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Title: Investigating the role of dynamic histone modification in the mechanism of action of lysine deacetylase inhibitor (KDACi)
Author: Huang, Li-Yao
ISNI:       0000 0004 9356 252X
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2019
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Methylation and acetylation of histones are tightly connected to the control of gene expression. Changes in patterns of methylation and acetylation of histones are associated with changes in gene expression during growth and development. It has become widely accepted that misregulation of histone modifications, including histone methylation and acetylation, can play a critical role in cancer cells. Consequently, inhibitors targeting histone-modifying enzymes, such as lysine deacetylase inhibitors (KDACis), have shown therapeutic potential against a number of different types of cancer. Multiple hydroxamate-based KDACis have been approved for clinical use. However, the exact mechanism of action of these compounds remains uncertain as do the mechanisms of resistance that are either intrinsic or acquired on KDACi treatment. Hydroxamate-based KDACis such as Trichostatin A (TSA) induces rapid initial acetylation of histone 3 (H3) proteins which are already modified by tri-methylation on lysine 4 (H3K4me3) while acetylation of bulk histones happens later. In this thesis, I reveal the role of dynamic acetylation in the mechanism of action of hydroxamates using the eukaryotic social amoeba Dictyostelium discoideum as a model. Loss of H3K4me3 in strains with mutations in the gene encoding the methylating enzyme or the histone molecules themselves confers resistance to KDACi-induced inhibition of development and slows the accumulation of histone acetylation. Furthermore, the dynamic rapid acetylation of H3K4me3 requires the Dictyostelium orthologue of Sgf29 which recognizes the H3K4me3 mark via its tandem Tudor domain. Disruption of the gene encoding Sgf29 abolished rapid dynamic acetylation of H3K4me3 and led to developmental resistance to TSA. However, loss of rapid acetylation of H3K4me3 did not provide resistance to growth inhibition caused by TSA. Aiming to identify genes involved in the process, a genome-wide screen was performed using a newly established technology REMI-seq ( This allows parallel phenotyping of thousands of insertional mutants in a population to identify strains with growth advantage under TSA treatment. The screen identified genes encoding proteins such as ABC transporters, transcription factors and protein kinases and a number were demonstrated to be resistant to TSA during growth as single clones but not resistant during development. The results of this thesis provide a previously unidentified role of dynamic acetylation of H3K4me3 in the mode of action of hydroxamates and prove that REMI-seq is a powerful tool in Dictyostelium to identify resistance-related genes when studying drug mechanisms.
Supervisor: Pears, Catherine Sponsor: Swire Scholarship Trust
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available