Methyl-CpG binding protein 2 (MeCP2) and histone H1 are important chromatin associated proteins. Both exhibit their own extent of complexity as MeCP2 is an intrinsically disordered protein (IDP) that interacts with many different partners involved in several cellular processes and histone H1 consists of 11 different subtypes each of them associated with different posttranslational modifications (PTMs). An interesting avenue for the study of these proteins is in neurons where MeCP2 is very abundant and histone H1 level is half that observed in other somatic tissues. Several reports in the past have proposed that this lower level of histone H1 is due to the abundance of MeCP2 which displaces histone H1. However, this hypothesis has been debated and there is no clear consensus. In an attempt to study this controversy, a cell model system ReNCell WT and MeCP2-KO was used that can be induced to differentiate into neurons. The protein levels, transcript levels and localization of histone H1 subtypes in these cells were analyzed using HPLC, RT-qPCR and immunofluorescence, respectively. The results show that ReNCell WT and MeCP2-KO do not exhibit significant differences in their relative amount of histone H1 protein and transcript level neither at the proliferative nor at the later differentiated stages. However, HPLC analyses show that the histone H1 subtypes of these two cell types exhibit significant elution differences probably resulting from differences in their PTM content. Immunofluorescence analyses show that WT ReNCell differentiation as determined by extension of dendritic or axonic processes can be seen to occur over the course of one week and there is a significant difference in the nuclear area of these two cells at 8 DIV. This study provides important preliminary data for future research in MeCP2 and histone H1 using this cell model system and show that MeCP2 may have a bearing on histone H1 PTMs. / Graduate

Epigenetic silencing is often altered in cancer and is a target for drug discovery. Unbiased screens in live cells are performed to identify potential novel targets of epigenetic therapy, and these screens have identified drugs that were not previously recognized to be involved in epigenetic reactivation of gene silencing such as cardiac glycosides and a CDK9 inhibitor. Recently, our lab performed a whole genome siRNA screen in combination with DNMT inhibition. One of the top targets revealed in this screen was the splicing factor SF3B1. SF3B1 is a well-known crucial splicing factor and is mutated in several cancers. However, its role in epigenetic regulation has not been well studied. I propose SF3B1 is a novel target for epigenetic therapy in cancer. In the YB5 colon cancer cell line where GFP is under the control of a methylated CMV promoter, I validated the screen results and found 0%, 1.0% and 5.3% GFP+ cells after treatment with siControl, siSF3B1 or the DNA methyltransferase inhibitor decitabine (DAC), respectively. DAC and siSF3B1 were synergistic, inducing 17.2% GFP+ cells. This synergy was also seen in an additional live cell assay and with other SF3B and SF3A family proteins. RNA-Seq analyses showed 423 genes upregulated by siSF3B1, 430 genes induced by DAC, and 1190 induced by the combination. siSF3B1 resulted in aberrant splicing of 695 genes, but there were only 27 genes overlapping between splicing alterations and gene expression changes, suggesting different mechanisms. Genes regulated upon siSF3B1 treatment were enriched for the TATA motif in their promoters, and the TATA-Box binding protein (TBP) was among the genes differentially spliced after siSF3B1. DNA methylation analyses showed demethylation synergy between siSF3B1 and DAC. Finally, the effects of siSF3B1 were phenocopied by treatment with the pan-SF3B inhibitor Pladienolide B (PB). GFP was reactivated in two separate colon cancer cell lines upon treatment with PB with synergistic activation when combined with DAC in YB5 cells. Thousands of genes were regulated and alternatively spliced with PB treatment alone, and among the differentially spliced genes was TBP. Furthermore, PB treatment with DAC induced demethylation significantly more than with DAC treatment alone. Genes regulated upon SF3B1 loss and inhibition were enriched for p53 target genes. Indeed, there was reduced cell proliferation and cell cycle arrest when SF3B1 was inhibited. This study demonstrates that the splicing factor SF3B1 has unexpected effects on gene transcription and targeting SF3B1 is synergistic with DNA methylation inhibition suggesting clinical potential for the combination. / Biomedical Sciences

