The cyclic nucleotide monophosphates (CNs), cAMP and cGMP, are second messengers that participate in the regulation of development, metabolism and adaptive responses. In plants, CNs are associated with the control of pathogen responses, pollen tube orientation, abiotic stress response, membrane transport regulation, stomatal movement and light perception. In this study, we hypothesize that cAMP and cGMP promote changes in the transcription level of genes related to photosynthesis, high light and membrane transport in Arabidopsis thaliana leaves and, that these changes at the molecular level can have functional biological consequences. For this reason we tested if CNs modulate the photosynthetic rate, responses to high light and root ion transport. Real time quantitative PCR was used to assess transcription levels of selected genes and infrared gas analyzers coupled to fluorescence sensors were used to measure the photosynthetic parameters. We present evidence that both cAMP and cGMP modulate foliar mRNA levels early after stimulation. The two CNs trigger different responses indicating that the signals have specificity. A comparison of proteomic and transcriptional changes suggest that both transcriptional and post-transcriptional mechanisms are modulated by CNs. cGMP up-regulates the mRNA levels of components of the photosynthesis and carbon metabolism. However, neither cAMP nor cGMP trigger differences in the rate of carbon assimilation, maximum efficiency of the photosystem II (PSII), or PSII operating efficiency. It was also demonstrated that CN regulate the expression of its own targets, the cyclic nucleotide gated channels - CNGC. Further studies are needed to identify the components of the signaling transduction pathway that mediate cellular changes and their respective regulatory and/or signaling roles.

Η σύγκριση του μεταγραφικού προφίλ με χρήση μικροσυστοιχιών DNA είναι μια τεχνική που βελτιστοποιήθηκε την τελευταία δεκαετία. Η διαδικασία μπορεί να διαχωριστεί σε δύο μέρη: το πειραματικό και το υπολογιστικό. Το πρώτο μέρος αφορά στα βήματα της επιλογής της μικροσυστοιχίας, της απομόνωσης του βιολογικού υλικού, της σήμανσης και της επέκτασης, της υβριδοποίησης και της σάρωσης. Το υπολογιστικό μέρος αφορά στην ποσοτικοποίηση της εικόνας, στην κανονικοποίηση των δεδομένων και στην ανάλυσή τους. Πριν από τα παραπάνω βήματα πρέπει να έχει διατυπωθεί το κατάλληλο βιολογικό ερώτημα. Το βιολογικό ερώτημα που τέθηκε αφορούσε στις διαφορές στη γονιδιακή έκφραση των γενετικά τροποποιημένων εμβρυικών ινοβλαστών του ποντικού οι οποίοι έφεραν έλλειψη του ενός αλληλομόρφου της πρωτεΐνης Geminin σε σύγκριση με ομόζυγους εμβρυικούς ινοβλάστες. Για το σκοπό αυτό επιλέχθηκε μικροσυστοιχία δοκιμής με 384 ανιχνευτές γονιδίων ποντικού σε διπλά αντίγραφα. Απομονώθηκε ολικό RNA από τα κύτταρα, σημάνθηκε με απ’ ευθείας σήμανση και οι cDNA στόχοι που προέκυψαν, υβριδοποιήθηκαν στη μικροσυστοιχία. Έπειτα από δοκιμές καθορίστηκαν οι κατάλληλες συνθήκες για ένα ολοκληρωμένο πείραμα σύγκρισης μεταγραφικού προφίλ. Στη συνέχεια, πραγματοποιήθηκε προκαταρκτική ανάλυση του πειράματος η οποία περιελάμβανε ποσοτικοποίηση της εικόνας που προέκυψε, κανονικοποίηση των δεδομένων και πολυπαραμετρική ανάλυσή τους. / Transcriptional profiling using DNA microarrays was optimized during the last decade. The process can be separated in two parts: the experimental part and the computational part. The first part includes the steps of microarray choice, isolation of the biological material, labeling and amplification, hybridization and scanning. The computational part includes image quantification, data normalization and data analysis. Before the above steps, an appropriate biological question should be formulated. We wished to study differences in the gene expression profile of genetically modified mouse embryonic fibroblasts bearing a knock – out allele of the Geminin gene (homozygote|+/- Gem), in comparison to wild type embryonic fibroblasts. For this reason, a trial microarray was chosen with 384 gene probes in duplicates. Total RNA was isolated from the cells, directly labeled and the cDNA targets synthesized were hybridized to the microarray. After a series of trials, optimal conditions for a complete transcriptional profiling experiment were determined. Initial analysis including quantification of the image, data normalization and further multifunctional analysis was then carried out.

