Russell O. Pieper

Methylation-related chromatin structure is associated with exclusion of transcription factors from and suppressed expression of the O-6-methylguanine DNA methyltransferase gene in human glioma cell lines.

There is considerable interest in identifying factors responsible for expression of the O-6-methylguanine DNA methyltransferase (MGMT) gene, as MGMT is a major determinant in the response of glioma cells to the chemotherapeutic agent 1,3 bis(2-chloroethyl)-1-nitrosourea. Recently we have shown that MGMT expression is correlated in a direct, graded fashion with methylation in the body of the MGMT gene and in an inverse, graded fashion with promoter methylation in human glioma cell lines. To determine if promoter methylation is an important component of MGMT expression, this study addressed the complex interactions between methylation, chromatin structure, and in vivo transcription factor occupancy in the MGMT promoter of glioma cell lines with different levels of MGMT expression. Our results show that the basal promoter in MGMT-expressing glioma cell lines, which is 100% unmethylated, was very accessible to restriction enzymes at all sites tested, suggesting that this region may be nucleosome free. The basal promoter in glioma cells with minimal MGMT expression, however, which is 75% unmethylated, was much less accessible, and the basal promoter in nonexpressing cells, which is 50% unmethylated, was entirely inaccessible to restriction enzymes. Despite the presence of the relevant transcription factors in all cell lines examined, in vivo footprinting showed DNA-protein interactions at six Sp1 binding sites and one novel binding site in MGMT-expressing cell lines but no such interactions in nonexpressors. We conclude that in contrast to findings of previous in vitro studies, Sp1 is an important component of MGMT transcription. These correlations also strongly suggest that methylation and chromatin structure, by determining whether Sp1 and other transcription factors can access the MGMT promoter, set the transcriptional state of the MGMT gene.

Methylation of CpG Island Transcription Factor Binding Sites Is Unnecessary for Aberrant Silencing of the Human MGMT Gene

Aberrant transcriptional inactivation of the non-X-linked human O-6-methylguanine DNA methyltransferase (MGMT) gene has been associated with loss of open chromatin structure and increases in cytosine methylation in the Sp1-binding region of the 5′-CpG island of the gene. To examine the necessity of these events for gene silencing, we have isolated and characterized a subline of human MGMT+ T98G glioma cells. The subline, T98Gs, does not express MGMT activity or MGMT mRNA, and exhibits no in vivo DNA-protein interactions at Sp1-like binding sites in the MGMT 5′-CpG island. While the MGMT CpG island is less accessible to exogenously added restriction enzymes in T98Gs nuclei than in T98G nuclei, it is similarly methylated in both T98G and T98Gs cell lines 5′ and 3′ to the transcription factor binding sites, and similarly unmethylated in the region encompassing the binding sites. Inappropriate transcriptional inactivation of MGMT, therefore, does not require methylation of transcription factor binding sites within the 5′-CpG island. Rather, MGMT gene silencing and transcription factor exclusion from T98Gs MGMT CpG island binding sites is most closely associated with condensed chromatin structure, which is in turn indirectly influenced by distant sites of methylation.

Aberrant silencing of the CpG island-containing human O6-methylguanine DNA methyltransferase gene is associated with the loss of nucleosome-like positioning.

Tumor-associated aberrant silencing of CpG island-containing genes has been correlated with increased cytosine methylation, a closed chromatin structure, and exclusion of transcription factor binding in the CpG island/promoter regions of affected genes. Given the lack of understanding of what constitutes a closed chromatin structure in CpG islands, however, it has been difficult to assess the relationship among cytosine methylation, chromatin structure, and inappropriate gene silencing. In this study, nuclease accessibility analysis was used to more clearly define the chromatin structure in the CpG island of the human O6-methylguanine DNA methyltransferase (MGMT) gene. Chromatin structure was then related to in vivo DNA-protein interactions and cytosine methylation status of the MGMT CpG island in human glioma cells varying in MGMT expression. The results of these studies indicated that the open chromatin structure associated with the MGMT CpG island in MGMT+ cells consisted of an approximately 250-bp transcription factor-binding, nuclease-accessible, nucleosome-free region of DNA, whose formation was associated with at least four flanking, precisely positioned nucleosome-like structures. In MGMT- cells, this precise nucleosomal array was lost and was replaced by randomly positioned nucleosomes (i.e., the closed chromatin structure), regardless of whether methylation of the CpG island was spread over the entire island or limited to regions outside the transcription factor binding region. These results suggest that CpG islands facilitate the expression of housekeeping genes by facilitating nucleosomal positioning and that the conditions that alter the formation of this array (such as perhaps methylation) may indirectly affect CpG island-containing gene expression.