Obesity rates are rising rapidly in the United States, reaching epidemic proportions. Insights into which genes predispose individuals to develop obesity are a necessity. If people at risk for obesity can be identified, individualized treatment programs can be designed based on the individuals' genetic and epigenetic predisposition to help decrease the rate of obesity and obesity-related diseases and deaths. This study will be focusing on the genes FTO, MAOA, SH2B1, CCKAR, NEGR1, LEPR, DNMT3B, and BDNF that have been previously associated with obesity risk and obesity-related phenotypes. Transcript levels of FTO and MAOA were analyzed using quantitative real-time RTPCR, promoter methylation was examined utilizing methylation-sensitive restriction enzyme digestion assays designed for each of the eight gene promoters, and the genotype at eight SNPs, previously associated with obesity, were examined. These data were compared to data gathered on body composition, eating behavior, and temperament. The goals of this project were to replicate results from previous research suggesting associations between certain genetic variants to body composition measures, to identify novel associations between genetic and epigenetic variations and body composition, eating behavior, and temperament, and to provide evidence that the genes previously correlated to obesity in adults is also correlated to measures of obesity and obesity-related phenotypes in children. Decreased levels of methylation in the promoter of BDNF were associated with different eating behaviors including, decreased food fussiness and decreased satiety response. These results were statistically significant after Bonferroni correction for multiple testing. Genotype analysis at the SNP, rs4923461, in BDNF identified an association between the G allele and increased emotional under-eating in males. This association also remained significant after Bonferroni correction. These data gathered for BDNF may suggest a novel role for BDNF in the regulation of energy balance and obesity. The data analysis for all expression, methylation, and genotype data identified associations with 16 different obesity-related phenotypes. These phenotypes included; three measures of body composition, seven eating behaviors, two measures of food intake, one measure of self-regulation, and three measures of temperament. These associations were held to a lower statistical standard and are considered suggestive pending replication in a larger sample. This research was able to provide novel insight into genetic and epigenetic alterations that modify obesity-related phenotypes in African American children. A cumulative genetic and epigenetic "obesity risk factor" score was derived using all significant and suggestive associations to obesity-related phenotypes. The score was derived from the methylation analysis from all eight gene promoters, SNPs from LEPR, DNMT3B, and BDNF, and expression data for MAOA and FTO. The "obesity-risk factor" score was significantly higher in obese compared to non-obese individuals, suggesting the combined genetic and epigenetic approach has value in the prediction of childhood obesity in African Americans. / Molecular Biology and Genetics

The dominantly held view in evolutionary theory focuses on gradual or punctuated change, primarily via natural selection, as the mechanism by which novel traits arise and evolution occurs. Noticeably absent from this portrayal of evolution is mention of the conservation of general characteristics, such as homologous morphological features or conserved nucleotide sequences, commonly observed across even distantly related groups at both the molecular and organismal levels. This raises at least the following questions: a) How does the evolution of conserved traits fit into an evolutionary theory that emphasizes change? b) What components of an evolving system provide the capacity for adaptation in spite of this apparent conservation of general traits? And c) How do these components affect the evolution of lineages? Here I suggest that heritable traits such as DNA methylation and histone modifications provide one place to look when addressing these questions. Current quantitative and population genetic models reflect the dominant view of evolution described above, and act as the foundation for both formal and informal descriptions and predictions of evolutionary change. Using results from recent work in molecular epigenetics, I consider the evolutionary implications for these traits, and show how current models of evolution fail to accurately capture this influence. In doing so, I also address some of the philosophical implications for how we conceptualize evolution, and what potential changes might be necessary for a more complete theory. / Master of Arts

