Obesity is an increasing health problem which is causally associated with insulin resistance and type 2 diabetes. Oxidative stress, i.e. overproduction of reactive oxygen species, is associated with insulin resistance and obesity and may be a major risk factor in the onset and progression of diabetes. Bernlohr Lab at University of Minnesota have study oxidative stress in adipocytes by silencing the enzyme glutathione S-transferase A-4 (GSTA4), an enzyme detoxifying 4-hydroxynonenal formed during oxidative stress. Their results indicate that lysine acetylation, an important post-translational modification, may be involved during oxidative stress. In this study lysine acetylation has been investigated in condition of oxidative stress in 3T3-L1 adipocytes and subcutaneous adipose tissue from mice using SDS-PAGE gel electrophoresis and western blot. Lysine acetylation was analyzed in different compartments of the cell such as in cytoplasm, mitochondria as well as in whole cell extracts. Silencing of GSTA4 and stimulation by TNF-α in 3T3-L1 adipocytes resulted in an increase of lysine acetylation in cytoplasm. Furthermore, stimulation by IL-6 did not have any effect on lysine acetylation. Surprisingly, subcutaneous adipose tissue from mice fed on a high-fat diet showed a decrease of lysine acetylation in cytoplasm compare to mice fed on a chow diet. In conclusion, lysine acetylation seems to change during oxidative stress and may be an important factor during insulin resistance, type 2 diabetes and obesity. Therefore, studying lysine acetylation and enzymes modulating acetylation may potentially increase our understanding of insulin resistance, type 2 diabetes and obesity and could lead to new therapies.

Epstein-Barr Virus (EBV) has two states of infection, latent and lytic. During the latent state the viral genome remains stable in cells as episomes and replicates with cellular DNA. During the lytic cycle the viral DNA becomes amplified and packaged in newly formed virions. An unsolved problem is whether newly replicated EBV DNA produced upon lytic cycle activation is associated with histones, and if so, whether these histones are acetylated. This question has biological significance as knowing the chromatin structure of genes is important in determining their function and expression profile. Our hypothesis is that newly synthesized EBV lytic DNA is associated with histones and the histone tails are selectively acetylated. To investigate our hypothesis we performed chromatin immunoprecipitation (ChIP) in HH514-16 cells, a Burkitts Lymphoma cell line, during latent and lytic replication. We used quantitative PCR (qPCR) to detect the relative concentration of DNA among the different samples. We tested three different variables: type of inducing agent, duration of treatment, and different regulatory regions in the genome of Epstein-Barr Virus. We found that in cells induced into the lytic cycle with Trichostatin A (TSA), a histone deacetylase inhibitor (HDACi), association of newly replicated EBV DNA with acetylated histone 3 (H3) increased ~ 6-10 fold. This increase in association was greatest 72 hrs after treatment. Furthermore, activation of lytic viral replication in HH514-16 cells using a different inducing agent, Azacytidine (AZC), which is known to function as a DNA methyltransferase inhibitor, increased binding of H3 with viral DNA ~8 fold. However, unlike TSA, AZC increased the acetylation state of histones bound to newly synthesized viral DNA only ~ 2 fold. Changing the regulatory region of the EBV genome analyzed in qPCR did not affect our results. Our results suggest that newly replicated viral DNA is associated with histones, a fraction of which are acetylated. The degree of acetylation likely depends on the agent used to induce the lytic cycle. H3 is highly acetylated when an HDACi is used and less acetylated when AZC is used. Our study provides new insight on the epigenetic profile of newly replicated viral DNA during the lytic cycle. It remains to be determined whether histones are packaged together with viral genomes into virions and whether the chromatin state of virion DNA affects gene expression after the virus enters uninfected cells.

Thesis (Ph. D.)--University of Chicago, Department of Molecular Genetics and Cell Biology, 2001. / Includes bibliographical references. Also available on the Internet.

Humans are exposed to arsenicals through many routes with the most common being drinking water. Exposure to arsenic has been associated with an increased incidence of skin, lung, liver, prostate, and bladder cancer. Although the relationship between arsenic exposure and carcinogenesis is well documented, the mechanisms by which arsenic participates in tumorigenesis are not fully elucidated. We evaluated the potential epigenetic component of arsenical action by assessing the histone acetylation and DNA methylation state of 13,000 human gene promoters in a cell line model of arsenical-mediated malignant transformation. We show changes in histone H3 acetylation and DNA methylation occur during arsenical-induced malignant transformation, each of which is linked to the expression state of the associated gene. These epigenetic changes occurred non-randomly and targeted common promoters whether the selection was performed with arsenite [As(III)] or with the As(III) metabolite monomethylarsonous acid [MMA(III)]. The epigenetic alterations of these promoters and associated malignant phenotypes were stable after the removal of the transforming arsenical. One of the affected regions was the promoter of WNT5A. This gene is transcriptionally activated during arsenical induced malignant transformation and its promoter region exhibited alterations in each of the four histone modifications examined which were linked to its transcriptional activation. Experimental reduction of WNT5A transcript levels resulted in abrogated anchorage independent growth, suggesting a participative role for the epigenetic remodeling of this promoter region in arsenical-induced malignant transformation. Taken together, these data suggest that arsenicals may participate in tumorigenesis by stably altering the DNA methylation and histone modifications associated with targeted genes, uncovering a likely set of participative genes and representing a mechanism to potentially explain the latency associated with arsenic-induced malignancy.

