Forkhead box Class O (FOXO), one subfamily of the Forkhead box (Fox) family, which is featured by the Forkhead (FH) DNA-binding domain, includes four human transcription factors: FOXO1, FOXO3a, FOXO4, and FOXO6. The tumor suppressor FOXO3a is involved in multiple physiological and pathological processes, such as breast cancer and acute myeloid leukemia, and is related to human longevity. It plays essential role in metabolism, cell cycle arrest, DNA repair, and apoptosis. Besides the FH domain, FOXO3a contains three other regions (CR1-3), conserved within FOXO subfamily. It specifically binds a consensus Forkhead response element (FRE) DNA sequence through the FH domain, and recruits transcriptional coactivator CBP/p300 to activate gene transcription. FOXO3a functions through interacting with other proteins as well. FOXO3a binds p53 through the FH domain and the CR3 region, which are also engaged in an intramolecular interaction, and the solution structure of the former one was determined. This intramolecular interaction regulates coactivator recruitment and is disrupted by FRE DNA. A novel transactivation domain (TAD) CR2C was identified in addition to the known TAD CR3, both of which promiscuously associate with the KIX domain of CBP/p300 in equilibrium between two conformational states, the structures of which were determined by NMR spectroscopy. These two TADs of FOXO3a form additional multivalent binding to the TAZ1 and TAZ2 domains of CBP/p300, further increasing the promiscuity and complexity of the interaction. The coactivator recruitment is modulated by AMPK phosphorylation, which enhances the multivalent interaction between FOXO3a and CBP/p300, and thus the transactivation. These results indicate the significance of intrinsically disordered regions (IDRs) of FOXO3a in transcriptional activation and protein interaction, provide insight of the role of FOXO3a in gene transcription and apoptosis under various conditions, and potentially contribute to the cancer therapy.

Forkhead box Class O (FOXO), one subfamily of the Forkhead box (Fox) family, which is featured by the Forkhead (FH) DNA-binding domain, includes four human transcription factors: FOXO1, FOXO3a, FOXO4, and FOXO6. The tumor suppressor FOXO3a is involved in multiple physiological and pathological processes, such as breast cancer and acute myeloid leukemia, and is related to human longevity. It plays essential role in metabolism, cell cycle arrest, DNA repair, and apoptosis. Besides the FH domain, FOXO3a contains three other regions (CR1-3), conserved within FOXO subfamily. It specifically binds a consensus Forkhead response element (FRE) DNA sequence through the FH domain, and recruits transcriptional coactivator CBP/p300 to activate gene transcription. FOXO3a functions through interacting with other proteins as well. FOXO3a binds p53 through the FH domain and the CR3 region, which are also engaged in an intramolecular interaction, and the solution structure of the former one was determined. This intramolecular interaction regulates coactivator recruitment and is disrupted by FRE DNA. A novel transactivation domain (TAD) CR2C was identified in addition to the known TAD CR3, both of which promiscuously associate with the KIX domain of CBP/p300 in equilibrium between two conformational states, the structures of which were determined by NMR spectroscopy. These two TADs of FOXO3a form additional multivalent binding to the TAZ1 and TAZ2 domains of CBP/p300, further increasing the promiscuity and complexity of the interaction. The coactivator recruitment is modulated by AMPK phosphorylation, which enhances the multivalent interaction between FOXO3a and CBP/p300, and thus the transactivation. These results indicate the significance of intrinsically disordered regions (IDRs) of FOXO3a in transcriptional activation and protein interaction, provide insight of the role of FOXO3a in gene transcription and apoptosis under various conditions, and potentially contribute to the cancer therapy.

In order to speedup the encoding process of H.264/AVC and Scalable Video Coding (SVC), Temporal and Spatial Correlation-based Merging and Splitting (TSCMS) fast mode decision algorithm and Coded Block Pattern (CBP)-based fast mode decision algorithm are proposed in this thesis. TSCMS and CBP-based fast mode decision algorithms are applied to H.264/AVC and SVC, respectively. In TSCMS, Temporal Correlation (TC) is used to predict the Motion Vectors (MVs) of 8¡Ñ8 blocks in each macroblock. In addition, the merging and splitting procedure is adopted to predict the motion vectors of other blocks. Afterwards, the spatial correlation is performed to merge 16¡Ñ16 blocks instead of the conventional merge scheme. CBP value is the syntax used at each Macroblock (MB) header to indicate whether an MB contains residual information or not in CBP-based fast mode decision algorithm. The proposed algorithm can exclude the invalid modes for the mode prediction of the current MB in Enhancement Layer (EL) through the CBP values and MB modes of adjacent MBs in EL and the co-located Base Layer (BL) MB modes. Experimental results show that the proposed algorithms reduce computations significantly with negligible PSNR degradation and bit increase when compared to JM 12.3, JSVM 9.12, and the other existing methods.

