Thesis (Ph. D.)--University of Missouri--Columbia, 1999. / Typescript. Vita. Includes bibliographical references (leaves 137-154). Also available on the Internet.

XPA (xeroderma pigmentosum group A) protein is an essential factor for NER (nucleotide excision repair) which is believed to be involved in DNA damage recognition/verification, NER factor recruiting and stabilization of repair intermediates. Past studies on the structure of XPA have focused primarily on XPA interaction with damaged DNA. However, how XPA interacts with other DNA structures remains unknown though recent evidence suggest that these structures could be important for its roles in both NER and non-NER activities. Previously, we reported that XPA recognizes undamaged DNA ds/ssDNA (double-strand/single-strandDNA) junctions with a binding affinity much higher than its ability to bind bulky DNA damage. To understand how this interaction occurs biochemically we implemented a structural determination of the interaction using a MS-based protein footprinting method and limited proteolysis. By monitoring surface accessibility of XPA lysines to NHS-biotin modification in the free protein and the DNA junction-bound complex we show that XPA physically interacts with the DNA junctions via two lysines, K168 and K179, located in the previously known XPA(98-219) DBD (DNA-binding domain). Importantly, we also uncovered new lysine residues, outside of the known DBD, involved in the binding. We found that residues K221, K222, K224 and K236 in the C-terminal domain are involved in DNA binding. Limited proteolysis analysis of XPA-DNA interactions further confirmed this observation. Structural modelling with these data suggests a clamp-like DBD for the XPA binding to ds/ssDNA junctions. Our results provide a novel structure-function view of XPA-DNA junction interactions.

published_or_final_version / abstract / Biochemistry / Doctoral / Doctor of Philosophy

Récemment, notre laboratoire a démontré pour la première fois, que la protéine Damaged DNA Binding 2 (DDB2) possédait une activité régulatrice négative de l’expression basale de la superoxyde dismutase mitochondriale (SOD Mn) en se fixant sur un élément de réponse dans la région promotrice de son gène. Cette protéine était connue jusque là pour sa participation dans le système de réparation de l’ADN par excision de nucléotides. L’objectif de ce travail a été de définir précisément l’implication de ces deux protéines dans la croissance des cellules d’adénocarcinome mammaire, en développant des modèles cellulaires dont l’expression de la SOD Mn ou de la DDB2 est modulée expérimentalement. Nos résultats montrent pour la 1ère fois, que la SOD Mn est surexprimée dans les cellules tumorales mammaires insensibles aux oestrogènes (ER-) et ayant un pouvoir métastatique, et non dans les cellules épithéliales mammaires normales et les cellules ER+. L’inhibition de l’expression de la SOD Mn entraîne une stimulation de la croissance et une diminution de l’invasivité cellulaires, associées à une activité réduite de la métalloprotéinase 9. L’addition d’antioxydants, éliminant spécifiquement l’H2O2 issu de l’activité élevée de la SOD Mn, entraîne à la fois une inhibition de la croissance et du pouvoir invasif des cellules ER-. Ces résultats révèlent que la SOD Mn participe aux capacités invasives des cellules ER- via la production d’H2O2. Nous avons également montré pour la 1ère fois, que la DDB2 présente une activité oncogénique dans les cellules tumorales mammaires sensibles aux oestrogènes (ER+), non seulement parce que son gène est surexprimé, mais également parce qu’elle active leur prolifération en agissant sur la phase de transition G1/S et sur la progression dans la phase S du cycle