BACKGROUND:Colony stimulating factor-1 (CSF-1) plays an important role in ovarian cancer biology and as a prognostic factor in ovarian cancer. Elevated levels of CSF-1 promote progression of ovarian cancer, by binding to CSF-1R (the tyrosine kinase receptor encoded by c-fms proto-oncogene).Post-transcriptional regulation of CSF-1 mRNA by its 3' untranslated region (3'UTR) has been studied previously. Several cis-acting elements in 3'UTR are involved in post-transcriptional regulation of CSF-1 mRNA. These include conserved protein-binding motifs as well as miRNA targets. miRNAs are 21-23nt single strand RNA which bind the complementary sequences in mRNAs, suppressing translation and enhancing mRNA degradation.RESULTS:In this report, we investigate the effect of miRNAs on post-transcriptional regulation of CSF-1 mRNA in human ovarian cancer. Bioinformatics analysis predicts at least 14 miRNAs targeting CSF-1 mRNA 3'UTR. By mutations in putative miRNA targets in CSF-1 mRNA 3'UTR, we identified a common target for both miR-128 and miR-152. We have also found that both miR-128 and miR-152 down-regulate CSF-1 mRNA and protein expression in ovarian cancer cells leading to decreased cell motility and adhesion in vitro, two major aspects of the metastatic potential of cancer cells.CONCLUSION:The major CSF-1 mRNA 3'UTR contains a common miRNA target which is involved in post-transcriptional regulation of CSF-1. Our results provide the evidence for a mechanism by which miR-128 and miR-152 down-regulate CSF-1, an important regulator of ovarian cancer.

<p>Salicylic acid (SA) is a central plant defense signal. It is not only required for closing the stomata upon infection to prevent pathogens from entering into the plant apoplast, but also mediates defense responses activated by pathogen-originated microbe-associated molecular patterns (MAMPs) and effectors in the infected tissues. In addition, SA is a necessary and sufficient signal for systemic acquired resistance (SAR). In <italic>Arabidopsis</italic> <italic>thaliana</italic>, SA level increases in response to pathogen attack, which is essential for activating defense responses. This SA accumulation involves transcriptional activation of several genes including <italic>ICS1</italic> (<italic>ISOCHORISMATE</italic> <italic>SYNTHASE</italic> <italic>1</italic>), <italic>EDS5</italic> (<italic>ENHANCED</italic> <italic>DISEASE</italic> <italic>SUSCEPTIBILITY</italic> <italic>5</italic>), <italic>EDS1</italic> (<italic>ENHANCED</italic> <italic>DISEASE</italic> <italic>SUSCEPTIBILITY</italic> <italic>1</italic>), <italic>PAD4</italic> (<italic>PHYTOALEXIN-DEFICIENT</italic> <italic>4</italic>) and <italic>PBS3</italic> (<italic>avrPphB</italic> <italic>SUSCEPTIBLE</italic> <italic>3</italic>). However, it is not well understood how pathogenic signals induce these SA accumulation genes. Interestingly, our time-course transcriptome analysis showed that these five genes share a similar pathogen-induced expression pattern, suggesting the existence of common transcription factors (TFs). Through yeast-one-hybrid screening, a TF NTL9 was identified for its interactions with the promoters of the SA accumulation genes. Preferentially expressed in guard cells, NTL9 activates the expression of SA accumulation genes in guard cells. The <italic>ntl9</italic> mutant is defective in pathogen-induced stomatal closure mediated by a well-characterized MAMP, flg22. Consistent with the stomatal closure defect, the <italic>ntl9</italic> mutant exhibits elevated susceptibility to surface-inoculated pathogens. The stomatal closure defect of the <italic>ntl9</italic> mutant can be rescued by exogenous application of SA, demonstrating that NTL9 acts upstream of SA in stomatal closure response. These results suggest that NTL9-mediated activation of SA accumulation genes is essential for MAMP-triggered stomatal closure.</p><p>While plants induce SA to activate defense responses, pathogens can also produce virulence factors to counteract the effects of SA. Coronatine is one such virulence factor produced by <italic>Pseudomonas</italic> <italic>syringae</italic>. Coronatine is known to promote opening of stomata for bacterial entry, bacterial growth in the apoplast, systemic susceptibility and development of disease symptoms such as chlorosis. In the process of examining the mechanisms underlying coronatine-mediated virulence, three homologous TFs, ANAC019, ANAC055 and ANAC072, were found to be activated by coronatine directly through the TF, MYC2. Genetic characterization of these three TF mutants revealed that these TFs mediate multiple virulence effects of coronatine by inhibiting SA accumulation. To exert this inhibitory effect, these TFs repress <italic>ICS1</italic> and activate <italic>BSMT1</italic>, genes involved in SA biosynthesis and inactivation modification, respectively. Thus, a signaling cascade downstream of coronatine was illustrated to dampen SA-mediated defense responses through differential transcriptional regulation of genes related to SA level.</p><p>Taken together, my dissertation studies revealed novel transcriptional regulation of SA production and demonstrated that this transcriptional regulation is a vital point not only for plant defense activation but also for pathogen manipulation to counteract defense responses. Further studies on the interplay of this transcriptional regulation by different TFs would broaden our understanding about the dynamics of plant-pathogen interaction.</p> / Dissertation

