defects in deadenylation, decapping, and exonucleolytic degradation in 5' to 3' and 3' to 5' directions. Replication stress inhibits transcription of histone genes by removing the histone genes-specific transcription factors Spt10p and Spt21p, disassembling the preinitiation complexes and evicting RNA Pol II from histone promoters by a mechanism that is facilitated by checkpoint kinase Rad53p and histone chaperone Asf1p. In contrast, replication stress does not affect occupancy of Swi4p, the DNA binding subunit of the SBF complex, at the histone promoters, suggesting that Spt10p and Spt21p are responsible for the transcriptional downregulation of histone genes during replication stress. In the second project, we determined the role of acetyl-CoA in histone transcription. Acetyl-CoA is a key metabolite linking catabolism and anabolism. This central position endows acetyl-CoA with an important regulatory and signaling role, and the acetyl-CoA level reflects the energetic and metabolic state of the cell. Acetyl-CoA also serves as a substrate for lysine acetyltransferases that catalyze the transfer of acetyl groups to lysines in a vast array of proteins, including histones. The level of nucleocytosolic acetyl-CoA regulates the global acetylation of chromatin histones and the transcription of many genes. Here we show that reduced synthesis of nucleocytosolic acetyl-CoA leads to reduced acetylation of chromatin histones in the promoters of histone genes, and decreased histone transcription. The globally altered chromatin structure triggers mitochondrial biogenesis and respiration and leads to increased synthesis of ATP.

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