This study examined the DNA replication timing patterns of endothelial cell (EC)-enriched genes. We especially focused on a unique set of EC-enriched mRNA transcripts that possess differentially methylated regions (DMRs) within proximal promoters. It was previously shown that this DNA methylation plays an important functional role in regulating EC-enriched patterns of gene expression. Since the maintenance of these silencing marks is necessary for the inheritance of cell identity, the cell should ensure the proper transmission of such marks during mitotic cell cycle. Here we show that EC-enriched genes with DMRs replicate early during S phase in both expressing and non-expressing cell types. EC-enriched genes that do not have DMRs followed the expected trend, being early replicating in expressing cell types and late in non-expressing cell types. The relationship between DNA replication and DNA methylation was also investigated. A delay between DNA replication and DNA methylation was observed.

Accumulated genetic and epigenetic abnormalities contribute to the development of colon cancer. We have shown that a combination of fish oil (containing decosahexaenoic acid, DHA, 22:6 n-3) and pectin (fermented to butyrate by colonic microflora) is protective against colon carcinogenesis in part by regulating the expression of genes involved in apoptosis, leading to apoptosis induction. To determine how FO/P enhances apoptosis, we measured the expression of genes involved in apoptosis. We performed a pathway analysis on differentially expressed genes identified at three times during colon tumorigenesis: initiation, aberrant crypt foci (ACF) formation, and tumor stage, and compared these results with phenotypic observations at those times. At initiation, FO/P down-regulated the expression of genes involved with cell adhesion and enhanced apoptosis compared with corn oil/cellulose (CO/C). At the ACF stage, expression of genes involved in cell cycle regulation was modulated by FO/P and proliferation was reduced in FO/P rats compared with CO/C rats. FO/P increased apoptosis and the expression of genes that promote apoptosis at the tumor endpoint compared with CO/C. We next determined if changes in expression of genes involved in apoptosis by FO/P are associated with changes in promoter methylation of a key apoptosis regulator, Bcl-2. Genomic DNA was isolated from carcinogen-induced colon tumors and non-involved tissues. FO/P increased Bcl-2 promoter methylation in tumor tissues and colonocyte apoptosis relative to those observed with CO/C. A negative correlation between Bcl-2 DNA methylation and Bcl-2 mRNA levels was observed in the tumors. Additionally, we examined gene specific promoter methylation of 24 apoptosis-related genes using human colon cancer cells. Cells were treated with DHA or linoleic acid (18:2 n-6), and select cultures were also treated with butyrate. The combination of DHA and butyrate led to a significant reduction in the methylation of pro-apoptotic genes and an increase in apoptosis. These data suggest that part of the mechanisms involved in the induction of apoptosis by FO/P may be through epigenetic regulation of genes involved in apoptosis throughout colon carcinogenesis.

Long terminal repeat (LTR) retrotransposons account for approximately 10% of mouse and 8% of human genomes and may play a role in modifying gene expression. Many species harbor retrotransposon families encompassing both autonomous and non-autonomous members. Specifically, the mouse Early Transposon (ETn) family members lack all retroviral genes but are transcriptionally and retrotranspositionally active, causing over 20 known insertional germline mutations. ETns owe their retrotransposition potential to proteins encoded by structurally intact MusD retrotransposons with whom they share LTRs. ETn elements are transcribed at a much higher level than MusD retrotransposons in embryos and undifferentiated cells, suggesting their evasion of host restriction mechanisms. However, mechanisms responsible for the replicative success of non-autonomous retrotransposon subfamilies over their coding-competent relatives are poorly understood. In the first stage of my research, I analyzed regulatory sequences in an ETn LTR responsible for its high promoter activity in the undifferentiated cell line P19. I found that three GC-boxes that may function as Sp1/Sp3 binding sites act synergistically and are indispensable for undifferentiated cell-specific promoter activity of the LTR. Sp1 binding partners may be responsible for the restricted ETn expression. Moreover, I have shown that unlike many retroviruses, ETn elements possess multiple transcription initiation sites and that they have amplified via intracellular retrotransposition in the P19 teratocarcinoma cell line. In the next step of my research, I performed analysis of epigenetic mechanisms as a means of ERV suppression. Specifically, I showed that in embryonic stem cells, autonomous MusD retrotransposons are epigenetically suppressed to a greater degree than non-autonomous ETn retrotransposons, illustrated by a higher level of DNA methylation and a lower level of active histone modifications. I hypothesize that MusD elements may be silenced by DNA methylation and repressive chromatin spreading into the LTR from the CpG-rich internal retroviral sequence absent in ETn elements. I propose that internal structure largely devoid of high CG content enables ETn elements to evade host-imposed transcriptional repression, contributing to their high mutagenic activity in the mouse germline.