cellulaire. Contrairement à la SOD Mn, l’expression de la DDB2 n’est pas observée dans les cellules tumorales mammaires ER-. De même à partir de biopsies provenant de patientes atteintes d’un cancer du sein, nous avons montré que la DDB2 est significativement plus exprimée dans les tumeurs les moins agressives et exprimant le récepteur aux oestrogènes. En montrant l’importance de la SOD Mn et la DDB2 dans la croissance et l’invasion des cellules tumorales mammaires, l’ensemble de ce travail révèle ainsi ces deux protéines comme des marqueurs prédictifs potentiels de la progression tumorale, et ouvre de nombreuses perspectives en cancérologie mammaire. / Recently, our laboratory demonstrated for the first time, that Damaged DNA Binding 2 (DDB2) played a role as a negative transcriptional regulator on the mitochondrial superoxide dismutase (MnSOD) expression through its binding to a specific DNA sequence located into the promoter of MnSOD gene. DDB2 was known as a protein which participates in the nucleotide excision repair of DNA. The goal of this study was to define precisely the involvement of the both proteins in the growth of mammary adenocarcinoma cells, using experimental procedures to modulate their expression in the breast cancer cell lines. Our results show for the first time that MnSOD is overexpressed in the estrogen receptor (ER) negative and metastatic breast tumor cells, but not in normal epithelial mammary cells and ER-positive tumor cells. Inhibition of MnSOD expression stimulates proliferation but decreases the invasive ability and the metalloproteinase 9 activity of tumor cells. Elimination of H2O2 from the elevated MnSOD activity by addition of specific antioxidants decreases proliferation as well as invasive ability of tumor cells, suggesting that the role of MnSOD in the invasive ability of tumor cells is mediated by H2O2. We have shown too for the first time that DDB2 has an oncogenic activity in the ER-positive breast tumor cells, because its gene is overexpressed and stimulates the proliferation by activating the entry of cells in the G1/S transition phase and the S phase progression. In contrast to MnSOD, DDB2 expression is not observed in ER-negative breast tumor cells, but is higher in ER-positive than in ER-negative tumor samples from patients with breast carcinoma. Taken together, our findings demonstrate that both MnSOD and DDB2 play a role in the growth and invasiveness of tumor cells and may become a promising candidate as a predictive markers in breast cancer. More studies will be need to define molecular mechanism controlling this activity of these both proteins.

Chan Kam Leung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 175-182). / Abstract also in Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / Abbreviations --- p.v / Table of Contents --- p.vii / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Drosophila as a model for studying development --- p.1 / Chapter 1.2 --- The formation of the body axis in Drosophila --- p.2 / Chapter 1.3 --- The maternal genes are essential for development --- p.9 / Chapter 1.4 --- Maternal gene bicoid is essential for formation of the anterior structures in the embryo --- p.11 / Chapter 1.5 --- The formation of the biocid protein gradient from anterior pole to posterior pole of the embryo --- p.13 / Chapter 1.6 --- The bed protein gradient controls the downstream zygotic target genes in a concentration-dependent manner --- p.15 / Chapter 1.7 --- The formation of the bed protein gradient in embryo --- p.17 / Chapter 1.8 --- Components required for bcd mRNA localization at anterior pole of oocyte --- p.21 / Chapter 1.8.1 --- Cis-acting elements --- p.21 / Chapter 1.8.2 --- Trans-acting elements --- p.21 / Chapter 1.9 --- The properties of exuperantia protein --- p.25 / Chapter 1.9.1 --- The function of exu protein --- p.25 / Chapter 1.9.2 --- Exuperantia is a phosphoprotein --- p.26 / Chapter 1.9.3 --- Phosphorylation pattern of exuperantia protein is stage-specific --- p.28 / Chapter 1.9.4 --- Reversible phosphorylation is one of the major mechanisms to control protein activity in all eukaryotic cells --- p.29 / Chapter 1.9.5 --- The relationship between the exu protein phosphorylation and the bcd mRNA localization --- p.30 / Chapter 1.10 --- Aim of project --- p.31 / Chapter CHAPTER 2 --- Preparation of the exuperantia genomic DNA and complement DNA (cDNA) mutant Constructs / Chapter 2.1 --- Introduction --- p.33 / Chapter 2.2 --- Materials and methods --- p.35 / Chapter 2.2.1 --- DNA preparation methods --- p.35 / Chapter 2.2.1.1 --- Preparation of double-stranded DNA by polyethylene glycol6000 --- p.35 / Chapter 2.2.1.2 --- Preparation of M13mp8 single-stranded DNA --- p.37 / Chapter 2.2.1.3 --- "Preparation of double-stranded DNA by Biol prep (Modified from Maniatis et al.,1989)" --- p.38 / Chapter 2.2.2 --- "Preparation of DH5α，JM109, TG1 competent cells" --- p.39 / Chapter 2.2.3 --- Bacteria transformation --- p.40 / Chapter 2.2.4 --- Restriction enzyme digestion --- p.40 / Chapter 2.2.5 --- Phenol/chloroform extraction --- p.41 / Chapter 2.2.6 --- Purification of DNA fragment by electro-elution --- p.42 / Chapter 2.2.7 --- DNA ligation --- p.43 / Chapter 2.2.8 --- DNA dephosphorylation --- p.43 / Chapter 2.2.9 --- In vitro site-directed mutagenesis --- p.44 / Chapter 2.2.9.1 --- The Sculptor´ёØ in vitro mutagenesis --- p.44 / Chapter 2.2.9.2 --- The GeneEditor´ёØ in vitro site-directed mutagenesis --- p.47 / Chapter 2.2.10 --- The double-stranded or single-stranded DNA sequencing by T7 DNA polymerase sequencing system --- p.50 / Chapter 2.2.11 --- Denatured polyacrylamide gel electorphoresis --- p.51 / Chapter 2.2.11 --- Nucleotide sequence of the sequencing primers and the mutageneic oligonucleotides --- p.54 / Chapter 2.3 --- Results --- p.55 / Chapter 2.3.1 --- Design exuperantia mutant constructs --- p.55 / Chapter 2.3.1.1 --- Comparison of exu protein amino acids sequence with different Drosophila species --- p.56 / Chapter 2.3.2 --- The exu genomic mutant constructs --- p.63 / Chapter 2.3.3 --- The exu cDNA mutant constructs --- p.63 / Chapter 2.4 --- Discussion --- p.76 / Chapter CHAPTER 3 --- Epitope tagging of exuperantia protein with c-myc eptiope / Chapter 3.1 --- Introduction --- p.79 / Chapter 3.2 --- Materials and methods --- p.84 / Chapter 3.2.1 --- Preparation of the c-myc eptiope DNA fragment --- p.84 / Chapter 3.2.2 --- End-filling of 5'overhang DNA fragment by Klenow fragment --- p.86 / Chapter 3.2.3 --- In vitro translation of protein by TNT® Quick coupled transcription and translation system --- p.86 / Chapter 3.2.4 --- Immunoprecipitation of recombinant exu protein --- p.87 / Chapter 3.2.5 --- Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) --- p.88 / Chapter 3.2.5.1 --- SDS-PAGE preparation --- p.88 / Chapter 3.2.5.2 --- SDS-PAGE electrophoresis --- p.90 / Chapter 3.2.6 --- Western blot analysis --- p.90 / Chapter 3.2.6.1 --- Transfer the protein to a nitro-cellulose membrane by semi-dried blotting --- p.90 / Chapter 3.2.6.2 --- Western blot blocking and antibody recognition --- p.91 / Chapter 3.3 --- Results --- p.92 / Chapter 3.3.1 --- Construction of the plasmid containing exu cDNA tagging with a c-myc epitope --- p.92 / Chapter 3.3.2 --- In vitro translation of c-myc epitope tagged exu protein --- p.102 / Chapter 3.3.3 --- Immunoprecipitation of c-myc labeled exu protein by a polyclonal rabbit anti-exu antibody and monoclonal mouse anti-myc antibody --- p.104 / Chapter 