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Embryogenesis in plants, as in animals, requires the regulated expression of sets of genes involved in developmental processes. To gain insight into the processes regulating gene expression during embryogenesis differential screening was used to identify embryo-specific sequences in a cDNA library constructed from Zea mays embryo RNA. Four embryo-specific sequences and one constitutive sequence were characterized further by RNA blot hybridization and DNA sequence determination. The constitutive sequence and two of the embryo-specific sequences were found to encode parts of the previously-reported chloroplast 23S rRNA, Oleosin KD-18, and RAB-17 genes. Two sequences, named Emb5 and Emb564, were found to encode novel maize homologs of a gene expressed during late embryogenesis in a wide range of seed plants. These 5 genes exhibited differential temporal and spatial accumulation during development. Moreover, analysis of RNA from cultured embryos suggested that 4 of these genes were regulated by abscisic acid. The ABA-responsive genes could be divided into 3 classes, based on their developmental expression, tissue-specificity, and sensitivity to ABA. Antibodies raised against a $ beta$-galactosidase:EMB564 fusion protein were used to analyze the accumulation of the EMB564 and/or EMB5 proteins. These polyclonal antibodies detected one or several polypeptides with a molecular weight less than 14 kD which exhibited patterns of developmental accumulation and regulation similar to Emb5 and Emb564 transcripts.

Troponin I (TnI), like many striated muscle contractile proteins, consists of multiple isoforms encoded by a multigene family whose members are differentially expressed in the different striated muscle cell types. Two TnI genes, TnIfast and TnIslow, are expressed in skeletal muscle the former in fast muscle fibers, the latter in slow fibers. The tissue- and fiber-type-specificities of the TnI fast and slow genes are driven by transcriptional enhancer elements: a Slow Upstream Regulatory Element (SURE) upstream of the TnIslow gene and a fast Intronic Regulatory Element (IRE) within the first intron of the TnIfast gene. Within the 144 bp IRE, there are 4 known cis elements, and the aim of this work was to initiate the studies to map the element(s) that are chiefly responsible for directing the fast-fiber-specificity of IRE-driven gene expression. This was approached by making IRE end-deletion constructs lacking either the left-most or right-most IRE cis-element. These IRE derivatives were coupled to a reporter gene consisting of a minimal (enhancer-dependent) TnIfast promoter linked to E. coli beta-galactosidase coding sequences. The transcriptional activity of these constructs was first evaluated in cell culture transfection experiments, and then by in vivo gene transfer into adult mouse skeletal muscles. The conclusion of these experiments was that fast-fiber-specificity of IRE-driven gene expression resides in the left-most 30 bp of the IRE, a region including an E-box binding site for myogenic regulatory factors of the MyoD family.

Quantitative analysis of Drosophila melanogaster gap gene expression data reveals valuable information about the nature and strengths of interactions in the gap gene network. We first explore different models for fitting the spatiotemporal gene expression data of Drosophila gap gene system and validate our results by computational analysis and comparison with the existing literature. A fundamental problem in systems biology is to associate these results with the inherent cause of gene regulation, namely the binding of the transcription factors (TF) to their respective binding sites. In order to relate these expression-based estimates of gap gene regulation with the sequence-based information of TF binding site composition, we also explore two related problems of (i) finding a set of regulatory weights that is proportional to the binding site occupancy matrix of the transcription factors in current literature and (ii) finding a set of position weight matrices of the TFs that produce a new binding site occupancy matrix showing a greater level of proportionality with our regulatory weights. Our solution to the first problem yielded a regulatory weight matrix incapable of explaining the true causes of gene expression profile despite its relative numerical accuracy in predicting the gene expressions. On the other hand, the second optimization problem could be solved up to a reasonable level of accuracy, but further analysis on the result demonstrated that this optimization problem may be under-constrained. We devise a simple regularization strategy that helps us to reduce the under-constrained nature of the problem.