There are two chief molecular pathways to sporadic colorectal cancer (CRC), the chromosomal instability (CIN) and the CpG island methylator phenotype (CIMP) pathways. A third pathway, the pure microsatellite instability pathway, is important in inherited CRC specifically hereditary non-polyposis colorectal cancer. The CIN pathway is characterized by an adenomatous pathological precursor, aneuploidy and microsatellite stability. CIMP pathway cancers, however, are frequently proximal, develop from serrated rather than adenomatous polyps and are strongly associated with BRAF mutation. The CIMP pathway is driven primarily by epigenetic rather than genetic instability. These pathway-specific molecular traits are evident within the pathological precursors to these cancers and thus pathway divergence must occur at the beginning of carcinogenesis or even before. Although DNA methylation is recognized as a key mechanism in colorectal carcinogenesis, relatively little is known about its pattern, regulation and relevance in normal colorectal mucosa. This PhD thesis characterized the profile of DNA methylation in the normal human colorectum and explored its associations with luminal, environmental, dietary and pathological factors. The genes methylated in CRC are characterized as “type A” (Age-related) genes and “type C” (Cancer-specific) genes. Generally, “type A” genes are methylated in both normal and neoplastic tissue with the degree of methylation proportional to the age of the tissue. The methylation of “type C” genes, however, is more specific for neoplastic tissue. The primary study recruited 166 patients undergoing colonoscopy. At colonoscopy, mucosal biopsies were taken from the caecum, transverse colon, sigmoid colon and rectum. DNA methylation was analysed by MethyLight at “type A” (ESR1, GATA5, HIC1, HPP1, SFRP1) and “type C” methylation markers (MGMT, MLH1, CDKN2A, MINT2, MINT31, IGF2, CACNA1G, NEUROG1, SOCS1, RUNX3). LINE-1 methylation was quantified by pyrosequencing. The last 5 “type C” markers comprise a CIMP panel used to identify CIMP cancers. Mean “type A” and CIMP panel methylation Z-scores were calculated. The PMR for each of these CpG island loci was compared to patient age, gender, previous colorectal polyps, smoking history and the presence of concomitant pathology. Most “type A” genes demonstrated strong and direct correlations between methylation and patient age (e.g. ESR1, ρ=0.66, p<0.0001) and had greater methylation within the distal compared to the proximal colorectum (e.g. ESR1, p<0.0001). On multivariate analysis, the mucosal “type A” methylation Z-score had a strong, independent, inverse association with the diagnosis of colorectal adenomas (OR=0.23, p<0.001), the precursor to CIN cancers. The mean CIMP methylation Z-score in normal mucosa, however, was significantly and independently associated with advanced proximal serrated polyps (OR=5.1, p=0.009), the precursor to CIMP cancers. The luminal and epithelial associations with colorectal methylation were explored by a randomized, double-blind, placebo-controlled trial. This experiment was undertaken to determine whether dietary supplementation could modulate epithelial DNA methylation. In addition, the study was designed to evaluate intra-individual reproducibility of the MethyLight technique. The study consisted of a 4 week cross-over trial of resistant starch and Bifidobacterium lactis either alone or as a combined synbiotic preparation, in 20 human volunteers. Rectal biopsies, faeces and serum were collected. Rectal mucosal endpoints included DNA methylation at the CpG island loci and LINE-1, epithelial proliferation (Ki67 immunohistochemistry) and crypt cellularity. Faecal short-chain fatty acid concentrations, pH, ammonia and microbiological profiles (by DGGE and sequencing) were examined. The synbiotic intervention fostered a significantly different faecal stream bacterial community than either the prebiotic or the probiotic interventions alone, but did not show any significant associations with the epithelial or luminal parameters. To explore possible associations between luminal and epithelial parameters and mucosal DNA methylation, the baseline indices were further analysed. There was a strong positive correlation between baseline epithelial proliferation and “type A” marker methylation (ρ = 0.7, p = 0.0001). Thus, “type A” methylation may reflect the cellular age or mitotic burden of a tissue, which is a function of both time and cell turnover. There were consistent inverse trends evident between faecal short-chain fatty acid levels and rectal mucosal DNA methylation. This PhD project found that DNA methylation within the normal colorectal mucosa varied with patient age and region and was strongly associated with the development of pathway-specific pathology, suggesting that the background colorectal field may predict both the at-risk patients and at-risk pathways. Diet and the luminal environment more broadly may influence levels of DNA methylation in the colorectal mucosa and could help to explain regional patterns of colorectal DNA methylation.

Thesis (Ph.D.). / Written for the Dept. of Pharmacology and Therapeutics. Title from title page of PDF (viewed 2008/05/09). Includes bibliographical references.

