A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree in Master of Science (Medicine) in the Division of Human Genetics / Foetal Alcohol Syndrome (FAS) is characterised by growth retardation, craniofacial dysmorphology and neurodevelopmental deficits. Whilst, not all alcohol exposed offspring display alcohol-related developmental anomalies, the percentage of affected offspring is greatly underestimated. Common behavioural disorders, such as ADHD and anxiety, are likely to be linked to the transgenerational effects of in utero alcohol exposure. Epigenetics has been highlighted as a potential mechanism in the aetiology of alcohol teratogenesis due to alcohol’s disruptive effects on the folate pathway, and subsequently DNA methylation. The imprinted H19/Igf2 domain is critical in foetal growth and development. The locus is regulated by the methylation-sensitive CTCF binding protein which binds to the H19 imprinting control region (ICR) upstream of the H19 locus. CTCF binding allows for the reciprocal expression of H19 and Igf2 in an allele-specific parent of origin manner. Due to the monoallelic expression of imprinted genes, DNA methylation changes within their control regions can lead to altered gene expression and possibly disease. Furthermore, if these alterations occur in the germline, disease states or susceptibility to disease may be transmittable to future generations. A mouse model was used to investigate the potential transgenerational effects of F0 chronic maternal ethanol exposure on parturition, growth, locomotor activity and anxiety. Furthermore, the transgenerational inheritance of H19 ICR DNA methylation was investigated and its possible contribution to the aforementioned phenotypes was determined. Phenotypic analysis revealed significantly reduced F1 fertility following alcohol exposure (P = 0.003) but no other significant perturbations in parturition. Although not significant at all generations, alcohol’s effects on growth and behaviour were apparent. DNA was extracted from tail biopsies, bisulfite modified and the CTCF1 and CTCF2 regions of the H19 ICR amplified. DNA methylation quantification via Pyrosequencing revealed significantly reduced mean methylation profiles at CTCF1 and CTCF2 within the F1 EtOH exposed group (P = 0.021), with CpG sites 1, 2, 4 and 6 of CTCF1 and CpG sites 1, 2, 3 (P = 0.021) and 5 (P = 0.043) of CTCF2 displaying statistically significant differences. In contrast, the EtOH group of the F2 generation showed an increase in CTCF1 mean methylation that trended towards significance (P = 0.083) suggesting a potential recovery or compensatory mechanism within the epigenetic machinery. The F3 generation EtOH exposed group displayed decreased CTCF1 mean methylation levels (P = 0.083). The F2 and F3 generations showed no significant difference in CTCF2 methylation levels between treatment groups. The significant change in CTCF1 methylation at the F1 generation and the trend towards significance in the F2 and F3 generations indicated potential transgenerational inheritance of altered H19 ICR DNA methylation. Correlations between DNA methylation at the H19 CTCF1 and CTCF2 binding sites with growth rate and behaviour measures revealed no significant relationships. This dissertation supports the involvement of epigenetic mechanisms in alcohol teratogenesis. In addition it contributes to the growing field of transgenerational epigenetic inheritance, with implications for the treatment of those with Foetal Alcohol Syndrome and/or Foetal Alcohol Spectrum Disorders and their progeny.

DNA methylation is increasingly recognised as a significant epigenetic event that may initiate and drive the process of neoplasia in humans. In the colon, DNA methylation of key genes is common in a subset of colorectal cancers. The extent to which DNA methylation at various genes contributes to initiation of colorectal neoplasms is less clear. This study sought to clarify the biological and clinicopathological significance of methylation of various genes in the development of sporadic and familial colorectal neoplasia. Quantitative methylation-specific PCR (qMSP) assays (capable of detecting down to a measureable proportion of 0.1% of the total input DNA) were developed to determine the presence of CpG methylation at a given gene. Methylation of MLH1-C was found in the apparently normal mucosa samples from seven of 104 (7%) of individuals with sporadic colorectal cancer (CRC) showing microsatellite instability (MSI). No methylation of MLH1-C was found in the biological samples of individuals with microsatellite stable (MSS) counterparts (n=131). MLH1-C methylation may be a field defect that predisposes to the development of sporadic colorectal neoplasia, particularly those demonstrating MSI. Methylation of three of five genes within the 3p22 region including AB002340, MLH1, ITGA9, PLCD1 and DLEC1 (regional 3p22 methylation) was found in 83% of sporadic MSI (n=86) and 12% of MSS cancers demonstrating BRAF V600E mutation (n=42). Regional 3p22 correlated strongly with CpG island methylator phenotype (CIMP), and other clinicopathological characteristics typical of CIMP. Thus, regional 3p22 methylation and CIMP may be overlapping phenomena. Regional 3p22 methylation and the BRAF V600E mutation were found in normal colonic mucosa of four individuals with sporadic MSI CRC, and these cases also had multiple synchronous serrated polyps. These molecular aberrancies may predispose some individuals to the development of metachronous serrated neoplasia. Germline epimutations of APC do not contribute towards the development of FAP, AFAP, or hyperplastic polyposis syndromes. However, APC methylation in normal colonic mucosa of these individuals may represent a field defect in the development of futher neoplasms. In conclusion, different patterns of DNA methylation in normal colonic mucosa may represent a field defect important in the development of different subtypes of colorectal neoplasia.

