PI3K signaling in pancreatic β cells has been shown to be important in modulating β cell mass and function under basal condition. Evidence suggests that a specific group of insulin promoter-expressing neurons also modulates glucose metabolism and energy homeostasis through their PI3K signaling. Thus we hypothesize that PI3K activation via PTEN deletion under the control of rat insulin promoter (RIP) in pancreatic β cells and RIP-expressing neurons will protect against hyperglycemia and diabetes in experimentally induced mouse models of type 2 diabetes. In Chapter IV, we showed that RIP-mediated PTEN deletion in pancreatic β cells led to PI3K activation and subsequent increased β cell mass and function, thus protected the mice from high fat diet (HFD)-induced diabetes. Furthermore in the absence of global leptin signaling, β cell-specific PTEN deletion maintained β cell function in the setting of severe insulin resistance, therefore prevented diabetes development. Interestingly, RIP-mediated PTEN deletion also resulted in increased peripheral insulin sensitivity due to PI3K activation in central nervous system. In Chapter V, we showed this increased insulin sensitivity was maintained after HFD feeding, which also contributed to the protection against diabetes. These mice also showed increased visceral adipogenesis and subcutaneous adiposity on HFD, which were dramatically attenuated in the absence of leptin signaling, indicated the essential role of peripheral leptin action in mediating the insulin sensitive phenotype from neuronal RIP PTEN deletion. Finally, we demonstrated that the insulin sensitizing phenotype in these mice was not mediated through ventromedial hypothalamic nuclei (VMH), such that VMH-specific PTEN deletion did not alter energy homeostasis or glucose metabolism. Together, the data from this thesis points to an inhibitory role of PTEN in both central nervous system and pancreatic β cells in glycemic control. Therefore, PTEN may represent a potential target for diabetes prevention and treatment.

Promoter hypermethylation mediated gene silencing is a frequent epigenetic finding in many cancers that affects genes known to have important roles in several aspects of cell biology. Hematological malignancies have been reported to harbor multiple genes aberrantly silenced by promoter hypermethylation and as a result, cytosine analogs known to inhibit the DNA methylation machinery are currently being evaluated in clinical trials. As such, the general goal of this thesis was to identify genes silenced by promoter hypermethylation in human acute myeloid leukemia (AML) and to study the mechanism of promoter hypermethylation mediated gene silencing. Interestingly, the cyclin dependent kinase inhibitor p15 was found to be methylated at a high frequency in AML patients and cell lines in association with a lack of detectable p15 mRNA. Treatment with the cytosine analog 5-Aza-2-deoxycytidine (5-Aza-dC) in vitro resulted in promoter demethylation and p15 mRNA re-expression, which was associated with a release of a transcriptionally repressive complex at the p15 promoter. Importantly, 5-Aza-dC treatment also reversed specific histone amino-terminal modifications at the p15 promoter which are normally associated with transcriptionally inactive chromatin regions, implicating chromatin remodeling in promoter hypermethylation mediated gene silencing. The recently discovered DNA methylation inhibitor, zebularine considered more stable than 5-Aza-dC was also able to reconstitute p15 mRNA in vitro in association with promoter demethylation, regional enrichment of histone acetylation, and growth inhibition. To identify novel genes silenced by promoter hypermethylation in AML, cDNA microarray analysis was employed following in vitro pharmacological inhibition of DNA methylation and histone deacetylation. Of note, four genes from the metallothionein family of cysteine rich small molecules were consistently upregulated following drug treatment and further evaluation identified the gene MT1H to be hypermethylated at a high frequency in AML patients and cell lines. Taken together, the data suggests that aberrant promoter hypermethylation mediated gene silencing occurs in multiple genes from different gene families during the molecular pathogenesis of human AML. Furthermore, the mechanism of promoter methylation mediated transcriptional silencing acts in concert with specific histone modifications which, importantly, can be reversed by treatment with pharmacological inhibitors of DNA methylation.