Thesis (Ph.D.). / Written for the Dept. of Pharmacology and Therapeutics. Title from title page of PDF (viewed 2008/07/23). Includes bibliographical references.

Dissertation (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Vita. Bibliography: p.215-229

Thesis (Ph.D.)--Medical University of Ohio, 2006. / "In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Medical Sciences." Major advisor: Michael A. Pereira. Includes abstract. Document formatted into pages: v, 152 p. Title from title page of PDF document. Title at ETD Web site: Involvement of DNA methylation and CpG endonuclease activity in environmental carcinogenesis and cancer chemoprevention. Bibliography: pages 65-66, 90-92, 123-125, 137-150.

Trimethylation of histone H3 lysine 9 (H3K9me3) and DNA methylation mark heterochromatin, contributing to gene silencing and normal cellular functions. My research investigated the control of H3K9me3 and DNA methylation in the filamentous fungus Neurospora crassa. The H3K9 methyltransferase complex, DCDC, consists of DIM-5, DIM-7, DIM-9, DDB1, and CUL4. Each component of DCDC is required for H3K9me3. The DIM-9/DDB1/CUL4 subunits are reminiscent of known cullin E3 ubiquitin ligases. I showed that core features of CUL4-based E3 ubiquitin ligases are not required for H3K9me3 and DNA methylation in Neurospora. H3K9me3 is bound by heterochromatin protein 1 (HP1) to recruit the DIM-2 DNA methyltransferase and the HCHC histone deacetylase complex. HCHC consists of HP1, CDP-2, HDA-1, and CHAP. Both HP1 and CDP-2 harbor conserved chromodomains that bind H3K9me3, and CHAP contains two putative AT-hook domains that bind A:T-rich DNA. To test the contributions of these domains to HCHC function, I deleted the chromodomains of HP1 and CDP-2. Deletion of the HP1 chromodomain resulted in a reduction of DNA methylation, which was not exacerbated by deletion of the CDP-2 chromodomain. A strain with deletions of chap and the HP1 chromodomain showed a DNA methylation phenotype comparable to the loss of the HDA-1 catalytic subunit. These findings support a model in which recognition of H3K9me3 and A:T-rich DNA by HP1 and CHAP, respectively, are required for proper HCHC function. To examine the relationships between H3K9me3, DNA methylation, and histone acetylation, I utilized in vivo protein tethering of core heterochromatin components. The requirement of DIM-7 for native heterochromatin, previously implicated in localizing the H3K9 methyltransferase DIM-5, was not bypassed by DIM-5 tethering, indicating that DIM-7 has additional roles within the DCDC. Artificial localization of the HCHC histone deacetylase, by tethering HP1 or HDA-1, resulted in induction of H3K9me3, DNA methylation, and gene silencing, but silencing did not require H3K9me3 or DNA methylation. HCHC-mediated establishment of H3K9me3 was not required for de novo heterochromatin formation at native heterochromatic loci suggesting a role in heterochromatin spreading. Together, this work implicates HDA-1 activity as a key driver of heterochromatin spreading and silencing. This dissertation includes previously published co-authored material.

DNA methylation is an epigenetic mark that is deposited throughout the genome of mammals and plays an important role in the maintenance of transcriptionally repressive states across cell divisions. There are two major mechanisms by which DNA methylation has been proposed to act: one involves the recognition of the mark by protein complexes containing histone deacetylases (HDACs) that can remodel the local chromatin. Alternatively, methylation has been suggested to directly affect the interaction between transcription factors and their cognate binding sequence. The aim of this research was to determine the contributions of these two mechanisms in cells. The importance of HDAC activity in mediating DNA methylation-dependent transcriptional repression was assessed by comparing the genes and retrotransposons that are upregulated in response to DNA methylation loss or the disruption of HDAC activity. To this purpose, we performed whole-genome transcriptional analysis in wild type and DNA methylation-deficient mouse embryonic stem cells (DNMT.TKO mESCs) in the presence and absence of the HDAC inhibitor trichostatin A. Our data suggests that there are few genes whose repression is solely dependent on the recruitment of HDACs by DNA methylation in mESCs. Rather it appears that DNA methylation and HDAC-mediated silencing represent two independent layers of repression that converge at certain transcriptional elements. To investigate the contribution of DNA methylation on the genome-wide occupancy of transcription factors, we compared the global chromatin accessibility landscape and the binding profile of candidate transcription factors in the absence or presence of DNA methylation. We found that loss of DNA methylation associates with localised gains in accessibility, some of which can be linked to the novel binding of transcription factors such as GABPA, MAX, NRF1 and YY1. Altogether, our results present new insights into the interplay between DNA methylation and histone deacetylation and their impact on the localisation of transcription factors from different families.