Pluripotent cells have the dual abilities to self-renewal and to differentiate into all three germ layers. Pluripotent cells can be isolated from two different stages of mouse embryogenesis. Embryonic stem cells (ESCs) are isolated from the inner cell mass (ICM) of the pre-implantation embryo and are considered to be in a naïve state. On the other hand, cells isolated from epiblast of the post-implantation embryo are referred as epiblast stem cells (EpiSC) and are representative of primed pluripotency. ESCs and EpiSCs are distinct from each other in terms of the morphology, the gene regulatory network and the signalling pathways regulating self-renewal. Under certain conditions, ESCs and EpiSCs can be transitioned into each other. However, the mechanism that regulates this transition from naïve to primed pluripotent state remains to be solved. Nanog, Oct4 and Sox2 form the core gene regulatory network of pluripotency. Additionally, the Id protein family is also important in the maintenance of pluripotency in ESCs. Id proteins function by inhibiting the activity of pro-differentiation factors. Tcf15 is identified as one of the targets of Id inhibition in ESCs. Moreover, Tcf15 has been identified as a repression target of Nanog. In this study, to understand the function of Tcf15, the expression of Tcf15 was characterized in differentiating ESCs. The transient upregulation of Tcf15 mRNA and protein was detected at early stages of differentiation before lineage commitment. Furthermore, Tcf15 protein was heterogeneously expressed in differentiating cells. Mutually exclusive expression of Nanog and Tcf15 proteins were demonstrated in both self-renewing and differentiating ESCs. Further characterization of the effect of Nanog on Tcf15 transcription showed that Tcf15 pre-mRNA was downregulated within 20 minute of Nanog induction. A Nanog binding site was identified at +32kb relative to the Tcf15 transcription start site (TSS). Initially, Nanog binding at this region was confirmed by performing ChIP-PCR experiments. Then, this Nanog binding region was further analysed for its enhancer activity related to the Tcf15 gene. Deletion of the Nanog binding region using CRISPR-Cas9 confirmed that this region acts as Tcf15 enhancer; it was shown that this region was required for the activation of Tcf15 transcription during differentiation. Tcf15 induction experiments were performed in order to the check whether Tcf15 affects Nanog transcription. The results indicate that Nanog is not a direct target of Tcf15, but Tcf15 contributes indirectly to the repression of Nanog. Additional analysis with the Tcf15 enhancer deletion cells showed that Tcf15 is not required for efficient downregulation of naïve markers and the upregulation of primed markers. However, the genes related to the regulation of adhesion properties of cells such as Zyc, Itga3 were induced with lower efficiency in the absence of Tcf15 compared to the wild type cells. In summary, I investigated the reciprocal regulation of Tcf15 and Nanog and the role of Tcf15 for the differentiation. My results suggest that Tcf15 is expressed in the cells that have initiated differentiation but are not lineage-committed. Additionally, Tcf15 can contribute to the regulation of adhesion related genes in order to help the epithelisation of the cells required during the differentiation from naïve to the primed pluripotent state. As a conclusion, Nanog is proposed to help to prevent certain aspects of ESCs differentiation by repressing Tcf15.