Epigenetic mechanisms play tremendous roles in the development and management of neural processing. The important mechanisms include inactivation of transcription via methylation, histone modification via acetylation/deacetylation, and miRNA regulation. These modifications allow for expression or silencing of genes, without manipulation of nucleotide sequence. An individual's internal and external environments provide input for quotidian epigenetic regulation. Aberrations in the form of regulation have been increasingly linked to neurological disorders, in addition to the established correlation to tumorigenesis. In recent years, deviations from normal epigenetic patterns have been observed in cases of Alzheimer's disease (AD). The brains of patients with AD have been shown to display significantly less methylation overall, as compared to age-matched controls. Of particular concern, the methylation, which normally keeps the promoter of the APP gene silenced, occur far less frequently in AD patient allowing for the progression of amyloid deposition and subsequent tau pathology. In addition to the hypomethylation present in AD, many AD cases present with a concurrent hypoacetylation on histones in the hippocampus. There is strong evidence suggesting that the reduced levels of acetylation are due to over-activation of histone deacetylases. Post-mortem examinations of the brains of AD patients have shown that the brain-derived neurotrophic gene, which is crucial for neural processing associated with maturation and memory, has low levels of acetylation halting its transcription. While low levels of methylation and acetylation seem to contribute to the pathogenesis of AD, regulatory miRNA levels can have adverse effects whether they are aberrantly reduced or increased. Patients with AD tend to show abnormally augmented expression of miRNA-125b, miRNA-128, and miRNA-9 in the hippocampus, while a reduced expression of miRNA-107. Deregulation of these miRNAs have been linked to the progression of AD and include amyloid deposition, tau pathology, and oxidative stress through inflammatory processes. The latter quandary of oxidative stress has been shown to be crucial for the early progression of AD. Reactive oxygen species disallow the methylation of genes due to steric hindrance at the CpG islands of DNA where DNA methyltransferases act. Research shows that increases in oxidative stress are correlated to decreases in methylation, which allows for APP expression. While these alterations to normal epigenetic patterns occur internally, there is a breadth of changes that the external environment imposes to exacerbated AD pathogenesis. Most heavily studied of these external environmental factors is lead exposure. There is a strong correlation between lead exposure in individuals who carry the ApoE4 gene and increased mRNA transcription of the APP gene. Lead is thought to demethylate the promoter of the APP gene and allow for amyloid processes to occur. Inadequate nutrition, specifically deficits in choline and folate, has been linked to hypomethylated states due to an inefficient "methylation/remethylation cycle" leading to an accumulation of homocysteine characteristic of AD. With the emphasis epigenetic deregulation has in the progression of AD, epigenetic treatments need to be seriously considered as therapeutic avenues. Current drugs treat the symptoms and acute conditions of AD, but through epigenetic modifications, the pathology of the diseases can be directly addressed. Potential therapeutic avenues include the use of methyl donors, highly specific histone deacetylase inhibitors, and miRNA biomarkers. Methyl donors can help alleviate the hypomethylated state and prevent further APP expression and amyloid deposition. Currently, the histone deacetylase inhibitors are being used as global inhibitors, but have adverse effects including non-specific and premature cell death. By further researching these inhibitors and finding a mechanism to attack specific histone deacetylases (such as HDAC6 in AD), the efficacy of this aspect of treatment will be greatly increased. The current use of miRNAs as epigenetic regulators to turn off unwanted genetic expression is ineffective due to a major problem of effective delivery to target zones. By using the gene sequences of miRNAs as biomarkers, an AD patient's genomic sequence can be mapped, marking which areas require regulation. This process is necessary because of the inter-individuality of miRNA regulation between each case of AD. Also, the problem of some anti-miRNA molecules not being able to cross the blood brain barrier needs to be addressed using a novel transport mechanism, as direct brain injections are not feasible. The simplest, and highly effective, therapeutic avenue is a healthy lifestyle. Daily exercise and proper nutrition hinder inflammatory process and oxidative stress and can prevent progression of AD through allowing higher brain perfusion for cognitive functioning.