Comparison of O-6-methylguanine DNA methyltransferase (MGMT) mRNA levels in Mer+ and Mer- human tumor cell lines containing the MGMT gene by the polymerase chain reaction technique.

O-6-Alkylguanine is a mutagenic and carcinogenic DNA lesion induced by a variety of alkylating agents, including the chloroethylnitrosoureas. The lesion is repaired by the alkyl-accepting suicide enzyme O-6-methylguanine DNA methyltransferase (MGMT). Approximately 25% of cell lines derived from human tumors are phenotypically deficient in this enzyme and are described as Mer-. Recent cloning of the human MGMT cDNA (Tano, K.; Shiota, S.; Collier, J.; Foote, R.S.; Mitra, S. Proc. Natl. Acad. Sci. USA 87:686-690; 1990) has allowed for a more detailed analysis of the basis of the Mer- phenotype in human Mer- tumor cell lines. Using the polymerase chain reaction (PCR) technique, an MGMT cDNA probe based on the published sequence was generated. The probe and the PCR technique were then used to analyze the presence and expression of the MGMT gene in two Mer+ and four Mer- lines, including one SV40-transformed Mer- line and three Mer- human tumor cell lines. The data demonstrate that while all six cell lines contained a relatively nonamplified, nonrearranged MGMT gene, Mer- lines contained levels of MGMT mRNA detectable only by PCR analysis. Of the three Mer- tumor cell lines examined, two (COLO 320 HSR, A1235) contained MGMT mRNA levels that were four to five orders of magnitude lower than that of the prototype Mer+ tumor line (HT-29), while one (BE) contained no consistently detectable MGMT mRNA. These results suggest that in the human Mer- tumor lines tested, the Mer- phenotype was mediated by a severe reduction in MGMT mRNA levels, despite the presence of the MGMT gene.

Direct correlation between methylation status and expression of the human O-6-methylguanine DNA methyltransferase gene

To assess the role of DNA cytosine methylation in the expression of the O-6-methylguanine DNA methyltransferase (MGMT) gene, the methylation status of selected CpG-containing dinucleotides in and surrounding the coding regions of the gene were examined and correlated with steady state expression of MGMT mRNA in 13 human cell lines. Additionally, tumor cells which exhibited very high levels of MGMT expression were chronically exposed to 5-azacytidine to assess the effects of changes in gene methylation on MGMT expression. Results of these studies demonstrate that the degree of methylation of multiple MGMT gene regions correlates with gene expression, but in a direct rather than an inverse fashion, and that 5-azacytidine-induced demethylation of the MGMT gene correlates with a significant reduction, rather than induction, of MGMT steady-state mRNA expression. These results suggest a unique, potentially alterable methylation-related regulatory mechanism for the MGMT gene.

DNA-damaging and transcription-terminating lesions induced by AF64A in vitro.

Abstract: Although immediate cholinergic deficits produced by AF64A can be explained adequately by inhibition of enzymes involved in acetylcholine metabolism, the structural similarity of AF64A to a number of DNA‐damaging anti‐tumor agents suggested that the observed long‐term cholin‐ergic deficits may involve damage to the cells informational molecules. This study was initiated to determine if AF64A can damage DNA and prematurely terminate RNA transcription in vitro, and to produce cytotoxic and DNA damaging effects in cells exposed to the drug in vivo. The ability of AF64A to produce N‐7 guanine alkylations in DNA in vitro was assessed using a modified Maxam and Gilbert DNA sequencing technique, and the ability of AF64A to terminate RNA transcription was assessed by an in vitro RNA transcription system. AF64A was capable of producing extensive dose‐dependent N‐7 guanine alkylations in DNA fragments exposed to AF64A in vitro, although no sequence specificity of AF64A attack could be discerned. Furthermore, AF64A was able to produce RNA transcription‐terminating lesions in vitro, also in a dose‐dependent fashion. Transcription of AF64A‐damaged DNA resulted in RNA molecules terminated not at every alkylated guanine, but at various discrete sites along the DNA template. AF64A was also found to be cytotoxic in a dose‐dependent manner in cultured mouse leukemia L1210 cells. The induced cytotoxicity was accompanied by DNA lesions which were detected as DNA single strand breaks using the DNA alkaline elution technique. The results of these experiments support the hypothesis that AF64A may alter the structure and function of cellular DNA and may help explain the observed long‐term cholinergic deficits.

Chapter 2 – Molecular and Cell Biology

The Department of Molecular and Cell Biology offers a program of graduate study leading to the Ph.D. in molecular and cell biology. This program provides advanced training in the research methods and concepts of the study of the molecular structures and processes of cellular life. The training is intellectually focused, but at the same time offers an unusually wide range of opportunities for varied disciplinary specialization.