TGF-β/Activin/Nodal 信號通路調節了許多重要的細胞生物學過程,例如,細胞分裂,增殖,分化,遷移和衰老凋亡。此外,它也在胚胎髮育,損傷修復,腫瘤發生,組織纖維化,糖尿病發生及其免疫方面也扮演了重要的角色。TGF-β家族信號分子,包括TGF-β, Activin 和 Nodal,通過結合到它們各自的受體從而啟動它們,而啟動後的受體又可以通絡磷酸化作用進一步激活Smad2 和Smad3 蛋白,激活後的Smad2 和Smad3 蛋白可以和Smad4 蛋白形成複合體,一起從細胞膜轉移到細胞核內調節下游基因的表達。 / 在人的胚胎幹細胞中,TGF-β/Activin/Nodal signaling 做為最關鍵的信號分子,調節了人胚胎幹細胞的自我更新以及胚胎幹細胞多能性的維持。而在小鼠胚胎幹細胞中,該信號通路的功能並沒有清楚的研究。在本論文中,我們分離以及建立了Smad3 突變體的小鼠胚胎幹細胞系(Smad3-/-),該突變體細胞能夠維持正常小鼠胚胎幹細胞的形態,在自我增殖更新方面也沒有缺。此外,幹細胞多能性相關的標記基因以及組織標記基因表達水準也與野生型細胞非常相似,但是,在擬胚體的生長過程中,Smad3 被敲除後導致了組織發育相關的標記基因出現了差異性的表達。與野生型相比,中胚層標記基因（T 和GSC）的表達明顯受到了抑制。另外令人驚奇的是,將Smad3 基因敲除的胚胎幹細胞皮下注射裸鼠後長出了惡性的未完全成熟的畸胎瘤,而野生型的幹細胞則更傾向于長成成熟的良性畸胎瘤。進一步的分析發現,Smad3 功能性缺失後,細胞的增殖速率明顯增加了;紫外(UV)誘變後,相對於野生型,突變體細胞的抗凋亡能力也明顯增強了;並且在分化過程中,突變體細胞的遷移能力也要明顯強于野生型細胞。所有以上的細胞特徵可以解釋為什麼Smad3 基因敲除後會長出惡性的畸胎瘤。 / Microarray 分析結果發現,一個DNA 損傷修復基因Rif1,在Smad3 突變體細胞中呈現出了很高的上調,這個基因的上調現象已經發現是和侵蝕性腫瘤的發生是相關的,而且該基因的上調水準也與乳腺癌的浸潤程度是非常相關的。染色質免疫共沉澱和螢光素酶活性實驗進一步證實了Smad3 可以結合到Rif1 的啟動子領域從而直接抑制該基因的表達。這些實驗進一步說明了Smad3 可能通過下調Rif1 基因的表達,從而抑制了小鼠胚胎幹細胞長出惡性畸胎瘤的發生。 / 總之,我們建立了Smad3-/-基因敲除的小鼠胚胎幹細胞系,並且發現該突變體細胞傾向于長出惡性的畸胎瘤。我們推測,在正常的情況下,Smad3 正是通過抑制了DNA 損傷修復因數基因Rif1 的表達,從而阻止了惡性畸胎瘤的發生。這些研究的結果不僅開闊了我們對於惡性腫瘤發生的認識,而且為我們在幹細胞或誘導多能幹細胞治療應用中防止畸胎瘤的發生提供了新的思路和策略。 / TGF-β/Activin/Nodal signaling controls many important biological procedures in cells, such as cell division, proliferation, differentiation, migration and apoptosis in mammalian cells. It also plays a critical role in embryo development, wound healing, tumorigenesis, tissue fibrosis, diabetes and immunity. TGF-β superfamily ligands, such as TGF-β, Activin and Nodal bind to their respective ligand receptors and activate them, which in turn activate the receptor related SMAD proteins by phosphorylation, including Smad2 and Smad3. Once phosphorylated, they can cooperate with Smad4 and enter nucleus to bind promoter DNA sequence and regulate the target gene expression. / In human embryonic stem (ES) cells, TGF-β/Activin/Nodal signaling has been demonstrated to be the most critical pathways for ES cell self-renewal and maintenance of undifferentiated state. However, in mouse ES cells, its role is yet to be clearly exploited. In this study, we reported the derivation and establishment of mouse Smad3 knockout embryonic stem cell lines (Smad3-/- ES cells). Smad3-/- ES cells maintain normal ES cell morphology and express higher level of mouse ES cell markers, alkaline phosphatase (AP) and stage-specific embryonic antigen 1(SSEA1), and display no defect on self-renewal capacity. In addition, both of them show similar expression profiles of pluripotent and lineage marker genes compared to wild type ES cells. However, Smad3 ablation results in transient different expression of germ layer markers during embryoid body (EB) development. The expression of mesoderm lineage marker, like T and GSC, is significantly reduced in the EBs developed by Smad3-/- ES cells compared to EBs formed by wild type ES cells. More interestingly, to investigate the differentiation potential of Smad3-/- ES in vivo, we subcutaneously injected both wild type and Smad3-/- ES cells into nude mice, and observed that Smad3-/- ES cells are prone to grow malignant immature teratomas, while wild type ES cells develop normal mature teratomas. Further characterization of Smad3-/- ES cells demonstrates that depletion of Smad3 increases ES cell proliferation; Smad3-/- ES cells show higher capacity of the anti-apoptosis after UV irradiation and the migration potential of Smad3-/- ES cell differentiated cells is enhanced compared to wild type ES cells in the wound healing assay. Therefore, Smad3-/- ES cells exhibit enhanced malignancy, which may underlie their teratoma malignancy. / Microarray analysis shows that Rif1, a DNA repair factor is highly upregulated in Smad3-/- ES cells. Upregulation of DNA repair factor is found to be associated with invasive tumor. And the expression level of Rif1 is linked to the invasive degree of breast cancer at certain level. Chromatin immunoprecipitation (ChIP) assay and luciferase assay confirm that Smad3 binds to Rif1 promoter region and directly represses its expression; knockdown Rif1 in Smad3-/- ES cells rescues the expression level of Ccnd2 and migration potential to wild type ES cell level. Taken together, all these data suggests that Smad3 may suppress the malignancy of mouse embryonic stem cell formed teratoma through downregulating Rif1 expression in normal condition. / In summary, we reported the establishment of Smad3-/- ES cells and characterization of these cells. We discovered that Smad3-/- ES cells are prone to grow malignant teratomas compared to wild type ES cells. We hypothesized that Smad3 may suppress the malignancy of teratoma through repressing a DNA repair factor, Rif1. This information will not only broaden our general knowledge of malignant teratomas, but also help us to develop strategies to prevent malignant teratoma formation in ES/iPS cell therapy. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Li, Peng. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 149-181). / Abstracts also in Chinese.