It is well known that DNA methylation in gene promoter regions inhibits gene transcription and that tissue-specific gene expression is partially under the control of this transcription regulatory mechanism. In this study, bovine mammary gland tissues were collected from individual animals in lactating and non-lactating stages to investigate the DNA methylation patterns in the kappa-casein gene and alpha-lactalbumin gene core promoter regions using the bisulphite treatment in combination with polymerase chain reaction (PCR) sequencing. Different methylation status of each sample was classified into three categories, namely methylation at known transcription factor binding domains, methylation at core promoter non-binding domains and the absence of cytosine methylation. Real-time quantitative PCR was used to quantify the transcription levels of the kappa-casein and alpha-lactalbumin genes from the collected samples. A comparative method was used and fold-change values were calculated based on the comparison of the normalized threshold values of samples from different physiological stages as well as on various methylation patterns observed in their core promoter regions. Statistical analyses showed that the expressions of the kappa-casein and alpha-lactalbumin genes were significantly different in lactating and non-lactating mammary gland tissues. The methylation observed in the core promoter region of bovine alpha-lactalbumin gene was found to be associated with its gene expression. On the other hand, the methylation found in the core promoter region of bovine kappa-casein gene did not have any effect on its gene transcript levels.

Previous studies have shown that transcriptional differences in the orf224-atp6 mitochondrial gene region are correlated with fertility restoration of the pol CMS trait by the dominant nuclear Rfp gene in Brassica napus. Recently, the recessive rfp allele, or a tightly linked gene, was found to act as a dominant gene, designated Mmt, in controlling the production of additional, smaller transcripts of two other mitochondrial loci. The results presented in this thesis reveal that Mmt-specific transcripts lack sequences found at the $5 sp prime$ end of the full-length transcripts of these loci and contain a common sequence, UUGUGG, which maps immediately downstream of their $5 sp prime$ termini. A similar sequence, UUGUUG, is found within orf224 downstream of the major Rfp-specific $5 sp prime$ transcript terminus; these hexanucleotide sequences may serve as recognition motifs in the generation of Mmt- and Rfp-specific transcripts. These results suggest that Rfp/Mmt is a novel nuclear locus affecting the expression of multiple mitochondrial gene regions, with different alleles or haplotypes affecting different mitochondrial genes.

SHP-1, a SH2 domain-containing protein-tyrosine phosphatase, plays a critical role in regulation of cell signal transduction. SHP-1 is expressed not only in cells of hematopoietic lineages, but also in many non-hematopoietic cells under the control of a tissue-specific promoter, P1. In the first part of this thesis, the activity of the P1 promoter was analyzed in a region spanning 3.5 kb upstream of the major transcription start site in non-hematopoietic MCF-7 cells. An upstream Sp1 element (-126 to -118) positively regulated this TATA-box-lacking promoter. Two inverted CCAAT-elements (-332 to -328 and -66 to -62) played the important, but opposite roles, and transcription factor NF-Y predominantly bound to the two CCAAT-elements to control SHP-1 gene expression. Furthermore, incubation of MCF7 cells with 100 ng/ml trichostatin A (TSA), an inhibitor of histone deacetylase, significantly increased the activity of the P1 promoter. Mutation in the proximal CCAAT-element, however, eliminated the activating effect of trichostatin A on the promoter. In the second part of this thesis, the mechanism by which SHP-1 modulated TSA-induced MCF-7 cell apoptosis was elucidated. Analysis of cell survival signaling pathways revealed that overexpression of SHP-1 inactivated Akt ( eg. diminished phosphorylation resulted from modulation of PI3K expression) and increased caspase-9 and caspase-7 activities. Interestingly, a parallel decrease was observed in the phosphorylation of the pro-apoptosic Bcl-2 family member Bad at Ser112 as well as in the stress-activated MAP kinase JNK, both of which have been implicated in Akt- as well as ERK1/2-mediated functions. It was not surprising, therefore, to detect a diminished level of phosphorylated ERK1/2 in SHP-1-overexpressiog cells and that this effect was exacerbated by TSA treatment. Taken together, the data presented in this thesis suggest that SHP-1 expression is regulated by Sp1 and NF-Y factors, and SHP-1 sensitizes MCF-7 cells to TS

