Access Type

Open Access Dissertation

Date of Award

January 2016

Degree Type

Dissertation

Degree Name

Ph.D.

Department

Biological Sciences

First Advisor

Lori A. Pile

Abstract

Chromatin modification and cellular metabolism are tightly connected. The mechanism for this cross-talk, however, remains incompletely understood. SIN3 controls histone acetylation through association with the histone deacetylase RPD3. In this study, my major goal is to explore the mechanism of how SIN3 regulates cellular metabolism.

Methionine metabolism generates the major methyl donor S-adenosylmethionine (SAM) for histone methylation. In collaboration with others, I report that reduced levels of some enzymes involved in methionine metabolism and histone demethylases lead to lethality, as well as wing development and cell proliferation defects in Drosophila melanogaster. Additionally, disruption of methionine metabolism can directly affect histone methylation levels. Reduction of little imaginal discs (LID) histone demethylase, but not lysine-specific demethylase 2 (KDM2) demethylase, is able to counter the effects on histone methylation due to reduction of SAM synthetase (SAM-S). Taken together, these results reveal an essential role of key enzymes that control methionine metabolism and histone methylation.

Next, we demonstrate the genetic interaction between Sin3A and methionine metabolic genes. We find that SIN3 binds to methionine metabolic genes, affects histone modifications at the promoter regions of these genes and regulates their expression. We provide evidence that alteration of SIN3 level influences the amount of SAM and global H3K4me3. Furthermore, reduction of SIN3 can restore decreased global H3K4me3 caused by knockdown of either SAM-S or the histone methyltransfase SET1 to near control levels. Collectively, these results indicate that SIN3 directly regulates expression of methionine metabolic genes to control SAM levels, which in turn affect global H3K4me3.

To further identify specific genes and cellular metabolic pathways requiring the activity of SIN3, we performed RNA-seq and metabolomics analysis when SIN3 and/or SAM-S is reduced. Moreover, we did correlation analysis between global H3K4me3 levels and the metabolic profiles to generate a list of metabolites whose concentration change significantly with the alteration in H3K4me3. We find glycolysis is a major pathway correlated with global H3K4me3 upon reduction of SIN3 and/or SAM-S. We demonstrate that SIN3 binds to glycolytic genes, affects H3K9ac, not H3K4me3, at the promoter regions of these genes and regulates their expression. Altogether, these results suggest that SIN3 directly regulates transcription of glycolytic genes to affect glycolysis, which is associated with H3K4me3 due to unknown mechanism.

Overall, our study reveals that SIN3 is an important epigenetic regulator connecting cellular metabolism and histone modification.

Supplementary files are included:

• Supplementary Data 1_ML – Excel spreadsheet containing detailed RNAseq differential expression analysis

• Supplementary Data 2_ML – Excel spreadsheet containing detailed gene ontology and KEGG pathway analyses

• Supplementary Data 3_ML – Excel spreadsheet containing detailed metabolomic analysis

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