Memory T cells are a critical component of immunological memory, which provides long-lasting immunological protection. These cells are characterized by a lower response threshold, rapid effector cytokine production, and prolonged longevity, and thus allow organisms to respond to pathogens more rapidly and effectively. However, the mechanisms that regulate the generation, function, homeostasis and tissue targeting of memory CD4+ T cells are not clear. This body of work investigated post-effector requirement for T-bet expression in determining the circulating and tissue resident memory CD4+ T cell fate and the implications of early T-bet deletion on lung CD4+ TRM development. We used mouse models with conditional expression of T-bet to delete T-bet in CD4+ T cells after priming and effector differentiation to analyze the development of resultant memory CD4+ T cells. We found that T-bet-ablation following cell priming and Th1 polarization did not impair the ability of Th1 effector cells to produce high levels of IFN-γ production, and moreover, there were dramatic increases in IL-2 production, suggesting post-effector T-bet expression is not required for functional maintenance in effector cells. Memory CD4+ T cells that developed from T-bet ablated effector cells after transfer to lymphocyte deficient RAG1/2-/- hosts or intact congenic hosts had increased persistence, and they maintained lower but substantial levels of IFN-γ and higher IL-2 production. We found elevation of IL-17 production and RORγt expression in T-bet ablated memory CD4+ T cells, and transcriptome analysis further showed that these cells upregulated genes expressed by other CD4+ T cell subsets, including Foxp3 and GATA3, indicating greater functional plasticity of T-bet-ablated memory CD4+ T cells. Increased localization of T-bet-ablated memory CD4+ T cells in the lung resident niche was found only in RAG1/2-/- hosts but not in congenic hosts, indicating the importance of the tissue environment in the development of TRM cells. Using antigen specific T-bet+/- OT-II and T-bet-/- OT-II cells, we found that T-bet+/- OT-II cells had increased persistence while T-bet-/- OT-II cells had decreased persistence compared with the wild type OT-II cells after PR8-OVA influenza virus infection. However, both T-bet+/- and T-bet-/- OT-II cells had normal TRM formation. Collectively, our results reveal the roles of T-bet in regulating the generation, function, maintenance and tissue targeting of memory CD4+ T cells.

Transcription factors control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in transcription factor binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here we developed a versatile maximum likelihood framework, named No Read Left Behind (NRLB), that fits a biophysical model of protein-DNA recognition to all in vitro selected DNA binding sites across the full affinity range. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. The model captures the specificity of p53 tetrameric binding sites and discovers multiple binding modes in a single sample. Additionally, we confirm that newly-identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

Remarkable progress has been made in our ability to design and produce synthetic DNA binding domains (TALE or Cas9-based), which can be further functionalized into synthetic transcription factors (sTFs). This technology is revolutionizing our ability to modulate expression of endogenous mammalian genes. Forced expression of cDNAs encoding transcription factors (TFs) is widely used to drive lineage conversions. However, this process is often inefficient and unreliable. Multiplex delivery of sTFs pool to activate endogenous master regulators and extinguish the expression profile of the host cell type could be a potential solution to this problem. We have developed a novel, simple TALE assembly method that enabled us to produce and screen large numbers of TAL effectors and compare their activity to dCas9-based TFs. During this process, we constructed many new functionally validated sTFs. Our ultimate goal is to test whether combining synthetic transcriptional activators and repressors can efficiently reprogram fibroblasts to NS cells or alternatively ‘program’ NS cell differentiation to neurons. We performed analyses of the transcriptome and chromatin accessibility of both fibroblasts and neural stem cells to unravel their core TF networks and their epigenetic state. This will allow us in the future the targeted design of sTFs and synthetic chromatin modifiers for specifically changing cell identity.