To maintain intracellular redox homeostasis, genes encoding many endogenous antioxidants and phase II detoxification enzymes are transcriptionally upregulated upon deleterious oxidative stress through the cis- antioxidant responsive elements (AREs) in their promoter regions. Nrf2 has emerged as the pivatol transcription factor responsible for ARE-dependent transcription, and has been shown to play critical roles in hepatotoxicity, chemical carcinogenesis, pulmonary inflammatory diseases, neurodegenerative diseases and aging. Therefore, understanding the molecular mechanism of the Nrf2-dependent cytoprotective system is important for development of drugs for therapeutic intervention.Nrf2 is targeted by Keap1 for ubiquitin-mediated degradation under basal conditions. Upon oxidative stress, distinct cysteine residues of Keap1 are alkylated, leading to inhibition of Keap1 and activation of Nrf2. However, it was not clear how Nrf2 is re-entered into the repression status when redox homeostasis is re-achieved. In this dissertation, we establish that the post-induction repression of Nrf2 is controlled by the nuclear export function of Keap1 in alliance with the cytoplasmic ubiquitination/ degradation machinery. We show that a nuclear export sequence (NES) in Keap1 is required for termination of Nrf2 signaling; ubiquitination of Nrf2 is carried out in the cytosol; Keap1 nuclear translocation is independent of Nrf2; and the Nrf2-Keap1 complex does not bind the ARE. Collectively, these results suggest that Keap1 translocates into the nucleus to dissociate Nrf2 from the ARE and mediates nuclear export of Nrf2 followed by ubiquitination and degradation of Nrf2 in the cytoplasm.In addition to Keap1-mediated negative regulation, we identified a novel positive regulatory mechanism of Nrf2 mediated by transcription co-activator p300/CBP. We show that p300/CBP directly binds and acetylates Nrf2 in response to oxidative stress. We have identified multiple acetylated lysine residues within the Nrf2 Neh1 DNA-binding domain. Combined lysine-to-arginine mutations on the acetylation sites, with no effects on Nrf2 protein stability, compromised the DNA-binding activity of Nrf2 in a promoter-specific manner both in vitro and in vivo. These findings demonstrated that acetylation of Nrf2 by p300/CBP augments promoter-specific DNA binding of Nrf2 and established acetylation as a novel regulatory mechanism that functions in concert with Keap1-mediated ubiquitination in modulating the Nrf2-dependent antioxidant response.

The budding yeast, Saccharomyces cerevisiae, serves as an excellent model for identifying fundamental mechanisms of DNA repair. A Local Coherence Detection (LCD) algorithm that uses biclustering to assign genes to multiple functional sub-groups was applied on the chromosome E-MAP containing genetic interactions among genes involved in nuclear processes. Using this method, we found that Asf1 and Rtt109, genes that are together required for histone H3K56 acetylation, cluster together with Ctf4, Ctf18, Ctf8 and Dcc1, genes important for efficient sister chromatid cohesion. It is known that H3K56 acetylation is required for post-repair chromatin reassembly at sites of DNA double-strand breaks (DSBs). The cohesion genes were previously implicated in the repair of some DNA DSBs, but the nature of their involvement has not been reported. The experimental data in my thesis work suggest that Ctf4, Ctf8, Ctf18 and Dcc1 function in the post-repair chromatin reassembly pathway.

The budding yeast, Saccharomyces cerevisiae, serves as an excellent model for identifying fundamental mechanisms of DNA repair. A Local Coherence Detection (LCD) algorithm that uses biclustering to assign genes to multiple functional sub-groups was applied on the chromosome E-MAP containing genetic interactions among genes involved in nuclear processes. Using this method, we found that Asf1 and Rtt109, genes that are together required for histone H3K56 acetylation, cluster together with Ctf4, Ctf18, Ctf8 and Dcc1, genes important for efficient sister chromatid cohesion. It is known that H3K56 acetylation is required for post-repair chromatin reassembly at sites of DNA double-strand breaks (DSBs). The cohesion genes were previously implicated in the repair of some DNA DSBs, but the nature of their involvement has not been reported. The experimental data in my thesis work suggest that Ctf4, Ctf8, Ctf18 and Dcc1 function in the post-repair chromatin reassembly pathway.