In mammals, epigenetic modifications and trans-acting effectors coordinate gene expression during development and impose transcriptional memories that define specific cell lineages and cell-types. Methylation at CpG dinucleotides is an epigenetic mechanism through which transcriptional silencing is established and heritably maintained through development. Functionally, DNA methylation regulates key biological processes such as X-chromosome inactivation, transposon repression and genomic imprinting. However, the extent to which DNA methylation is the primary regulator of single-copy gene expression and the precise mechanism of methylation-dependent silencing remain undetermined. Here, I identify a novel set of germline-specific candidate genes putatively regulated by DNA methylation. Analysis of one candidate gene, Tex19, demonstrates that promoter CpG methylation is the primary and exclusive mechanism for regulating developmental silencing in somatic lineages. Genetic or pharmacological removal of CpG methylation triggers robust de-repression of Tex19 and loss of transcriptional memory. Moreover, Tex19 critically relies on de novo methylation, mediated by Dnmt3b, to impose silencing in differentiating ES cells and somatic cells in vivo from embryonic day (E)7.5. Reporter gene and ChIP analysis demonstrate that Tex19 is strongly activated by general transcription factors and is not marked by repressive histone modifications in somatic lineages, consistent with differential DNA methylation per se being the primary mechanism of regulating expression. Full transcriptional silencing of Tex19 is critically dependent on the methyl-binding protein (MBP) Kaiso, which is only recruited to methylated Tex19 promoter. The reliance on DNA methylation and Kaiso for silencing in somatic cells establishes an epigenetic memory responsible for maintaining expression in germline and pluripotent cell types through successive developmental cycles. This thesis represents the first causal report of lineagespecific promoter DNA methylation directing silencing of an in vivo gene through recruitment of an MBP.

Genome-wide association studies have been used extensively to study hundreds of phenotypes and have determined thousands of associated SNPs whose underlying biology and causation is as yet largely unknown. Many previous studies attempted to clarify the causal biology by investigating overlaps of trait-associated variants with functional annotations, but lacked statistical rigor and examined incomplete subsets of available functional annotations. Additionally, it has been difficult to disentangle the relative contributions of different annotations that may show strong correlations with one another. In this thesis, we address these shortcomings and strengthen and extend the obtained results. Two methods, permutations and logistic regression, are applied in statistically rigorous analyses of genomic annotations and their observed enrichment or depletion of trait-associated SNPs. The genomic annotations range from genic regions and regulatory features to measures of conservation and aspects of chromatin structure. Logistic regressions in a number of trait-specific subsets identify genomic annotations influencing SNPs associated with both normal variation (e.g., eye or hair colour) and diseases, suggesting some generalities in the biological underpinnings of phenotypes. SNPs associated with phenotypes of the immune system are investigated and the results highlight the distinct aetiology for this subset. Despite the heterogeneity of the studied cancers, SNPs associated to different cancers are particularly enriched for conserved regions, unlike all other trait-subsets. Nonetheless, chromatin states are, perhaps surprisingly, among the most influential genomic annotations in all trait-subsets. Evolutionary conserved regions are rarely within the top genomic annotations despite their widespread use in prioritisation methods for follow-up studies. We identify a common set of enriched or depleted genomic annotations that significantly influence all traits, but also highlight trait-­‐specific differences. These annotations may be used for the computational prioritisation of variants implicated in phenotypes of interest. The approaches developed for this thesis are further applied to studies of a specific human complex trait (height) and gene expression in atherosclerosis.

Virtually all multicellular organisms are capable of developing differently in response to environmental variation. At the molecular level, such developmental plasticity requires interpretation and perpetuation of environmental signals without changing the underlying genotype. Such non-genetic, heritable information is known as epigenetic information. This dissertation examines epigenetic information among social insects, and how differences in such information relate to phenotypic caste differences. The studies included herein primarily focus on one form of epigenetic information: DNA methylation. In particular, these studies explore DNA methylation as it relates to and impacts (i) alternative phenotype and particular gene expression differences in two social insect species, (ii) histone modifications, another important form of epigenetic information, in insect genomes, and (iii) molecular evolutionary rate of underlying actively transcribed gene sequences. We find that DNA methylation exhibits marked epigenetic and evolutionary associations, and is associated with alternative phenotype in multiple insect species. Thus, DNA methylation is emerging as one important epigenetic mediator of phenotypic plasticity in social insects.