To maintain intracellular redox homeostasis, genes encoding many endogenous antioxidants and phase II detoxification enzymes are transcriptionally upregulated upon deleterious oxidative stress through the cis- antioxidant responsive elements (AREs) in their promoter regions. Nrf2 has emerged as the pivatol transcription factor responsible for ARE-dependent transcription, and has been shown to play critical roles in hepatotoxicity, chemical carcinogenesis, pulmonary inflammatory diseases, neurodegenerative diseases and aging. Therefore, understanding the molecular mechanism of the Nrf2-dependent cytoprotective system is important for development of drugs for therapeutic intervention.Nrf2 is targeted by Keap1 for ubiquitin-mediated degradation under basal conditions. Upon oxidative stress, distinct cysteine residues of Keap1 are alkylated, leading to inhibition of Keap1 and activation of Nrf2. However, it was not clear how Nrf2 is re-entered into the repression status when redox homeostasis is re-achieved. In this dissertation, we establish that the post-induction repression of Nrf2 is controlled by the nuclear export function of Keap1 in alliance with the cytoplasmic ubiquitination/ degradation machinery. We show that a nuclear export sequence (NES) in Keap1 is required for termination of Nrf2 signaling; ubiquitination of Nrf2 is carried out in the cytosol; Keap1 nuclear translocation is independent of Nrf2; and the Nrf2-Keap1 complex does not bind the ARE. Collectively, these results suggest that Keap1 translocates into the nucleus to dissociate Nrf2 from the ARE and mediates nuclear export of Nrf2 followed by ubiquitination and degradation of Nrf2 in the cytoplasm.In addition to Keap1-mediated negative regulation, we identified a novel positive regulatory mechanism of Nrf2 mediated by transcription co-activator p300/CBP. We show that p300/CBP directly binds and acetylates Nrf2 in response to oxidative stress. We have identified multiple acetylated lysine residues within the Nrf2 Neh1 DNA-binding domain. Combined lysine-to-arginine mutations on the acetylation sites, with no effects on Nrf2 protein stability, compromised the DNA-binding activity of Nrf2 in a promoter-specific manner both in vitro and in vivo. These findings demonstrated that acetylation of Nrf2 by p300/CBP augments promoter-specific DNA binding of Nrf2 and established acetylation as a novel regulatory mechanism that functions in concert with Keap1-mediated ubiquitination in modulating the Nrf2-dependent antioxidant response.

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

L’oestradiol est l’une des hormones sécrétées par les ovaires. Non seulement impliquée dans le développement des organes sexuels chez les femmes, cette hormone aurait également un rôle important dans la carcinogénèse. En effet, l’oestradiol agit comme facteur de croissance dans le cancer, et c’est pourquoi la thérapie anti-hormone apparaît efficace dans le traitement du cancer du sein. Dans ce projet, nous avons étudié comment une seule molécule pouvait être aussi polyvalente, en modifiant certains cofacteurs altérant ainsi l’expression de certains gènes. L'Œstradiol agit sur l’ADN en recrutant le récepteur aux œstrogènes via les éléments hormonaux-sensibles. La liaison des œstrogènes sur leurs récepteurs induit un changement dans leur conformation et déclenche le recrutement de co-activateurs. Ces co-activateurs, tels CARM1 et CBP qui sont des enzymes épigénétiques majeures, sont recrutés par les gènes cibles des œstrogènes. Bien que ce mécanisme soit connu, la signification fonctionnelle du recrutement d’HAT et d’une méthyltransférase restait toujours non élucidée. Au cours de ma thèse, j’ai démontré que la protéine CBP est spécifiquement et exclusivement méthylée par CARM1 in vivo et qu’il existe plusieurs formes de méthyl-CBP qui recrutent et régulent différents gènes clefs dans la voie de signalisation des œstrogènes. Pour la première fois, nous avons défini un « code