Transcription factors regulate distinct macrophage functions by regulating gene expression in response to micro-environmental cues. This functional plasticity is critical for regulating innate and adaptive immune responses during infection and during chronic disease processes including inflammatory diseases and cancer. Microarray analysis of macrophages polarized to a pro-inflammatory (M1) phenotype with LPS and IFNγ revealed that basic leucine zipper transcription factor ATF-like 2 (Batf2), a member of the AP1 transcription factors, is selectively upregulated in M1 macrophages compared to anti-inflammatory IL-4-polarized (M2) macrophages. The initial hypothesis was that Batf2 is a master regulator of gene expression that orchestrates M1 polarization. To investigate a potential role of Batf2 during macrophage polarization, its expression in M1 polarized macrophages was examined. Batf2 mRNA appears within 60 minutes following LPS/ IFNγ treatment and is sustained for at least 48 hours. To address the hypothesis that Batf2 acts as a master transcriptional factor driving a functional M1 phenotype, we have established macrophage cell lines that constitutively express Batf2. Batf2 overexpression did not enhance key M1-associated genes, including iNOS and H2-Aa, but did enhance LPS/IFNγ-driven Cxcl10. Batf2 overexpression also failed to suppress key M2-associated genes including Fizz1 and Mrc1. Batf2 overexpression also failed to alter multiple non-immunity-related genes established or predicted to be downstream of Batf2 in macrophages or other cells. Overall, contrary to our initial hypothesis, constitutive Batf2 expression by itself does not appear to broadly induce M1 gene expression; rather, it appears to enhance only select genes. Since other Batf family members interact with members of the IRF family, I discuss the possibility that Batf2 works in conjunction with a limiting cofactor, possibly Irf family members and/or other regulatory proteins.

ISWI is a member of a versatile family of ATP-dependent chromatin remodelling complexes involved not only in transcription regulation (initiation, elongation and termination), but also in other cellular functions like maintenance of higher order chromatin structure and DNA replication. TbISWI, a novel ATPase of the ISWI family in Trypanosoma brucei, is involved in the transcriptional repression of silent VSG expression sites (ESs) in both bloodstream form (BF) and procyclic form (PF) life cycle stages of the parasite. Using in silico analysis, I have found that TbISWI is well conserved across the eukaryotic lineage, including those members of the order Kinetoplastida that do not exhibit antigenic variation. Compared to the ISWIs of higher eukaryotes, TbISWI has greater representation of random coils within its structure, an indicator of more structural fluidity and flexibility of interaction with multiple protein partners. Using an eGFP reporter based assay, I have studied the role of TbISWI in transcriptional repression of silent areas of the T. brucei genome. TbISWI was found to be involved in preventing inappropriate transcription of the silent VSG repertoires. TbISWI was also found to downregulate transcription in RNA pol I, but not pol II, transcription units. These results argue for the presence of at least two functionally distinct TbISWI complexes in T. brucei. Using DNA staining and fluorescence in situ hybridisation (FISH), I have investigated the potential effect of TbISWI depletion on cell cycle progression and minichromosome segregation. I did not find any evidence for the role of TbISWI in the maintenance of centromeric heterochromatin in T. brucei.