Background: Gene expression is regulated via highly coordinated epigenetic changes, the most studied of which is DNA methylation (DNAm). Many studies have shown that DNAm is linearly associated with age, and some have even used DNAm data to build predictive models of human age, which are immensely important considering that DNAm can predict health outcomes, such as all-cause mortality, better than chronological age. Nevertheless, few studies have investigated non-linear relationships between DNAm and age, which could potentially improve these predictive models. While such investigations are relevant to predicting health outcomes, non-linear relationships between DNAm and age can also add to our understanding of biological responses to late-life events, such as diseases that afflict the elderly. Objectives: We aim to (1) examine non-linear relationships between DNAm and age at specific loci on the genome and (2) build upon regularization methods by comparing prediction errors between models with both non-transformed and square-root transformed predictors to models that include only non-transformed predictors. We used both the sparse partial least squares (SPLS) regression model and the lasso regression model to make our comparisons. Results: We found two age-differentially methylated sites implicated in the regulation of a gene known as KLF14, which could be involved in an immunosenescent phenotype. Inclusion of the square-root transformed variables had little effect on the prediction error of the SPLS model. On the other hand, the prediction error increased substantially in the lasso regression model, particularly when few predictors (70) were included. Conclusion: The growing amount and complexity of biological data coupled with advances in computational technology are indispensable to our understanding of biological pathways and perplexing biological phenomena. Moreover, high-dimensional biological data have enormous implications for clinical practice. Our findings implicate a possible biological pathway involved in immunosenescence. While we were unable to improve the predictive models of human age, future research should investigate other possible non-linear relationships between DNAm and human age, considering that such statistical methods can improve predictions of health outcomes.

Epigenetic deregulation contributes significantly to the development of multiple human diseases, including cancer. While great effort has been made to elucidate the underlying mechanism, our knowledge on epigenetic regulation is still fragmentary, an important gap being how the diverse epigenetic events coordinate to control gene transcription. In the first part of our study, we demonstrated an important link between Snail-mediated transcriptional control and epigenetic regulation during cancer development. Specifically, we found that the highly conserved SNAG domain of Snail sequentially and structurally mimics the N-terminal tail of histone H3, thereby functions as a molecular “hook”, or pseudo substrate, for recruiting histone lysine specific demethylase 1 (LSD1) repressor complex to the E-cadherin promoter. Furthermore, we showed that Snail and LSD1 are both required for E-cadherin repression and EMT induction, and their expression is highly correlated with each other in multiple human tumor tissues. Our findings have important clinical ramifications in that compounds mimicking the SNAG domain may disrupt Snail-LSD1 interaction and inhibit EMT and metastasis. In the second part of our study, we designed a batch of compounds based on the structure of the SNAG domain and are currently screening for candidates capable of competing with SNAG peptide for LSD1 binding. In addition, we applied a peptide pulldown/mass spectrometry-coupled analysis to identify SNAG-interacting proteins, among which are many chromatin enzymes and modulators. Functional characterization of these proteins will help to elucidate the Snail-mediated epigenetic regulation process. In the third part of our study, we found that Snail interacts with poly(ADP-ribose) polymerase 1 (PARP1) through a potential pADPr-binding motif and is subject to poly(ADP-ribosyl)ation, which can stabilize the Snail-LSD1 complex for enhanced PTEN suppression under DNA damage condition. Our findings added another layer to the delicate Snail transcriptional machinery, and indicated that PARP inhibitors may be applied in combination with conventional chemotherapies to target cancers with high expression of Snail and LSD1. In summary, we demonstrated that Snail cooperates with multiple epigenetic machineries to induce EMT as well as survival of tumor cells. Our findings contribute to a better appreciation of Snail-mediated epigenetic network as well as diversification of therapeutic strategies against cancer.