3.4 --- Discussion --- p.109 / Chapter CHAPTER 4 --- In vitro phosphorylation of exuperantia Protein / Chapter 4.1 --- Introduction --- p.111 / Chapter 4.2 --- Materials and methods --- p.113 / Chapter 4.2.1 --- Exogenous kinase phsophorylation reactions --- p.113 / Chapter 4.2.2 --- Separation of the phosphorylated exu protein variants by SDS- PAGE --- p.114 / Chapter 4.3 --- Results --- p.115 / Chapter 4.3.1 --- Western blot analysis of in vitro translated exu protein variants --- p.115 / Chapter 4.3.2 --- Phosphorylation of in vitro translated exu protein variants by exogenous cAMP-dependent protein kinase --- p.118 / Chapter 4.3.3 --- Phosphorylation of in vitro translated exu protein variants by exogenous cGMP-dependent protein kinase --- p.123 / Chapter 4.3.4 --- Phosphorylation of in vitro translated exu protein variants by exogenous protein kinase C --- p.128 / Chapter 4.4 --- Discussion --- p.133 / Chapter CHAPTER 5 --- Introduction of the exuperantia genomic constrcuts into the germline of Drosophila by P element-mediated transformation / Chapter 5.1 --- Introduction --- p.136 / Chapter 5.2 --- Materials and methods --- p.138 / Chapter 5.2.1 --- Construction of a genomic construct for production of transgenic flies --- p.138 / Chapter 5.2.2 --- Preparation of double-stranded DNA by ultra-centrifugation --- p.142 / Chapter 5.2.3 --- P-element mediated transformation --- p.143 / Chapter 5.2.3.1 --- Eggs collection --- p.143 / Chapter 5.2.3.2 --- Dechorionating the eggs --- p.143 / Chapter 5.2.3.3 --- Orientating the eggs --- p.144 / Chapter 5.2.3.4 --- Microinjection --- p.145 / Chapter 5.2.4 --- Collecting virgin female Drosophila --- p.146 / Chapter 5.2.5 --- Setup a crossing experiment --- p.146 / Chapter 5.2.6 --- Preparation of total ovaries and testes extracts exu protein from Female and male Drosophila --- p.147 / Chapter 5.2.7 --- Immunohistochemical distribution of exuperantia protein --- p.147 / Chapter 5.3 --- Results --- p.150 / Chapter 5.3.1 --- Insertion of the mutated exu fragments into the Drosophila Transformation vector (pCaSpeR) --- p.150 / Chapter 5.3.2 --- Introduction of the mutated exu gene into the genome of Drosophila by P-element mediated transformation --- p.153 / Chapter 5.3.3 --- Western blot analysis of the exu protein in the exu (ES2.1) transgenic fly --- p.160 / Chapter 5.3.4 --- Immunohistochemical distribution of exu protein in exuES21 mutants --- p.162 / Chapter 5.3.5 --- Rescue test of exuES2.1 trangenic flies --- p.165 / Chapter 5.4 --- Discussion --- p.168 / Chapter CHAPTER 6 --- General Discussion --- p.171 / References --- p.173 / Chapter Appendix I: --- List of reagents --- p.183 / Chapter Appendix II: --- Publication --- p.187

High fidelity double strand break repair is paramount for the maintenance of genome integrity and faithful passage of genetic information to the following generation. Homologous recombination (HR) and non-homologous end joining (C-NHEJ) have evolved as the two major pathways for the efficient and accurate repair of double strand breaks (DSBs). In addition, a minor Ku- and Ligase IV-independent end-joining pathway has been identified and implicated in the formation of chromosomal translocations. This alternative end-joining pathway occurs by bridging the break ends through annealing between short microhomologies, hence the name microhomology-mediated end joining (MMEJ). In addition to these defined DSB repair pathways, a broken DNA end possesses immense mutagenic potential to generate chromosomal rearrangements. Diverse and complex rearrangements are a commonly observed feature amongst cancer cells. The focus of this thesis is to examine the role of Replication Protein A (RPA) in binding single-stranded DNA (ssDNA) repair