<p>Transcription initiation is a key component in the regulation of gene expression. Recent high-throughput sequencing techniques have enhanced our understanding of mammalian transcription by revealing narrow and broad patterns of transcription start sites (TSSs). Transcription initiation is central to the determination of condition specificity, as distinct repertoires of transcription factors (TFs) that assist in the recruitment of the RNA polymerase II to the DNA are present under different conditions. However, our understanding of the presence and spatiotemporal architecture of the promoter patterns in the fruit fly remains in its infancy. Nucleosome organization and transcription initiation have been considered hallmarks of gene expression, but their cooperative regulation is also not yet understood.</p> <p>In this work, we applied a hierarchical clustering strategy on available 5' expressed sequence tags (ESTs), and developed an improved paired-end sequencing strategy to explore the transcription initiation landscape of the D.melanogaster genome. We distinguished three initiation patterns: 'Peaked or Narrow Peak TSSs&#8219;, 'Broad Peak TSSs&#8219;, and 'Broad TSS cluster groups or Weak Peak TSSs&#8219;. The promoters of peaked TSSs contained the location specific sequence elements, and were bound by TATA Binding Protein (TBP), while the promoters of broad TSS cluster groups were associated with non-location-specific elements, and were bound by the TATA-box related Factor 2 (TRF2).</p> <p>Available ESTs and a tiling array time series enabled us to show that TSSs had distinct associations to conditions, and temporal patterns of embryonic activity differed across the majority of alternative promoters. Peaked promoters had an association to maternally inherited transcripts, and broad TSS cluster group promoters were more highly associated to zygotic utilization. The paired-end sequencing strategy identified a large number of 5' capped transcripts originating from coding exons that were unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications.</p> <p>We applied an innovative search program called FREE to embryo, head, and testes specific core promoter sequences and identified 123 motifs: 16 novel and 107 supported by other motif sources. Motifs in the embryo specific core promoters were found at location hotspots from the TSS. A family of oligos was discovered that matched the Pause Button motif that is associated with RNA pol II stalling.</p> <p>Lastly, we analyzed nucleosome organization, chromatin structure, and insulators across the three promoter patterns in the fruit fly and human genomes. The WP promoters showed higher associations with H2A.Z, DNase Hypersensitivity Sites (DHS), H3K4 methylations, and Class I insulators CTCF/BEAF32/CP190. Conversely, NP promoters had higher associations with polII and GAF binding. BP promoters exhibited a combination of features from both promoter patterns. Our study provides a comprehensive map of initiation sites and the conditions under which they are utilized in D. melanogaster. The presence of promoter specific histone replacements, chromatin modifications, and insulator elements support the existence of two divergent strategies of transcriptional regulation in higher eukaryotes. Together, these data illustrate the complex regulatory code of transcription initiation.</p> / Dissertation

Reversion-inducing cysteine-rich with Kazal motif (RECK) is a cell surface anchoring protein, which known for the ability to inhibit matrix metalloproteinases (MMPs) and participate in angiogenesis regulation. The inhibition of membrane type-1 matrix metalloproteinase (MT1-MMP), MMP-2, MMP-7 and, MMP-9 by RECK has been demonstrated. Our previous studies show that RECK expression is suppressed by Ras and Her-2/neu oncogene. In addition, oncogenic Ras activates downstream ERK signaling pathway to increase Sp1/HDAC promoter binding affinity which results in reduction of RECK gene transcription and increase of tumor progression and metastasis. From the clinical investigation, RECK expression is down-regulated in a number of cancer types. In breast cancer, RECK expression is associated with the prognosis of the patients. Recently, single nucleotide polymorphisms (SNPs) of RECK promoter have been suggested to be linked with survival rate and prognosis of breast cancer patients. Whether SNP of the RECK promoter has any effect on RECK expression and its clinical significance is still unclear. . In this study, we investigate -402 SNP at RECK promoter and find this SNP directly affects RECK expression through progesterone receptor binding. Additionally, we also address the -402 SNP in the sample collected from patients and analyze its association with clinicopathological parameters to clarify its clinical significance. Our results suggest that RECK SNP may be an valuable prognosis factor for breast cancer.

Gene expression analyses using native populations can provide information on the genetic and molecular mechanisms that determine intraspecific variation and contribute to the understanding of plant development and adaptation in multiple ways. Using quantitative real time – polymerase chain reaction (qRT-PCR), we analyzed the expression of 111 genes with probable roles in wood development in 400 loblolly pine individuals belonging to a population covering much of the natural range. Association mapping techniques are increasingly being used in plants to dissect complex genetic traits and identify genes responsible for the quantitative variation of these traits. We used candidate-gene based association studies to associate single nucleotide polymorphisms (SNPs) in candidate genes with the variation in gene expression. The specific objectives established for this study were to study natural variation in expression of xylem development genes in loblolly pine (Pinus taeda L.) using qRT-PCR, to associate SNPs in candidate genes with the variation in gene expression using candidate-gene based association analyses and to detect loblolly pine promoter polymorphisms and study their effect on gene expression. Out of the 111 genes analyzed using qRT-PCR, there were significant differences in expression among clones for 106 genes. Candidate-gene based association studies were performed between 3937 single nucleotide polymorphisms (SNPs) and gene expression to associate SNPs in candidate genes with the variation in gene expression. To the best of our knowledge, this is the first association genetic study where expression of a large number of genes, analyzed in a natural population, has been the phenotypic trait of interest. We cloned and sequenced promoters of 19 genes, 16 of which are transcription factors involved in wood development and drought response. SNP discovery was done in 13 of these promoters using a panel of 24 loblolly pine clones (unique genotypes). SNP genotyping is underway in the entire association population and association analyses will be done to study the effects of promoter SNPs on gene expression. The results from this project are promising and once these associations have been tested and proved, we believe that they will help in our understanding of the genetics of complex traits.

