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Although the human brain has been studied over past decades at morphological and histological levels, much remains unknown about its molecular and genetic mechanisms. Furthermore, when compared with our closest relative the chimpanzee, the human brain strikingly shows great morphological changes that have been often associated with our cognitive specializations and skills. Nevertheless, such drastic changes in the human brain may have arisen not only through morphological changes but also through changes in the expression levels of genes and transcripts. Gene regulatory networks are complex and large-scale sets of protein interactions that play a fundamental role at the core of cellular and tissue functions. Among the most important players of such regulatory networks are transcription factors (TFs) and the transcriptional circuitries in which TFs are the central nodes. Over past decades, several studies have focused on the functional characterization of brain-specific TFs, highlighting their pathways, interactions, and target genes implicated in brain development and often disorders. However, one of the main limitations of such studies is the data collection which is generally based on an individual experiment using a single TF. To understand how TFs might contribute to such human-specific cognitive abilities, it is necessary to integrate the TFs into a system level network to emphasize their potential pathways and circuitry. This thesis proceeds with a novel systems biology approach to infer the evolution of these networks. Using human, chimpanzee, and rhesus macaque, we spanned circa 35 million years of evolution to infer ancestral TF networks and the TF-TF interactions that are conserved or shared in important brain regions. Additionally, we developed a novel method to integrate multiple TF networks derived from human frontal lobe next-generation sequencing data into a high confidence consensus network. In this study, we also integrated a manually curated list of TFs important for brain function and disorders. Interestingly, such “Brain-TFs” are important hubs of the consensus network, emphasizing their biological role in TF circuitry in the human frontal lobe. This thesis describes two major studies in which DNA microarray and RNA-sequencing (RNA-seq) datasets have been mined, directing the TFs and their potential target genes into co-expression networks in human and non-human primate brain genome-wide expression datasets. In a third study we functionally characterized ZEB2, a TF implicated in brain development and linked with Mowat-Wilson syndrome, using human, chimpanzee, and orangutan cell lines. This work introduces not only an accurate analysis of ZEB2 targets, but also an analysis of the evolution of ZEB2 binding sites and the regulatory network controlled by ZEB2 in great apes, spanning circa 16 million years of evolution. In summary, those studies demonstrated the critical role of TFs on the gene regulatory networks of human frontal lobe evolution and functions, emphasizing the potential relationships between TF circuitries and such cognitive skills that make humans unique.

Further investigation of possible regulatory pathway of NYD-SP24 demonstrated that the cell cycle of NYD-SP24 overexpressing cells was incompletely blocked at G2/M phase, and one of cell cycle-related genes, p21, shown to be an inducer of differentiation in different types of cell system, was found upregulated in a p53-independent manner, consistent with a role of NYD-SP24 in differentiation. (Abstract shortened by UMI.) / Spermatogenesis is a unique cell differentiation process consisting of three main phrases, namely mitosis, meiosis and postmeiosis. The differentiation of germ cells in the process involves distinct transcriptional programs, each under control of different transcription factor network. Many testis-specific transcription factors have been reported previously, however, few detailed studies have been done. This thesis describes the characterization and functional studies of a newly discovered testis-specific transcription factor, NYD-SP24, and the investigation of the possible regulatory pathway of NYD-SP24 in spermatogenesis. / The results demonstrated that in normal human tissues, NYD-SP24 was specifically and highly expressed in the testis but not in other somatic tissues, indicating its possible role in spermatogenesis. In the mouse model, mRNA and protein of NYD-SP24 mouse homolog gene (mNYD-SP24) were increased in the first wave of spermatogenesis. During the differentiation of germ cells, mNYD-SP24 mRNA and protein were confined to spermatocyte, round spermatid and spermatozoa. In hyperthermic mouse model, expression of mNYD-SP24 was decreased following the damage to germ cells by heat shock, but returned to normal level upon recovery of spermatogenesis. These results suggest the involvement of NYD-SP24 in spermatogenesis. / To identify the possible downstream targets of NYD-SP24, microarray and two-dimension gel technologies were performed in NYD-SP24 overexpressing cells and control cells. The results of microarray showed that 16 genes were upregulated and 4 genes were downregulated in NYD-SP24 overexpressing cells. In the two-dimension gel analysis, 12 protein spots were found to be altered significantly, with 8 increased and 4 decreased. Among these proteins, 3 were successfully identified by mass spectrometry. The nuclei localization in germ cells and the ability of NYD-SP24 to alter gene expression profile suggest that NYD-SP24 may be a testis-specific transcription factor, involved in gene regulation in spermatogenesis. / Zhu Hu. / "June 2005." / Adviser: Chan Hsiao Chang. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3607. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 136-146). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