The Centromere is a vital chromosomal structure that ensures faithful segregation of replicated chromosomes to their respective daughter cells. With such an important structure, one would expect the underlying centromeric DNA sequence would be highly conserved across all species. It turns out that the underlying centromeric DNA sequences between species ranging from the yeast, fly, mouse to humans are in fact highly diverged suggesting a DNA sequence independent or an epigenetic mechanism of centromere formation. / Neocentromeres are centromeres that form de-novo at genomic locations that are devoid of highly repetitive a-satellite DNA sequences of which normal centromeres are usually comprised from. To date, the 10q25 neocentromere is the most well-characterised, fully functional human centromere that has been used previously to characterise the extent of a number of centromeric protein binding domains and characterise the properties of the underlying DNA sequence. Along with other factors, the existence of neocentromeres has given rise to a hypothesis where centromeres are defined by epigenetic or DNA sequence independent mechanisms. / The putative 10q25 neocentromere domain was recently redefined by high resolution mapping of Centromeric protein A (CENP-A) binding through a chromatin immunoprecipitation and array (CIA) analysis. The underlying DNA sequence was investigated to determine and confirm that the formation of the 10q25 neocentromere was through an epigenetic mechanism. Through a high-density restriction fragment length polymorphism (RFLP) analysis using overlapping PCR amplified DNA derived from genomic DNA representing the 10q25 region before and after neocentromere activation. No sequence polymorphisms, large insertions or deletions were detected and confirmed the epigenetic hypothesis of centromere formation. / DNA methylation is one of many epigenetic factors that are important for cellular differentiation, gene regulation and genomic imprinting. As the mechanisms and functions of DNA methylation have been well characterised, its role at the 10q25 neocentromere was investigated to try and identify the candidate epigenetic mechanism involved in the formation of centromeres. DNA methylation across the neocentromere was assessed using sodium bisulfite PCR and sequencing of selected CpG islands located across the 10q25 neocentromere. Overall, the methylation level of the selected CpG islands demonstrated no difference in DNA methylation before and after neocentromere activation. However, significant hypomethylation upon neocentromere formation was detected close to the protein-binding domain boundaries mapped previously suggesting that this may have a role in demarcating protein binding domains at the neocentromere. / Further analysis of DNA methylation investigated non-CpG island methylation at sites defined as CpG islets and CpG orphans. Interestingly, the DNA methylation level measured at selected CpG islets and CpG orphans across the 10q25 neocentromere were not completely hypermethylated as previously thought, but demonstrated variable methylation that became fully hypermethylated upon neocentromere activation in most sites investigated. These results suggested that a role for DNA methylation existed at the 10q25 neocentromere and that it occurred at sites devoid of CpG islands. / This study has found that DNA methylation at non-CpG island sites was variable contrary to popular belief and, was linked with neocentromere formation through the observation of increased DNA methylation at the 10q25 neocentromere. Inhibition of DNA methylation demonstrated increased neocentromere instability and a decrease in methylation of these CpG islets and CpG orphans confirming the importance of DNA methylation at neocentromeres. This study has characterised a new class of sequences that are involved in the maintenance of chromatin structure through DNA methylation at the 10q25 neocentromere.

Graduation date: 1995

Regulation of gene expression is vital for proper growth and prevention of disease states. In eukaryotes this regulation occurs in the context of chromatin which creates an inherent barrier for the binding of trans-acting factors, such as transcription factors and RNA polymerase. This dissertation focuses on the role of transcriptional activators and chromatin remodeling coactivators in the regulation of the repressible acid phosphatase gene PHO5. Our studies show that histone methylation at lysine 4 of histone H3 is required for the full repression of PHO5and GAL1-10. We show that bromodomains, a domain conserved in chromatin remodeling coactivators, may function to stabilize binding. Finally, we present a strategy using DNA methyltransferases as in vivo probes to detect DNA-protein interactions and examine chromatin structure. We extend this strategy to zinc-finger proteins which can be engineered to bind to any desired DNA sequence as a means of targeting methylation with potential use in epigenetic silencing.

This study examined DNA methylation patterns at promoters of endothelial cell (EC)-enriched genes during differentiation of mouse ES cells towards the EC. We have previously shown that eNOS, CD31, VE-cadherin and vWF, which have an EC-enriched pattern of gene expression are differentially methylated between EC and vascular smooth muscle cells. Given that differential promoter DNA methylation is functionally important we asked when these distinct patterns are established. Using the hanging drop method to differentiate ES cells, followed by FACS, we isolated early (EB-day4 VEGFR2-positive) and late (EB-day7 CD31-positive) endothelial progenitor cells. Though current paradigms suggest that lineage-restricted genes are methylated in ES cells, we show heterogeneous promoter DNA methylation. We show DNA demethylation at the CD31 promoter in EB-day 7 CD31-positive cells. In contrast, the eNOS promoter is still heavily methylated in EB-day 7 CD31 positive cells compared with murine EC where there is no DNA methylation.