miRNAs are short, non-coding RNA molecules that regulate gene expression posttranscriptionally through inhibition of translation and/or mRNA degradation. Mammalian development is a complex series of developmental transitions, which relies on accurate spatial and temporal regulation of gene expression and we are interested in the role that miRNAs may play in these developmental transitions. An initial objective was to establish which, if any, miRNAs were dynamically regulated in a cell model of an early developmental transition, and to establish whether differential expression of any particular miRNA played a functional role in this developmental process. Having established a role for specific miRNAs, further objectives were to assess the reliability of current miRNA-mRNA target identification procedures and to assess the general role of miRNAs in cellular differentiation. In order to explore the roles of miRNAs during an early developmental transition, an embryonic stem (ES) cell model of trophectoderm differentiation was used. In this model system the expression of the key ES cell regulatory gene, Oct4, can be conditionally repressed, which induces the ES cells to differentiate down the trophectoderm lineage. The expression of microRNAs was profiled in this model system by cloning and sequencing of small RNAs. This approach identified miRNAs that were dynamically regulated during differentiation. The expression patterns of differentially regulated miRNAs were confirmed by miRNA northern analysis. The miRNA profiling data showed that mmu-miR-294 and mmu-mir-295 are expressed at similar levels in ES cells and differentiated cells, which disagrees with previous reports that these miRNAs are ES cell specific. Several of the miRNAs with higher expression levels in differentiated cells are encoded within a placental-enriched polycomb group gene, Sfmbt2, suggesting an important role for these miRNAs in extraembryonic development. One of the miRNAs that was expressed at higher levels in ES cells than in differentiated cells, mmu-miR-92a, was shown to play a role in regulation of cell proliferation. Three current methods of identifying miRNA targets were assessed. A sequencebased method using the web-based utility miRecords, which amalgamates results from numerous target prediction databases, was used to generate lists of potential targets of the Sfmbt2 miRNA cluster and of mmu-miR-92a. Amalgamating results from multiple target prediction programs may improve the likelihood that the predicted targets are real. Exemplifying this, the single mmu-miR-92a target that was predicted by six different target prediction programs had been previously experimentally verified. An experimental method of identifying direct miRNA targets, PAR-CLIP, was investigated but proved technically limiting for routine use in the laboratory. A proteome-based experimental method for identifying potential miRNA targets, called SILAC, was successfully used to identify proteins that were differentially expressed in the cell model of trophectoderm differentiation. Differential expression of two of these proteins, CTBP2 and CKB, was confirmed by western analysis. miRecords was then used to assess whether the differentially expressed proteins were likely to be targets of the differentially expressed miRNAs that had been identified in the miRNA profiling analysis. The general role of miRNAs in cell differentiation was investigated using a cell line that does not express miRNAs. This ES cell line is deficient for the miRNAprocessing enzyme DGCR8, which results in loss of expression of mature miRNAs in these cells. Compared to wild type ES cells, miRNA-deficient ES cells expressed normal levels of the ES cell marker genes Oct4 and Sox2 but elevated levels of Nanog. In contrast to wild type ES cells, miRNA-deficient ES cells did not upregulate the mesoderm marker gene Brachyury during embryoid body differentiation and showed reduced upregulation of the endoderm marker gene Gata6. These findings suggest that miRNAs are not required for maintenance of pluripotency, but are essential for proper ES cell differentiation. The results presented in this thesis show that miRNAs are dynamically expressed during a mammalian developmental transition and are involved in regulating early developmental processes. We believe that miRNAs act as an additional level of genetic regulation to ensure canalisation during embryonic development.

Positioning of nucleosomes within the 30nm fiber is fundamental in understanding how DNA compaction regulates gene expression. Numerous studies have focused on determining the structure, however; no studies have assessed the structure genome-wide. In this study, a new in silico methodology for genome-wide nucleosome arrangement was assessed through the use of randomly generating in silico datasets for the solenoid, solenoid-interdigitated, cross-linker (with odd and even n), twisted ribbon, and twisted ribbon-interdigitated. A PERL script was written to generate six in silico datasets from the human genome based on patterns and probabilities of close proximity nucleosomes, and align various length terminal ends of the sequences to the genome. A graphical representation was used to assess the genome-wide pattern of paired sequence alignments for each model. Whole genome sequence data from formaldehyde fixed HeLa cells were filtered, aligned, and compared to the models. Lack of sufficient experimental alignments yielded inconclusive model determination. / DNA compaction and the 30nm chromatin fiber -- Development of in silico method for analysis of the 30nm fiber on a genome-wide scale -- Experimental analysis of the 30nm chromatin fiber on a genome-wide scale -- Future directions. / Department of Biology