Production of large numbers of desirable human cell types in the laboratory is one of the major goals of stem cell research. Current experimental approaches have focused on the strategy of recapitulating the events of normal embryogenesis in culture, by treating cells - either tissue stem cells or pluripotent stem cells (iPS/ES cells) - with cocktails of growth factors, matrix proteins or pharmacological agents. This is challenging and often requires weeks or months of elaborate cell culture regimes. An alternative approach is the forced expression of master regulatory transcription factors; this can bypass developmental programs and drive conversion to the target cell type. Each of these strategies is inefficient and unreliable. Recently a new opportunity has arisen to exploit synthetic transcription factors (sTFs) to program and reprogram cell fate. To create such sTFs the CRISPR/Cas9 system is repurposed through tethering of catalytically dead Cas9 to various transcriptional regulatory effector domains (e.g. VP16, KRAB). In this thesis, we have explored sTFs as tools to reset transcriptional regulatory networks in neural stem cells and mouse embryonic fibroblasts. We tested transcriptional activation of key neural lineage target genes (e.g Olig2, Sox10 and Nkx6.2). We designed and validated a series of sTFs that could effectively activity these. We have found that activation of Sox10 by dCas9-VP160 in mouse neural stem cells can increase the amount of arising oligodendrocyte and oligodendrocyte precursors cells during the differentiation. The activity of sTFs strongly depends on cellular context: i.e. a specific sTF might work well in one cell type but not another. Importantly, these biological barriers are not easily overcome by increasing the strength of the sTF - either through levels or types of effector domains used. Our data inspecting single cells suggests that multiplex delivery of sTFs can indeed cooperate by both increasing the number of cells that activated the gene of interest and increasing the level of transcriptional activation in a given cell. To fully exploit these new technologies, we therefore developed a new construction pipeline that allows easy and efficient assembly of multiple sTFs. Using this approach, we were able to successfully activate three different target genes from a single expression plasmid (Olig2, Sox10 and Nkx6.2) in fibroblasts. These sTFs we able to force fibroblast transdifferentiation towards oligodendrocyte lineage. Future studies will explore further how to exploit these sTFs to augment or replace current reprograming strategies.