Chromatin is the combination of DNA and proteins in the nucleus that is used to aid in the compaction of DNA. Histones are a group of proteins used to condense DNA by forming a complex (nucleosome) around which DNA wraps around; there are two of each type of histone in a nucleosome: H2A, H2B, H3 and H4. Once the DNA is wrapped around the histones, the genome is further compacted. A shortened, "clipped" version of histone H3 has been found in some organisms including yeasts, flies, mammalian stem cells, and the ciliated protozoan, Tetrahymena thermophila. In each organism, clipping occurs at a different site on the N-terminus, usually before an alanine residue. Clipping is important as it may affect other epigenetic modifications and gene regulation in cell differentiation, but the regulation of this histone proteolysis has remained largely unstudied. In Tetrahymena thermophila, approximately half of the histone H3 molecules are clipped between residues 6 and 7 on histone H3, solely in the transcriptionally silent micronucleus. The histones in the micronuclei are deacetylated, while histones in the macronuclei can be acetylated or deacetylated. It is hypothesized that the post-translational acetylation modification to the histone tails may inhibit histone H3 clipping. Immunoblot analyses were carried out with acetylated and deacetylated micronuclei, demonstrating an increase of clipping when acetylated. Additionally, mutations were created at lysine 9 upstream of the clip site on the histone H3 tails to mimic acetylation and deacetylation to study whether the modification of that site has a regulatory effect.

Loss of function of the WRN protein causes the genetic disorder Werner Syndrome that is characterized by increased cancer and premature aging. WRN belongs to the RecQ helicase family that plays key roles in preventing genome instability. In response to treatment with genotoxins, WRN is subject to post-translational modification. The relationship of post-translational modification of WRN with its function in DNA metabolism is unknown. There is accumulating evidence suggesting that WRN contributes to the maintenance of genomic integrity through its involvement in DNA replication. Consistent with this notion, WS cells are sensitive to DNA replication inhibitors and DNA damaging agents that tend to block replication fork progression. The cells exhibit an extended S phase, as well as defects in normal bi-directional progression of replication forks diverging from the majority of replication origins. To elucidate the relationship between post-translational modifications of WRN with its function in DNA metabolism, here the acetylation of WRN was studied. In our studies, we provide evidence that WRN acetylation is a dynamic process that strongly correlates to blockage of replication by persistent DNA damage. We also determined the effect of WRN acetylation on its specificity and enzymatic functions. In addition, our studies reveal how agents that block replication regulate the nature of WRN interactions with RPA, a factor known to bind to single-stranded DNA generated at blocked replication forks. Our results demonstrated that WRN and RPA form a stable direct association under normal physiological conditions and treatments that block replication fork progression increase their association, further supporting the idea that WRN is involved in DNA replication through its action at blocked or stalled replication forks. Thus, these studies point to both 1) an important role for acetylation of WRN and 2) its interaction with RPA in the putative function of WRN in response to blocked replication. Overall, our results impact knowledge regarding the relationship between DNA damage, genome instability and the development and progression of aging and cancer.

Histone phosphorylation is often a direct outcome of activated intracellular signaling pathways, and functions to translate extracellular signals into appropriate biological outputs such as changes in gene expression. Growth factors and cellular stress trigger rapid and transient expression of immediate-early genes (such as c-fos, c-jun) in mammalian cells, and their induction strongly correlates with a transient phosphorylation of S10 and S28 on histone H3. While many signaling cascades that lead to H3 phosphorylation have been mapped out, mechanistic details of the downstream events and how H3 phosphorylation contributes to transcriptional activation are still poorly defined. To investigate the direct effects of H3 phosphorylation on transcription, we targeted the H3 kinase MSK1 to endogenous c-fos promoter, and found that this is sufficient to activate its expression. Moreover, targeting MSK1 to the tissue-specific -globin gene induces H3S28 phosphorylation and reactivates expression of this polycomb-silenced gene. Mechanistically, H3S28 phosphorylation not only disrupts binding of polycomb repressive complexes, but also induces a methyl-acetylation switch of the adjacent K27 residue. This provides the first indication that H3 phosphorylation is involved in antagonizing polycomb silencing. To further identify post-translational modifications (PTMs) that function together with MSK1-mediated H3 phosphorylation, I developed a novel nucleosome purification approach called Biotinylation-assisted Isolation of CO-modified Nucleosomes (BICON). This technique combines in vivo biotinylation by BirA and H3 phosphorylation by MSK1, allowing enrichment of phosphorylated nucleosomes using streptavidin. I found that MSK1-phosphorylated nucleosomes are hyper-acetylated on H3 and H4, and importantly, I identified a trans-tail crosstalk between H3 phosphorylation and H4 acetylation on K12. This proof-of-principle study demonstrates that BICON can be further adapted to study PTMs and crosstalks associated with other histone-modifying enzymes. Taken together, work described in this thesis shows that histone H3 phosphorylation can initiate additional PTM changes on other residues within the nucleosome, and such crosstalk plays an important role in regulating gene expression.