For cancer cells to initiate cell migration and progress to metastasize, epithelial genes must be silenced and the expression of mesenchymal genes must be upregulated. During prostate carcinogenesis, E-cadherin expression is downregulated through multiple mechanisms, the majority of which combine to silence E-cadherin expression through transcriptional regulation at the level of the E-cadherin promoter. Recently it has been discovered that there is transcriptional upregulation of the mesenchymal cadherin, N-cadherin during prostate cancer metastasis. Although N-cadherin expression can be detected in human prostate cancer and in prostate carcinoma cell lines, the mechanisms controlling the transcriptional regulation of N-cadherin in cancer are uncharacterized. This body of work offers the first evidence for the mechanisms controlling the transcriptional upregulation of N-cadherin expression in prostate carcinoma. We utilized anchorage independent culture to induce downregulation of N-cadherin expression, and then analyzed the necessary events for N-cadherin upregulation when cells attached to Fibronetin (FN). In order to determine the functional regions of the N-cadherin proximal promoter that were involved in the upregulation of N-cadherin expression, we cloned regions of the human N-cadherin 5’ proximal promoter, and regions of the first intron of the N-cadherin gene into a luciferase reporter vector. It was determined that the bHLH transcription factor Twist1 controlled the upregulation of N-cadherin transcription in PC-3 cells, through β1 integrin dependent nuclear localization of Twist1. A cis-element located in the first intron of the N-cadherin gene was shown to be necessary for Twist1 mediated effects on the N-cadherin promoter. We then determined the requirements for cell-type specific expression of the N-cadherin promoter. It was determined that an additional cis-element located in the first intron of the N-cadherin gene was necessary to repress N-cadherin promoter activity in cells lacking N-cadherin. Through deletion analysis of the N-cadherin promoter luciferase construct, a DNA binding site for the transcription factor FoxP1 was discovered. FoxP1 binds to the repressive cis-element in vitro, and mutation of the FoxP1 DNA binding site eliminated cell-type specific activity of the N-cadherin promoter. Therefore, we have documented that the aberrant expression of N-cadherin in prostate carcinoma involves alterations in both positive and negative transcriptional regulators.

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.

<p><italic>Cryptococcus neoformans </italic>is a human fungal pathogen that is also ubiquitous in the environment. To cause disease inside a human host, <italic>C. neoformans</italic> must be able to sense and respond to a multitude of stresses. One of the major responses to the host is the induction of a polysaccharide capsule, which allows the fungus to resist damage and evade the host immune response. This capsule is regulated by a number of signal transduction cascades, but a major contributor is the conserved cAMP/PKA pathway. </p><p> Using genetic and molecular biology techniques, I identified Gcn5 and Rim101 as key transcriptional regulators of capsule within the host. I determined that <italic>C. neoformans</italic> Rim101 is activated by a combination of the canonical pH sensing pathway and the cAMP/PKA pathway. This novel connection potentially gives the pathogen greater flexibility in responding to environmental stimuli, thus allowing for a greater capacity for disease. </p><p> I determined that the Rim101 transcription factor regulates cell wall remodeling in the context of the host by deep mRNA sequencing, electron microscopy, and biochemical assays. Using chromatin immunoprecipitation, I confirmed that these cell wall changes are under direct control of Rim101. I then confirmed the importance of cell wall changes in the host by nanoString profiling of fungal RNA in the context of a murine lung infection. I also examined the lungs of infected mice for cytokine and immune cell infiltrate and determined that <italic>C. neoformans</italic> cell wall changes are important in avoiding triggering an aberrant host response. I hypothesize that this cell wall remodeling via Rim101 activation is required for full capsule attachment and for masking immunogenic molecules from the host immune system.</p> / Dissertation