pour les modifications des co-activateurs », qui est impliqué dans la réponse endocrinienne et pourrait être dérégulé dans la progression tumorale du cancer du sein. Ces résultats mettent en évidence la régulation croisée entre les deux enzymes épigénétiques CARM1 et CBP comme une réponse essentielle aux œstrogènes et révèlent pour la première fois le mécanisme singulier par lequel les gènes cibles des œstrogènes sont régulés. / Estradiol is one of the hormones secreted by the ovaries. Not only involved in sexual development of women, this hormone would also have a significant role in carcinogenesis. Indeed estradiol acts as growth factor in cancer and this is why anti-hormone therapy is effective in breast cancer. In this project we investigated how a single molecule can be so diverse with respect to modulating certain cofactors and thus altering gene expression. Estradiol acts on DNA by recruiting the estrogen receptor on the hormone responsive elements. The binding of estrogen to its receptor induces a conformation change on the receptor which mediates the recruitment of co-activators. Coactivators such as CARM1 and CBP which are major epigenetic enzymes are recruited on estrogen target genes. Although this mechanism was known, the functional significance of recruiting a HAT and a methyltrasferase was still impending. In my thesis, I have shown that CBP is specifically and exclusively methylated by CARM1 in vivo and that there are several combinations of methyl CBP species which recruit and regulate distinct gene hubs in estrogen signaling. For the first time we define a “code for coactivator modifications”, which is involved in endocrine response and could be deregulated in tumor progression in breast cancer. These results identify the cross regulation between the two epigenetic enzymes CARM1 and CBP as a pivotal response to estrogen and reveal for the first time a distinct mechanism by which estrogen target genes are regulated.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

L’étude de la plasticité cellulaire est un puissant outil pour comprendre le choix du destin cellulaire pendant la différenciation et dans les processus cancéreux lors de la transformation d’une cellule normale en une cellule maligne. Chez la drosophile, le facteur de transcription Gcm contrôle la détermination du destin glial. Dans des mutants gcm, les cellules qui se développent normalement en glie entrent dans la voie de différenciation neuronale alors que l’expression ectopique de gcm dans des progéniteurs neuronaux induit de la glie. Ces données font de Gcm un outil important pour comprendre les bases de la plasticité cellulaire. Mon projet de thèse vise à comprendre les mécanismes contrôlant la plasticité des cellules souches neurales. Nous avons ainsi montré que la capacité des CSNs à se convertir en glie après expression forcée de Glide/Gcm décline avec l'âge et que lors de l'entrée en phase quiescente ou apoptotique, ils ne peuvent plus être convertis. Nous avons aussi découvert que le processus de conversion du destin ne se manifeste pas uniquement par l’expression de marqueurs gliaux mais aussi par des changements spécifiques au niveau de la chromatine. D’une manière intéressante, nous avons aussi montré que la stabilité de la protéine Glide/Gcm est contrôlée par deux voies opposées, où Repo et l’histone acetyltransférase CBP jouent un rôle majeur. / The study of cellular plasticity is a powerful tool to understand the mechanisms directing cell fate choice during differentiation and transformation of a normal cell into a cancerous one. In Drosophila, the transcription factor Gcm control glial fate determination. In gcm mutants, cells that normally develop into glia enter the path of neuronal differentiation, whereas ectopic expression of gcm in neural progenitors induces glia. These properties make gcm an important tool for understanding the basics of cellular plasticity. My thesis project aims to understand the mechanisms