名古屋大学博士学位論文 学位の種類:博士（医療技術学） (課程) 学位授与年月日　平成22年3月25日

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Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that affects several organs in the human body including the brain, heart, kidneys, eyes, skin, spleen, liver and lungs [Roach, et al., 1999]. TSC is characterized by hamartomas that rarely progress to malignancy in the affected organs. Clinical symptoms of TSC include cortical tubers and subependymal nodules in the brain, seizures, mental retardation, ungual and periungual fibromas, angiofibromas of the face, and angiomyolipomas in the kidneys [Roach, et al., 1999]. TSC displays genetic heterogeneity with two known loci: TSC1 on chromosome 9q34 [Fryer, et al., 1987a] and TSC2 on chromosome 16p13.3 [Kandt, et al., 1992]. The genes for both loci have been isolated and characterized [ The European Chromosome 16 Tuberous Sclerosis Consortium, 1993; van Slegtenhorst, et al., 1997]. The TSC1 gene contains 21 coding and two non-coding exons and encodes for an 8.6 kb mRNA. It spans 45 kb of genomic DNA and codes for hamartin, a 1,164 amino acid protein of 130 kDa. The TSC2 encodes for a 200 kDa protein, tuberin, and spans 43 kb of genomic DNA. The TSC2 gene consists of 41 coding exons and one non-coding exon and encodes for a 5.4 kb mRNA. Both genes are known to function as tumor suppressors [Carbonara, et al., 1994; Green, et al., 1994a; Green, et al., 1994b]. Several groups have performed mutation analysis of both the genes in patients mainly from the western and Japanese populations. A total of 133 mutations in the TSC1 gene and 350 mutations in the TSC2 gene have been reported so far (Human Gene Mutation Database; http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html). However, there is no report on the mutation analysis of the TSC genes from the Indian population. In this study, a total of 24 TSC cases were ascertained from the Indian population and a comprehensive mutation analysis of both the TSC genes was carried out in them to understand the function of both the genes, to locate important domains and also to find the mutational hotspots for molecular diagnosis of TSC. A total of 12 mutations, including seven novel mutations were identified. It was also shown that the most recurrent mutations (c.1831C>T and c.1832G>A) are, in part, due to methylation of the CpG dinucleotide. There are still 15-25% TSC cases in western populations with undetected mutations [Cheadle, et al., 2000a]. Further, there are familial TSC cases linked either to the TSC1 on 9q34 or TSC2 on 16p13.3 which fail to show any mutations in the coding sequences of both genes [Cheadle, et al., 2000a]. The failure to detect mutations in these cases could be due to several reasons. First, it could be that the mutations lie in the regulatory regions (promoters and enhancers) of both the genes, presently unidentified for the TSC1 gene [Cheadle, et al., 2000a]. Second, it is possible that the mutations lie outside of the coding sequences, within intronic sequences, or in the 5’ or 3’ UTRs [Cheadle, et al., 2000a]. Third, it may be due to the limitation of the techniques used to identify mutations [Cheadle, et al., 2000a]. In order to look for mutations in the promoter, the TSC1 gene promoter was characterized using luciferase reporter gene transfection assay. The promoter for the TSC2 gene is known [Kobayashi, et al., 1997]. The promoters of both TSC1 and TSC2 genes were sequenced in all the 24 cases to look for mutations. During the characterization of the TSC1 gene promoter, a novel isoform involving the non-coding exon 1 of the TSC1 gene was discovered serendipitously.

Thesis (Ph. D.)--University of Missouri--Columbia, 2000. / "December 2000." Typescript. Vita. Includes bibliographical references (leaves 133-147). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri--Columbia, 2001. / "August 2001." Typescript. Vita. Includes bibliographical references (leaves 135-149). Also available on the Internet.