Computational systems biology is an emerging area of research that focuses on understanding the holistic view of complex biological systems with the help of statistical, mathematical and computational techniques. The regulation of gene expression in gene regulatory network is a fundamental task performed by all known forms of life. In this subsystem, modelling the behaviour of the components and their interactions can provide useful biological insights. Statistical approaches for understanding biological phenomena such as gene regulation are proving to be useful for understanding the biological processes that are otherwise not comprehensible due to multitude of information and experimental difficulties. A combination of both the experimental and computational biology can potentially lead to system level understanding of biological systems. This thesis focuses on the problem of inferring the dynamics of gene regulation from the observed output of gene expression. Understanding of the dynamics of regulatory proteins in regulating the gene expression is a fundamental task in elucidating the hidden regulatory mechanisms. For this task, an initial fixed structure of the network is obtained using experimental biology techniques. Given this network structure, the proposed inference algorithms make use of the expression data to predict the latent dynamics of transcription factor proteins. The thesis starts with an introductory chapter that familiarises the reader with the physical entities in biological systems; then we present the basic framework for inference in transcriptional regulation and highlight the main features of our approach. Then we introduce the methods and techniques that we use for inference in biological networks in chapter 2; it sets the foundation for the remaining chapters of the thesis. Chapter 3 describes four well-known methods for inference in transcriptional regulation with pros and cons of each method. Main contributions of the thesis are presented in the following three chapters. Chapter 4 describes a model for inference in transcriptional regulation using state space models. We extend this method to cope with the expression data obtained from multiple independent experiments where time dynamics are not present. We believe that the time has arrived to package methods like these into customised software packages tailored for biologists for analysing the expression data. So, we developed an open-sources, platform independent implementation of this method (TFInfer) that can process expression measurements with biological replicates to predict the activities of proteins and their influence on gene expression in gene regulatory network. The proteins in the regulatory network are known to interact with one another in regulating the expression of their downstream target genes. To take this into account, we propose a novel method to infer combinatorial effect of the proteins on gene expression using a variant of factorial hidden Markov model. We describe the inference mechanism in combinatorial factorial hidden model (cFHMM) using an efficient variational Bayesian expectation maximisation algorithm. We study the performance of the proposed model using simulated data analysis and identify its limitation in different noise conditions; then we use three real expression datasets to find the extent of combinatorial transcriptional regulation present in these datasets. This constitutes chapter 5 of the thesis. In chapter 6, we focus on problem of inferring the groups of proteins that are under the influence of same external signals and thus have similar effects on their downstream targets. Main objectives for this work are two fold: firstly, identifying the clusters of proteins with similar dynamics indicate their role is specific biological mechanisms and therefore potentially useful for novel biological insights; secondly, clustering naturally leads to better estimation of the transition rates of activity profiles of the regulatory proteins. The method we propose uses Dirichlet process mixtures to cluster the latent activity profiles of regulatory proteins that are modelled as latent Markov chain of a factorial hidden Markov model; we refer to this method as DPM-FHMM. We extensively test our methods using simulated and real datasets and show that our model shows better results for inference in transcriptional regulation compared to a standard factorial hidden Markov model. In the last chapter, we present conclusions about the work presented in this thesis and propose future directions for extending this work.