The nervous system integrates multiple sources of sensory information that ultimately controls motor neurons to generate complex movements. Motor neurons form topographically organised ‘myotopic maps’ between the nerve cord and muscles in the periphery to ensure that correct pre-motor inputs into motor dendrites are relayed through corresponding axons to the appropriate muscle groups. Therefore understanding the development and assembly of motor neuronss is crucial for understanding how animals execute various motor outputs. In adult Drosophila, ~50 motor neurons are topographically organized between each leg and the nerve cord in a highly stereotyped manner (Baek and Mann, 2009). In this thesis, I describe a novel group of transcription factors that act in a combinatorial manner to specify the projections of distinct Drosophila leg motor neurons. Our studies suggest that morphological transcription factors regulate various downstream cell-surface genes that are involved in the assembly of motor circuitry. Using in vivo live imaging I describe the developmental steps involved in Drosophila leg motor neuron axon targeting during metamorphosis and the spatial expression patterns of a novel hetero-binding Ig domain transmembrane protein family – the DIPs and Dprs (Ozkan et al., 2013) in leg neuro-musculature. I further describe a function between interacting partners DIP-alpha and Dpr10, expressed in subsets of leg motor neurons and muscles respectively, in establishing the final stereotyped terminal axon branching of corresponding motor neurons. The combinations of such interactions throughout development between leg motor neurons, not only with muscles in the periphery, but also among themselves, with leg sensory neurons and other components in the central nervous system may ultimately lead to synaptic specificity and stereotyped morphologies of Drosophila leg motor neurons.

In Type 1 diabetes, beta-cells is subjected to an autoimmune-mediated apoptotic and inflammatory attack. Whilst lymphocytes are the primary contributor of beta-cell death, exposure of beta-cells to stress signals such as cytokines, transform these cells into an inflammatory state activating transcripts for toxic agents. Demonstrating a significant role for beta-cells in participating in their own destruction through the elaboration of toxins and chemotactic molecules that could contribute to increased cellular infiltration. The Nuclear Factor-kappa B (NF-kB) is a transcription factor that provides for early immediate stress responses governing inflammation and cell survival. In islets, NF-kB is thought to have an important role in beta-cell inflammation and apoptosis. Few studies however, have explored the role of NF-kB in beta-cell protection. Indeed, we found that the expression NF-kB is responsible for the islet-intrinsic immediate-early pro-inflammatory gene expression. Importantly however, we also found that in islets, NF-kB is responsible for the expression and regulation of anti-apoptotic genes. We demonstrated for the first time that similar to other cells, the expression and regulation of the anti-inflammatory/ anti-apoptotic gene A20, in islets, is regulated by NF-kB. Consequently, we found a somewhat paradoxical role for NF-kB, where on the one hand it is responsible for beta-cell death, whilst on the other hand it is also responsible for beta-cell survival. In vivo however, we found that islet survival and function was severely impaired in the absence of NF-kB activity. We observed that blockade of NF-kB abrogate cytokine-induced A20 expression, and inhibited the activation of glucose-stimulated insulin secretion in vitro. In contrast, blockade of NF-kB by over-expression of A20 resulted in an improved islet allograft survival with good metabolic control. Thus demonstrating the importance of NF-kB-dependent anti-apoptotic genes for islet survival and function. The findings presented in this thesis demonstrate a fundamental bimodal role for NF-kB in maintaining the balance of survival of beta-cells in the context of T1D. These data, uncovers a sophisticated molecular mechanism in the regulation of beta-cell death, survival, and metabolic function. Thus providing a better understanding of the role of NF-kB in beta-cells in the context of T1D.

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references. Also available on the World Wide Web.

<p>Transcriptional regulation largely determines which proteins and the protein levels that are found in a cell, and this is crucial in development, differentiation and responses to environmental stimuli. The major effectors of transcriptional regulation are a group of proteins known as transcription factors, which importance is supported by their frequent involvement in mendelian and complex diseases.</p><p>In paper I, we attempted to establish the importance of DNA sequence variation in transcriptional control, by analyzing the potential functionality of polymorphic short repetitive elements as cis-regulatory elements. However, the relevance of this study was constrained by the limited number of analyzed sequences and the <i>in vitro</i> nature of the experiments. To overcome these limitations, (paper II) we optimized an <i>in vivo</i> large-scale technology named ChIP-chip, which couples chromatin immunoprecipitation and microarray hybridization. We successfully identified the binding profiles of metabolic-disease associated transcription factors in 1% of the human genome, using a liver cellular model, and inferred the binding sites at base pair resolution.</p><p>Another important characteristic of transcriptional regulation is its plasticity, which allows adjusting the cellular transcriptome to cellular and environmental stimuli. In paper III, we investigated such plasticity by treating HepG2 cells with butyrate, a histone deacetylase inhibitor (HDACi) and interrogating the changes in histone H3 and H4 acetylation levels in 1% of the genome. Observation of frequent deacetylation around transcription start sites and hyperacetylation at the nuclear periphery challenges pre-assumed HDACi mechanisms of action.</p><p>Finally, in paper IV we extended the DNA binding profiles of the medically relevant transcription factors, USF1 and USF2, and H3 acetylation to the whole non-repetitive fraction of the human genome. Using motif finding tools and chromatin profiling, we uncovered the major determinants of USF-DNA interactions. Furthermore, USFs and H3ac were clearly localized around transcription start sites, frequently in the context of bidirectional promoters.</p>

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 130-153).