Au, Yee Man Candy. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 128-144). / Abstracts in English and Chinese. / Abstract --- p.i / 摘要 --- p.iii / Acknowledgements --- p.v / List of Tables --- p.x / List of Figures --- p.xi / List of Abbreviations --- p.xiii / Chapter 1. --- Chapter One Introduction / Chapter 1.1 --- Homeostasis and detoxification of metal ions --- p.1 / Chapter 1.2 --- Biochemistry of metallothionein --- p.3 / Chapter 1.2.1 --- Structure of metallothionein --- p.4 / Chapter 1.2.2 --- Isoforms of metallothionein --- p.5 / Chapter 1.2.3 --- Roles of metallothionein --- p.6 / Chapter 1.2.4 --- Structure of metallothionein gene --- p.9 / Chapter 1.2.5 --- Metal responsive element (MRE) --- p.10 / Chapter 1.2.6 --- Regulation of MT gene --- p.11 / Chapter 1.3 --- Metal responsive element-binding transcription factor 1 (MTF-1) --- p.16 / Chapter 1.3.1 --- Structure of MTF-1 --- p.16 / Chapter 1.3.2 --- Target genes of MTF-1 --- p.18 / Chapter 1.4 --- Teleost MT and MTF-1 --- p.20 / Chapter 1.5 --- Tilapia --- p.26 / Chapter 1.6 --- Tilapia MT and MTF-1 --- p.26 / Chapter 1.7 --- Aims of study --- p.30 / Chapter 2. --- Chapter Two Materials and Methods / Chapter 2.1 --- Quantification of MTF-1 isoforms and MT mRNA levels in tilapia and Hepa-Tl cells by real-time PCR --- p.32 / Chapter 2.1.1 --- Heavy metal exposure on tilapia --- p.32 / Chapter 2.1.1.1 --- Animals --- p.32 / Chapter 2.1.1.2 --- Heavy metal exposure --- p.32 / Chapter 2.1.1.3 --- Total RNA extraction --- p.33 / Chapter 2.1.1.4 --- Reverse Transcription --- p.35 / Chapter 2.1.2 --- Heavy metal exposure on Hepa-Tl cells --- p.36 / Chapter 2.1.2.1 --- Cell Culture --- p.36 / Chapter 2.1.2.2 --- Metal treatment on Hepa-Tl cells --- p.37 / Chapter 2.1.3 --- SYBR green --- p.39 / Chapter 2.1.3.1 --- Primer Design --- p.39 / Chapter 2.1.3.2 --- Validation of cycling condition --- p.41 / Chapter 2.1.3.3 --- Determination of relative amount of target gene present in the samples --- p.43 / Chapter 2.1.3.4 --- Statistical analysis --- p.44 / Chapter 2.1.4 --- TaqMan probes --- p.44 / Chapter 2.1.4.1 --- Primer Design --- p.44 / Chapter 2.1.4.2 --- Validation of cycling condition --- p.45 / Chapter 2.2 --- Localization study of MTF-1 isoforms --- p.46 / Chapter 2.2.1 --- Amplification of the full length tilapia MTF-1 isoforms --- p.46 / Chapter 2.2.2 --- Preparation of Escherichia coli competent cells --- p.48 / Chapter 2.2.3 --- Transformation --- p.49 / Chapter 2.2.4 --- Confirmation of the insert of the ligation products --- p.50 / Chapter 2.2.5 --- Cloning of MTF-1-L and MTF-1-S gene into phrGFPII-1 vector --- p.51 / Chapter 2.2.6 --- Transient transfection of plasmids to Hepa-Tl cells --- p.54 / Chapter 2.2.7 --- Staining of the nucleus by Hoechst 33342 --- p.55 / Chapter 2.2.8 --- Metal treatment on Hepa-Tl cells --- p.55 / Chapter 2.3 --- Electrophoretic mobility shift assay (EMSA) --- p.56 / Chapter 2.3.1 --- Preparation of Hepa-Tl whole-cell protein extract --- p.56 / Chapter 2.3.2 --- In vitro transcription/translation of tilapia MTF-1 isoforms --- p.57 / Chapter 2.3.3 --- Annealing of the tiMREg oligonucleotides --- p.58 / Chapter 2.3.4 --- Labeling of the annealed tiMREg oligonucleotides --- p.58 / Chapter 2.3.5 --- Electrophoretic mobility shift assay --- p.59 / Chapter 3. --- Chapter Three Results / Chapter 3.1 --- Quantification of MTF-1 isoforms and MT mRNA levels in tilapia and Hepa-Tl cells by real-time PCR --- p.62 / Chapter 3.1.1 --- Validation of primers for real-time PCR --- p.62 / Chapter 3.1.2 --- Tissue distribution of MTF-1 isoforms in tilapia and Hepa-Tl cell-line --- p.63 / Chapter 3.1.3 --- Effect of metal treatment on MTF-1 isoforms and MT gene expression level in different tissues of tilapia and Hepa-Tl cell-line --- p.68 / Chapter 3.2 --- Localization study of MTF-1 isoforms --- p.82 / Chapter 3.2.1 --- Cloning of MTF-1 isoforms into phrGFPII-1 vector --- p.82 / Chapter 3.2.2 --- Transient transfection of phrGFPII-1 plasmids to Hepa-Tl cells --- p.82 / Chapter 3.3 --- Electrophoretic mobility shift assay (EMSA) --- p.96 / Chapter 4. --- Chapter Four Discussion / Chapter 4.1 --- Tissue distribution of MTF-1 isoforms --- p.104 / Chapter 4.2 --- Effect of metal stress on the mRNA expression level of MT and MTF-1 isoforms --- p.106 / Chapter 4.3 --- In vitro study of the localization of the MTF-1 isoforms --- p.114 / Chapter 4.4 --- DNA binding of MTF-1 synthesized by in vitro transcription/translation method --- p.121 / Chapter 4.5 --- Conclusion --- p.125 / Chapter 5. --- REFERENCES --- p.128

