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Transcriptional Regulation by Set1-Catalyzed H3K4 Methylation in S. cerevisiae
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of DNA around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators and histone-modifying enzymes coordinate to make DNA accessible to RNA polymerase. This study focuses on understanding the role of Set1, a histone methyltransferase, in the regulation of gene transcription in S. cerevisiae.
Set1 catalyzes mono-, di-, and trimethylation of the fourth lysine on the N-terminal tail of histone H3. Plate growth assays using wildtype SET1^+, a set1Δ null mutant and hypomorphic mutants of SET1, set1-G951A and set1-R1013H revealed that the null mutant exhibits a growth defect under conditions of histidine and isoleucine-valine starvation which is rescued by cells expressing wildtype SET1^+ or the hypomorphic mutants of set1. Under nutrient stress, loss of Set1 caused a defect in induction of several genes involved in the biosynthesis of histidine, isoleucine and valine. Cells expressing H3K4me1 alone (set1-G951A) or H3K4me1 and H3K4me2 together (set1-R1013H) were able to support transcription in the absence of H3K4me3.
To understand how loss of Set1 affects transcription of the HIS3 gene in vivo, chromatin immunoprecipitation experiments were performed. Loss of H3K4 methylation caused a reduction in acetylated histone H3 levels at the HIS3 promoter under histidine starvation. In wild-type SET1^+ and the hypomorphic set1 mutants set1-G951A and set1-R1013H, the levels of acetylated histone H3 and histone H4 were increased at the HIS3 promoter upon histidine starvation. Loss of H3K4 methylation also reduced the association of chromatin remodelers Isw1 and Snf2 with the HIS3 gene promoter.
RNA sequencing was performed to determine the impact of loss of Set1 on genome wide transcription in cells grown with and without nutrient stress induced by 3AT. In agreement with previous reports, H3K4 methylation was found to be largely repressive for transcription irrespective of the presence of stress. Under nutrient stress, loss of Set1 caused a defect in the induction of genes involved in metabolism of histidine, aromatic amino acids, the cofactor NAD, and other classes of genes.
This study enhances the knowledge of gene regulation executed by evolutionarily conserved histone methyl transferases like Set1.
Citation
Deshpande, Neha (2023). Transcriptional Regulation by Set1-Catalyzed H3K4 Methylation in S. cerevisiae. Doctoral dissertation, Texas A&M University. Available electronically from https : / /hdl .handle .net /1969 .1 /199049.