This study examined the DNA methylation profile of endothelial nitric oxide synthase (eNOS) in the placental villous trophoblast in first, second trimester and healthy term placentas. Syncytiotrophoblast DNA revealed a heterogeneous methylation pattern in the first trimester eNOS proximal promoter and transitioned to a densely methylated pattern at term. Healthy, term syncytiotrophoblast and cytotrophoblast obtained through cytotrophoblast isolation technique provided purified cell samples for RNA and DNA extraction. Real-time PCR (rt-PCR) verified the presence and quantity of eNOS mRNA. In summary, the main findings of this thesis are heterogeneous methylation in first trimester compared to hypermethylation at term; greater eNOS expression and variable methylation in term syncytiotrophoblast compared to cytotrophoblast. A heterogeneous methylation pattern in eNOS has been identified in this study and recent stem cell studies in our lab, and we propose it represents plasticity in gene expression, particularly in early development.

This study examined DNA methylation patterns at promoters of endothelial cell (EC)-enriched genes during differentiation of mouse ES cells towards the EC. We have previously shown that eNOS, CD31, VE-cadherin and vWF, which have an EC-enriched pattern of gene expression are differentially methylated between EC and vascular smooth muscle cells. Given that differential promoter DNA methylation is functionally important we asked when these distinct patterns are established. Using the hanging drop method to differentiate ES cells, followed by FACS, we isolated early (EB-day4 VEGFR2-positive) and late (EB-day7 CD31-positive) endothelial progenitor cells. Though current paradigms suggest that lineage-restricted genes are methylated in ES cells, we show heterogeneous promoter DNA methylation. We show DNA demethylation at the CD31 promoter in EB-day 7 CD31-positive cells. In contrast, the eNOS promoter is still heavily methylated in EB-day 7 CD31 positive cells compared with murine EC where there is no DNA methylation.

This study examined the DNA methylation profile of endothelial nitric oxide synthase (eNOS) in the placental villous trophoblast in first, second trimester and healthy term placentas. Syncytiotrophoblast DNA revealed a heterogeneous methylation pattern in the first trimester eNOS proximal promoter and transitioned to a densely methylated pattern at term. Healthy, term syncytiotrophoblast and cytotrophoblast obtained through cytotrophoblast isolation technique provided purified cell samples for RNA and DNA extraction. Real-time PCR (rt-PCR) verified the presence and quantity of eNOS mRNA. In summary, the main findings of this thesis are heterogeneous methylation in first trimester compared to hypermethylation at term; greater eNOS expression and variable methylation in term syncytiotrophoblast compared to cytotrophoblast. A heterogeneous methylation pattern in eNOS has been identified in this study and recent stem cell studies in our lab, and we propose it represents plasticity in gene expression, particularly in early development.

During early mammalian embryogenesis, the embryonic genome undergoes critical reprogramming events that include changes in both DNA methylation and histone modifications necessary to control chromatin structure and thus, gene expression. Improper reprogramming of the epigenome during this window of development can lead to a vast number of imprinting anomalies, which are increased in children and livestock conceived in vitro. In the bovine, which closely resembles human preimplantation development, epigenetic changes occur from fertilization through the blastocyst stages. In particular, and concurrent with embryonic genome activation (EGA), de novo DNA methylation begins at the 8-cell stage. In order to explore the roles of histone-modifying enzymes during this crucial period of development, we characterized the transcript expression of several enzymes key enzymes across in vitro bovine preimplantation development using quantitative real-time PCR. Two of the 7 genes analyzed (Suz12 and Lsh) exhibited notable increases at the 8-16 cell stages, with basal levels observed both before and after this. These increases coincided with both EGA and de novo DNA methylation. We further explored their roles in bovine preimplantation embryos by knocking down expression via the use of gene-specific targeting siRNAs. Independent suppression of either Suz12 or Lsh via cytoplasmic microinjection of targeting siRNAs resulted in lower development rates (p < 0.0001), and poorer embryo quality of the morulas and blastocysts that survived. In addition, Suz12 suppression led to reductions in both H3K27 (p < 0.0001) and H3K9 (p = 0.07) trimethylation, and an increase in DNA methylation levels (p < 0.0001), as compared to the null-injected controls. Lsh suppression did not change H3K27, but led to a reduction in H3K9 trimethylation (p = 0.006) and an increase in DNA methylation (p < 0.0001). Clearly our data demonstrate that these epigenetic modifiers play a critical role in formation of the embryonic epigenome, but further research would be necessary in order to fully characterize gene activities during this developmental window.