Plants respond to and defend themselves against a wide range of disease-causing microbes. In order to do so, massive reprogramming of cellular protein expression patterns, which underpin various defense pathways, must occur. A family of basic leucine zipper transcription factors, called TGA factors, has been implicated in mediating this response. The TGA factors themselves are subject to complex regulation; of note, TGA1 and TGA4 are regulated via a reduction of conserved cysteines after treatment with the phenolic signaling molecular salicylic acid, which accumulates following pathogen challenge. Previous studies indicate that TGA factors physically interact in the yeast two-hybrid system with the plant-specific CC-type of glutaredoxin (Grx)-like proteins. Grx are a family of oxidoreductases that are important for maintaining the cellular redox status and often are required to modulate protein activity. The goal of this study was to ascertain the role of these Grx-like proteins in regulating TGA1 redox state. To this end, the expression patterns of several Grx genes were analyzed.<p> Quantitative-reverse-transcriptase PCR (q-RT-PCR) experiments indicated that TGA1 and TGA4 may be involved in down-regulating levels Grx-like gene transcripts after exposure to pathogens or salicylic acid (SA). Furthermore, qRT-PCR experiments also indicated that expression of some Grx-like genes is induced by SA, jasmonic acid (JA), and <i>Pseudomonas syringae</i>. Overexpression of the Grx-like protein, CXXC9, in <i>Arabidopsis thaliana</i> revealed that it is a regulatory factor in the cross-talk between vi theSA/JA pathways as it is able to suppress expression of PDF1.2, a marker for the JA defense pathway, as determined by qRT-PCR. The â-hydroxy ethyl disulfide (HED) assay was utilized to determine if the CC-type of Grx-like proteins have oxidoreductase activity <i>in vitro</i>. These studies revealed that that the Grx-like proteins do not exhibit oxidoreductase activity in this assay.

Plants respond to and defend themselves against a wide range of disease-causing microbes. In order to do so, massive reprogramming of cellular protein expression patterns, which underpin various defense pathways, must occur. A family of basic leucine zipper transcription factors, called TGA factors, has been implicated in mediating this response. The TGA factors themselves are subject to complex regulation; of note, TGA1 and TGA4 are regulated via a reduction of conserved cysteines after treatment with the phenolic signaling molecular salicylic acid, which accumulates following pathogen challenge. Previous studies indicate that TGA factors physically interact in the yeast two-hybrid system with the plant-specific CC-type of glutaredoxin (Grx)-like proteins. Grx are a family of oxidoreductases that are important for maintaining the cellular redox status and often are required to modulate protein activity. The goal of this study was to ascertain the role of these Grx-like proteins in regulating TGA1 redox state. To this end, the expression patterns of several Grx genes were analyzed.<p> Quantitative-reverse-transcriptase PCR (q-RT-PCR) experiments indicated that TGA1 and TGA4 may be involved in down-regulating levels Grx-like gene transcripts after exposure to pathogens or salicylic acid (SA). Furthermore, qRT-PCR experiments also indicated that expression of some Grx-like genes is induced by SA, jasmonic acid (JA), and <i>Pseudomonas syringae</i>. Overexpression of the Grx-like protein, CXXC9, in <i>Arabidopsis thaliana</i> revealed that it is a regulatory factor in the cross-talk between vi theSA/JA pathways as it is able to suppress expression of PDF1.2, a marker for the JA defense pathway, as determined by qRT-PCR. The â-hydroxy ethyl disulfide (HED) assay was utilized to determine if the CC-type of Grx-like proteins have oxidoreductase activity <i>in vitro</i>. These studies revealed that that the Grx-like proteins do not exhibit oxidoreductase activity in this assay.

Thesis (Ph.D.)--Memorial University of Newfoundland, 2002. / Includes bibliographical references.

Thesis (Ph. D.)--University of Missouri--Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 181-212). Also available on the Internet.