HuR est une protéine liant l’ARN, qui contrôle l’expression des gènes au niveau post-transcriptionnel. Dans le cytoplasme, HuR module la stabilité et la capacité de traduction des ARNm sur lesquels elle se fixe. Nos résultats montrent que HuR est surexprimée dans le carcinome hépatocellulaire (CHC) humain et dans des lignées de CHC en culture. HuR est anormalement retrouvée dans le cytoplasme des cellules hépatiques tumorales, et participe à leur prolifération. En combinant l’analyse globale des gènes régulés par l’extinction d’HuR, celle des ARNm liés à HuR et celle du transcriptome des CHC humains, nous avons identifié 2 gènes dont l’expression est régulée par HuR. Ces gènes sont sous-exprimés dans les tissus de CHC et participent à la mise en place du phénotype cancéreux (résistance à l’apoptose, prolifération cellulaire, invasion,...). / HuR is a RNA binding protein that controls gene expression at post-transcriptional level. In the cytoplasm, HuR modulates the stability and capacity of mRNA translation upon which it binds. Our results show that HuR is overexpressed in hepatocellular carcinoma (HCC) and in human HCC cell lines in culture. HuR is abnormally found in the cytoplasm of liver tumor cells, and contribute to their proliferation. By combining the global analysis of genes regulated by the extinction of HuR, the mRNAs associated with HuR and the transcriptome of human HCC, we identified two genes whose expression is regulated by HuR. These genes are under-expressed in HCC tissues and participate in the development of cancerous phenotype (resistance to apoptosis, cell proliferation, invasion ,...).

The human genome consists of over 3 billion nucleotides and would be around 2 meters long if uncoiled and laid out. Each human somatic cell contains all this in their nucleus which is only around 5 µm across. This extreme compaction is largely achieved by wrapping the DNA around a histone octamer, the nucleosome. Still, the DNA is accessible to the transcriptional machinery and this regulation is highly dynamic and change rapidly with, e.g. exposure to drugs. The individual histone proteins can carry specific modifications such as methylations and acetylations. These modifications are a major part of the epigenetic status of the DNA which contributes significantly to the transcriptional status of a gene - certain modifications repress transcription and others are necessary for transcription to occur. Specific histone methylations and acetylations have also been implicated in more detailed regulation such as inclusion/exclusion of individual exons, i.e. splicing. Thus, the nucleosome is involved in chromatin remodeling and transcriptional regulation – both directly from steric hindrance but also as a signaling platform via the epigenetic modifications. In this work, we have developed tools for storage (Paper I) and normalization (Paper II) of next generation sequencing data in general, and analyzed nucleosome locations and histone modification in particular (Paper I, III and IV). The computational tools developed allowed us as one of the first groups to discover well positioned nucleosomes over internal exons in such wide spread organisms as worm, mouse and human. We have also provided biological insight into how the epigenetic histone modifications can control exon expression in a combinatorial way. This was achieved by applying a Monte Carlo feature selection system in combination with rule based modeling of exon expression. The constructed model was validated on data generated in three additional cell types suggesting a general mechanism.

Development of the nervous system is a highly organized process that utilizes genetic mechanisms conserved across the animal kingdom. Components of the nervous system such as inhibitory GABAergic neural networks are common among most multicellular animals. The nematode Caenorhabditis elegans, utilizes similar genetic pathways to that of mice and humans to develop its GABAergic neural networks. These GABAergic neural networks are composed of two types of GABAergic motor neurons: the VD and DD sub-classes. The GABAergic differentiation of both these sub-classes requires the conserved transcription factor, Pitx/UNC-30. The VD sub-class is differentiated from the DD motor neurons by the expression of another transcription factor, COUP TFII/UNC-55. The transcriptional mechanisms regulating the expression of Pitx/UNC-30 and Coup TFII are unknown. We sought to determine how Pitx/UNC-30 and COUP TF-II/UNC-55 were transcriptionally regulated in an attempt to understand how mechanisms of GABAergic fate specification and class specification may be connected. We hypothesized there would be different mechanisms regulating the GABAergic differentiation and sub-class specification of the two sub-classes of GABAergic motor neurons. To test this, we dissected the transcriptional mechanisms responsible for the expression of Pitx/UNC-30 and COUP TFII/UNC-55. We found that different isoforms of the Hox cofactor Meis/UNC-62 stabilize and activate the expression of UNC-55. Furthermore, we conclude that Pitx/UNC-30 expression is regulated differently between the two motor neuron sub-classes by Meis/UNC-62, Hox-B7/MAB-5 and NeuroD/CND-1, each of which are vital to the development of different components of the nervous system in vertebrates. Our findings suggest that the GABAergic identity and the sub-class specification of neurons are under the control of multiple conserved transcription factors responsible for neuron fate determination and post mitotic identities.