The E2A-PBX1 fusion gene results from the t(1;19) chromosomal translocation that is found in 25% of pre-B-cell cases of acute lymphoblastic leukemia (ALL). The resulting encoded product contains the transactivation domains of E2A, a Class I basic helix-loop-helix transcription factor, and most of PBX1. PBX1 is a major cofactor for most members of the HOX family of homeodomain proteins and is necessary for regulating the essential role that HOX proteins play in development and tissue homeostasis. We have identified an interaction between the E2A-encoded portion of E2A-PBX1 and the CREB-binding domain (KIX) of the transcriptional coactivator CBP and demonstrated a requirement for this interaction in leukemia induction. Others have shown that HOX proteins and CBP also interact directly, with resulting inhibitory effects on the DNA-binding ability of HOX proteins and on the acetylation of substrate proteins by CBP. Several publications have also identified the interaction of HOX proteins with the PBX1 portion of E2A-PBX1 and the result is a potent transcriptional activator at PBX1/HOX target sequences. In an attempt to develop a molecular model for the induction of ALL by E2A-PBX1, we hypothesize that the addition of CBP interactive peptide elements encoded by E2A to PBX1 allows E2A-PBX1 to stabilize a ternary complex involving E2A-PBX1, HOX, and CBP resulting in the deregulated expression of critical PBX1 or HOX target genes. I demonstrate using in vitro protein-protein interactions that this ternary complex involving E2A-PBX1, HOXB4 (chosen as a representative member of the HOX family), and CBP does form. This direct interaction appears to reduce transcriptional activation by E2A-PBX1/HOXB4 heterodimers from PBX1/HOX enhancer elements. I also show that this suppression of transactivation appears to involve CBP antagonism of DNA binding by E2A-PBX1/HOXB4 heterodimers. My results are consistent with the idea that E2A-PBX1 contributes to ALL induction by promoting the redistribution of CBP away from DNA sites bound by E2A-PBX1/HOXB4 heterodimers and in favour of those sites bound by E2A-PBX1 homodimers. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2008-09-29 13:57:25.324

Serratia marcescens, a member of Enterobacteriaceae family, is a causative agent of nosocomial and opportunistic infections. Numerous reports show that the multidrug resistance among S. marcescens is growing. This organism has high-level intrinsic resistance to a variety of antimicrobial agents, which makes the treatment of infections caused by this bacterium very difficult. The major mechanism for antibiotic resistance, especially to fluoroquinolones, in Gram-negative organisms is the active efflux of the antibiotic molecule mediated by efflux pumps belonging to the Resistance-Nodulation-Cell Division (RND) family. It was previously shown that the SdeAB and SdeXY multidrug efflux pumps are important for conferring the intrinsic drug resistance in S.marcescens. In Escherichia coli, the up-regulation of transcriptional activators, such as MarA, SoxS and Rob, affect transcription of acrAB, tolC and micF. Over-expression of Rob results in increased expression of the E. coli AcrAB-TolC efflux pump and decreases outer membrane permeability through up-regulation of micF, resulting in multidrug, organic solvent and heavy metal resistance. In the present study, we report the identification of a rob gene in S. marcescens which has a 70% identity at the DNA level and 71% identity at the amino acid level to that of E. coli. Moreover, the S. marcescens rob demonstrated similar properties to the E. coli rob including having an effect on expression of outer membrane protein F (OmpF) and over-expression of SdeAB and SdeXY, conferring antibiotic resistance to divergent antibacterial agents and tolerance to organic solvents. We performed rob promoter evaluations using transcriptional fusions to the Green Fluorescence Protein (GFP) in the vector pGlow-TOPO and constructed a rob knock-out using the TargeTron Gene Knockout System. Promoter activity assessment, using the pGlow-TOPO reporter plasmid, showed that rob had higher promoter activity at 37°C than 30°C. In the presence of 2,2’-dipyridyl, rob promoter activity was observed to be slightly increased in the early and mid-log phase by 1.4 and 1.1 fold, respectively. We also showed that sodium decanoate and sodium salicylate can reduce the transcription of rob at 30°C and 37°C. This reduction was observed more potently when rob was exposed to sodium decanoate at 30°C. Minimum inhibitory concentration (MIC) for various antibiotics of the S. marcescens rob knock-out demonstrated a decrease in susceptibility to nalidixic acid, tetracycline, chloramphenicol, ciprofloxacin, norfloxacin, and ofloxacin. Over-expression of rob resulted in an increased resistance by 4, 2, and 2-fold to nalidixic acid, tetracycline and chloramphenicol, respectively. In addition, rob over-production displayed 8, 4, and 4-fold increase in resistance to ciprofloxacin, norfloxacin, ofloxacin, respectively. To discover the role of rob in the efflux mechanism, we performed ethidium bromide accumulation assays on over-expressing and knock-out strains. Organic solvent tolerance assays were carried out using n-hexane to determine if rob is involved in expression of efflux pumps. We found the rob null mutant to be sensitive to n-hexane while the over-expression of rob resulted in resistance to n-hexane. RT-PCR of the rob knock-out strain showed a decrease in expression of micF, ompC, sdeXY, sdeAB and tolC, respectively, and an increase in the expression of ompF. To conclude, we identified a rob homolog in S. marcescens which contributes to resistance to multiple antibiotics and tolerance to organic solvent.