controlling the plasticity of neural stem cells (NSCs). Based on this aim, we showed that the ability of NSCs to be transformed into glia, after forced expression of Gcm, declines with age and that upon entry into quiescence or apoptosis, they cannot be converted. We also found that the process of fate conversion does not manifest itself only through the expression of glial markers but also by specific changes in the level of chromatin. Remarkably, we also showed that the stability of the protein Gcm is controlled by two opposite and interconnected loops, where Repo and the histone acetyltransferase CBP play a major role.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Objective: P300/CBP Associated Factor (PCAF) is a histone acetyltransferase, and has been reported to interact with nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) and to stimulate cyclooxygenase-2 (COX-2) transcriptional activation. The aim of this study was to determine the role of PCAF in chronic pain modulation. / Method: In an in vitro experiment, PCAF small-interfering RNA (siRNA) was used to knock down PCAF. Interleukin-1 β (IL1β) was applied as COX-2 inducer in SK-N-SH neuroblastoma cells. Luciferase assay and chromatin immunoprecipitation (ChIP) were performed regarding COX-2 promoter region. / In an in vivo experiment, PCAF was examined for its distribution in dorsal horn of Spraque-Dawley rats. COX-2 level in the spinal cord was determined after inhibition of PCAF in rats with Complete Freund's Adjuvant (CFA)-induced pain. ChIP was also performed. / Finally, we tested whether genetic variations in the PCAF gene affected the risk of chronic pain in a gene association study of 267 surgical patients. The associations of pain with genotypes (58 single nucleotide polymorphisms, SNPs)/haplotypes were analyzed by χ² and Fisher exact tests. / Results: Knock-down of PCAF reduced COX-2 level and NF-κB activity. PCAF and acetylated histone 3 lysine 14 (H3K14) were enriched at COX-2 promoter when IL1β was applied. / PCAF was expressed in neurons at superficial layers of rat dorsal horn. In the in vivo experiment, COX-2 was reduced with the inhibition of PCAF in CFA rats. PCAF was enhanced at COX-2 promoter when CFA was injected. Anacardic acid and PCAF siRNA significantly alleviated thermal nociception and mechanical allodynia. / In the gene association study, 6 SNPs and 5 haplotypes were significantly associated with higher risk of severe chronic postsurgical pain. Multivariable analysis showed that patients with a SNP rs6763504 had a higher risk of developing severe chronic postsurgical pain (p = 0.001). / Conclusion: PCAF regulated COX-2 transcription and reduction or inhibition in PCAF resulted in a decrease in COX-2 and less chronic inflammatory pain. Genetic variations in the PCAF gene increased risk of severe chronic post-surgical pain in patients. / 實驗目的：P300/CBP相關蛋白（PCAF）是一種組蛋白乙酰化轉移酶。這種蛋白已被報道可以和核因子活化B細胞κ輕鏈增強子(NF-κB)相互作用，以及增進環氧合酶-2（COX-2）的轉錄激活。本實驗的目的在於研究PCAF在疼痛調節中的作用。 / 實驗方法：在細胞實驗中，我們使用了小干擾RNA（siRNA）來降低PCAF的含量。同時我們使用了白細胞介素-1β（IL1β）來作為SK-N-SH神經母細胞瘤細胞中COX-2的誘導劑。我們使用了熒光素酶試劑和染色質免疫沉澱來研究COX-2啟動子區域。 / 在體內實驗中，我們檢測了PCAF在大鼠脊椎背角部位的分佈。在弗氏完全佐劑（CFA）致痛的大鼠模型中，我們在PCAF抑制的情況下檢測脊髓中COX-2的水平。我們還進行了染色質免疫沉澱。 / 最後，在招募了267位手術患者的基因關聯試驗中，我們對PCAF基因中的基因變異對慢性疼痛風險的影響進行了分析。我們運用卡方檢驗和費雪精確性檢驗對疼痛與基因型（58個單核苷酸多態性）和單倍型的關係進行分析。 / 實驗結果：減少的PCAF降低了COX-2的水平以及NF-κB的活性。當添加了IL1β時PCAF和乙酰化第三組蛋白14號賴胺酸（H3K14）在COX-2啟動子處富集。 / PCAF在大鼠脊椎背角部位的淺表層（第一層和第二層）的神經細胞里表達。在動物實驗中，注射了CFA的大鼠顯示COX-2會隨著PCAF的抑制而下降。大鼠注射了CFA后PCAF在COX-2啟動子處有所增加。漆樹酸和PCAF siRNA顯著地減輕了熱痛和機械痛提高了機械痛閾值。 / 在該基因關聯試驗中，我們鑒定出六個單核苷酸多態性和五種單倍型與較高風險的嚴重術後慢性痛有顯著的相關性。多元回歸分析表明在PCAF基因上具有rs6763504遺傳變異的病人在術後發展嚴重慢性痛的幾率會較高(p = 0.001)。 / 結論：PCAF調節COX-2的轉錄，而且PCAF的減少或者抑制導致了COX-2的降低同時慢性炎症痛的減少。PCAF基因上的遺傳變異提高了術後病人嚴重慢性痛的風險。 / Meng, Zhaoyu. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 117-134). / Abstracts also in Chinese. / Title from PDF title page (viewed on 30, December, 2016). / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only.