In humans, the functional regulation of facilitative glucose transporters (GLUTs) by insulin plays a central role in the maintenance of glucose homeostasis. The insensitivity of tissues to this regulation results in diabetes mellitus, however, the underlying mechanisms remain largely unknown. To establish Caenorhabditis elegans (C. elegans) as a model system to study the mechanisms of insulin regulation of GLUTs because of the well-conserved insulin/IGF-like signaling (IIS) and many unique advantages of this organism, we functionally characterized 9 candidate genes of human GLUT homologues in C. elegans based on their sequence homologies to GLUTs. We found that FGT-1 is the only functional GLUT homologue with the ability to transport 2-deoxy-D-glucose (2DG) in Xenopus oocytes. FGT-1 mediated 2DG transport could be inhibited by the GLUT inhibitor phloretin and exhibited a Michaelis constant (Km) of 2.8 mM, which is smaller than the Km values of human GLUT1 and GLUT4. In addition to glucose, FGT-1 could also transport mannose, galactose, and fructose. Using a FGT-1::GFP fusion construct under the control of the 5 kb promoter sequence of the fgt-1a gene, FGT-1 was shown to be ubiquitously expressed in C. elegans tissues and cells, including the digestive tract, neurons, and body wall muscle. Two FGT-1 alternative splicing isoforms, FGT-1A and FGT-1B, showed similar transport activity and tissue localization. To study the function of FGT-1 and its regulation by IIS, the changes in several phenotypes that are known to be regulated by IIS were observed in FGT-1-knockdown worms or null strains in the presence or absence of IIS activity. FGT-1 knockdown resulted in fat accumulation but had no effects on dauer formation or brood size in both wild-type and daf-2 (insulin receptor) gene mutant strains. However, the function of FGT-1 in animal growth and aging was dependent on the IIS background, suggesting IIS regulation of FGT-1 function. Consistently, FGT-1 mediated glucose uptake was almost completely defective in the daf-2 and age-1 (PI3 kinase) mutants, and phloretin could only marginally inhibit 2DG uptake in these strains. This defect was only partially related to the approximately 60% decrease in FGT-1 protein levels in these mutants, suggesting the involvements of both post-transcriptional and post-translational regulatory mechanisms. We also found that OGA-1, an O-GlcNAcase, is essential for the function of FGT-1, implying possible regulation of FGT-1 function by glycosylation. In summary, our study has established C. elegans as a powerful model to study the mechanism by which insulin regulates glucose transporters and has provided insights into the mechanism of defective glucose uptake by tissues in patients with diabetes.

Diabetic embryopathy is one of many serious complications associated with diabetes. It is known that maternal diabetes increases the frequency of congenital defects up to ten times. The most common defects are cardiovascular and neural tube defects. Molecular mechanisms of diabetic embryopathy are still not known. This work contributes to elucidation of molecular processes leading to development of cardiovascular defects in diabetic embryopathy. This study is based on observation that maternal diabetes affects transcriptional regulation of hypoxia-inducible factor 1 (HIF-1) in developing embryo. To study the influence of maternal diabetes on HIF-1 signaling pathway, we used mouse model heterozygous for "knock-out" of Hif1α gene. Our analyses showed the negative combinational effects of maternal diabetes and Hif1α+/- genotype on embryonic development and increased risk of diabetic embryopathy. Histological analysis demonstrated the increased incidence of cardiovascular defects, particularly defects of interventricular septum and hypoplastic compact left ventricular wall in embryonic day (E) 14.5 Hif1α+/- embryos compared to wt littermates from the diabetic pregnancy. Using qPCR, we analyzed gene expression changes in the embryonic hearts at E9.5 and E10.5. We selected genes important for the...