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.

The Drosophila hindsight (hnt) gene encodes a C2H2-type zinc-finger (ZNF) protein crucial for epithelial morphogenesis. The human HNT homologue, RREB1, functions as a transcriptional modulator and regulates several tumor suppressor genes. HNT’s functional motifs, target genes and its regulatory abilities have not been elucidated. Here I showed that the C-terminal region of HNT containing the last five of 14 ZNFs (ZNF 10-14) binds in vitro to DNA-elements similar to those identified for RREB-1. I then mapped HNT’s endogenous binding sites on polytene chromosomes and focus on two, at 4C and 60C, which are associated with the hnt and nervy (nvy) loci, respectively. Sequence analysis of the bound fragments shows conservation of motifs similar to those bound by HNT in vitro. Data from both hnt loss- and gain-of-function experiments show that HNT attenuates the transcription of the hnt and nvy genes in several tissues and developmental stages. I show that the identified HNT C-terminal DNA binding domain ZNF 10-14 is not required for these regulatory functions. I further delineate the minimal functional motifs of HNT in transcriptional regulation and show that its ninth ZNF in isolation has a repressive activity and is sufficient to confer many regulatory functions of HNT. On the other hand, mutation of ZNF 9 in the context of the full-length protein indicates that it is not necessary for HNT functions. Interestingly, ZNF 9 has been lost from HNT vertebrate homologues. I propose two redundant mechanisms of transcriptional regulation by HNT: one is mediated by the potential protein-interaction abilities of ZNF 9; another is through cooperation of other ZNF motifs of HNT; the DNA binding abilities conferred by the C-terminal five fingers may be essential for the latter mechanism.

The Drosophila hindsight (hnt) gene encodes a C2H2-type zinc-finger (ZNF) protein crucial for epithelial morphogenesis. The human HNT homologue, RREB1, functions as a transcriptional modulator and regulates several tumor suppressor genes. HNT’s functional motifs, target genes and its regulatory abilities have not been elucidated. Here I showed that the C-terminal region of HNT containing the last five of 14 ZNFs (ZNF 10-14) binds in vitro to DNA-elements similar to those identified for RREB-1. I then mapped HNT’s endogenous binding sites on polytene chromosomes and focus on two, at 4C and 60C, which are associated with the hnt and nervy (nvy) loci, respectively. Sequence analysis of the bound fragments shows conservation of motifs similar to those bound by HNT in vitro. Data from both hnt loss- and gain-of-function experiments show that HNT attenuates the transcription of the hnt and nvy genes in several tissues and developmental stages. I show that the identified HNT C-terminal DNA binding domain ZNF 10-14 is not required for these regulatory functions. I further delineate the minimal functional motifs of HNT in transcriptional regulation and show that its ninth ZNF in isolation has a repressive activity and is sufficient to confer many regulatory functions of HNT. On the other hand, mutation of ZNF 9 in the context of the full-length protein indicates that it is not necessary for HNT functions. Interestingly, ZNF 9 has been lost from HNT vertebrate homologues. I propose two redundant mechanisms of transcriptional regulation by HNT: one is mediated by the potential protein-interaction abilities of ZNF 9; another is through cooperation of other ZNF motifs of HNT; the DNA binding abilities conferred by the C-terminal five fingers may be essential for the latter mechanism.