intermediates to promote error free repair and to prevent mutagenic chromosomal deletions and rearrangements. RPA is a highly conserved, heterotrimeric ssDNA binding protein with a ubiquitous role in all DNA transactions involving ssDNA intermediates. RPA promotes resection at DSBs to facilitate HR and abrogation of this function has severe consequences. Defective RPA can lead to the formation of secondary structures and impair loading of homology search proteins such as Rad52 and Rad51. Using a chromosomal end-joining assay, we demonstrate that hypomorphic rfa1 mutants exhibit elevated frequencies of MMEJ by up to 350-fold. Biochemical characterization of RPAt33 and RPAt48 complexes show these mutants are compromised for their ability to prevent spontaneous annealing and the removal of secondary structures to fully extend ssDNA. These results demonstrate that annealing between MHs defines a critical control to regulate MMEJ repair. Therefore, RPA bound to ssDNA intermediates shields complementary sequences from annealing to promote error-free HR and prevents repair by mutagenic MMEJ, thereby preserving genomic integrity. RPA also impedes intrastrand annealing between short inverted repeat sequences to prevent the formation of foldback structures. Foldbacks have been proposed to drive palindromic gene amplification, a genome destabilizing rearrangement that can disrupt the protein expression equilibrium and is a prevalent phenomenon within tumor cells. Palindromic duplications are elevated ~1000-fold in rfa1-t33 sae2Δ and rfa1-t33 mre11-H125N mutants compared to sae2Δ or mre11-H125N, yet we did not detect these events in the hypomorphic rfa1-t33 mutant. This suggests that Mre11 and Sae2 play critical roles in preventing palindromic amplification through regulation of the Mre11 structure-specific endonuclease to process DNA foldbacks (also called DNA hairpins). Therefore, Mre11-Sae2 together with RPA prevent palindromic gene amplification. Together, these data focus the spotlight on RPA playing active central and supporting roles to sustain genome stability. This additionally raises that notion that secondary structures are potent instigators and mediators of many genome rearrangements and their prevention by RPA is absolutely crucial.

Forkhead domain基因家族編碼了很多對於胚胎發育至關重要的轉錄因子，而Foxp4則屬於p-subtype forkhead轉錄因子其中一員。Foxp4在胚胎發育期間的表達十分活躍，在發育中的腦部的不同地方表達，但其於中樞神經系統發育中的調控角色並不清楚。Foxp4基因剔除小鼠在出生前死於心臟的缺陷表型(心二分支) ，在此時間段，腦部的發育才剛剛開始，因此我們無法利用Foxp4基因剔除小鼠作為研究中樞神經系統發育的動物模型。最近，我們的團隊利用小腦組織培養技術及siRNA發佈的研究顯示，Foxp4在小鼠小腦中的蒲金氏細胞(Purkinje cell)中擔當著重要的維持作用。這項研究結果加深了我們對研究Foxp4在中樞神經系統發育中的調控角色的決心。 / 本論文旨在利用斑馬魚作為實驗模型，研究foxp4在斑馬魚中樞神經系統發育中的表達及調控角色。RT-PCR結果顯示foxp4在斑馬魚發育中的bud stage開始表達，並在及後的階段維持其表達水平。利用原位雜交技術 (whole mount in-situ hybridization)，我們發現foxp4表達的地區主要集中於發育中的腦部。在成年斑馬魚中，foxp4表達在不同組織和器官，包括腦部，眼睛和心臟。成年斑馬魚腦部切片原位雜交 (sectioned in-situ hybridization)則顯示，foxp4在小腦的蒲金氏細胞和視頂蓋(optic tectum)的periventricular gray zone表達。 / 為了進一步探究foxp4對於胚胎發育過程中的功能，我們利用微注射技術，把反義嗎啉 (morpholino) MO1注射到斑馬魚胚胎中，大幅度抑制foxp4的表達水平。胚胎受精後48小時，MO1注入的胚胎顯示出第四腦室腦積水的缺陷表型。組織學分析顯示，第四腦室以下的延髓被壓縮致形態異常。此外，利用原位雜交技術及不同的分子標記，我們發現胚胎的中後腦邊界也會出現輕度畸形，而後腦的神經元數量及排列亦受到影響。 / 本項研究展示foxp4在胚胎中樞神經系統的發展的重要性，亦提供了新的見解。我們認為foxp4可能是調控腦室發育的重要成員，但在此方面與foxp4相關的分子機制仍須作更深入的研究。 / The forkhead domain gene family encodes a large group of transcription factors that play essential roles in development. Foxp4 is one of the members in the Foxp subfamily that expressed in different parts of developing central nervous system (CNS) and its function is less characterized. Previous study on Foxp4-knockout mice resulted in early embryonic lethality due to defective heart tube development that hindered the functional study of Foxp4 in CNS development. Recently, our laboratory reported that Foxp4 functions as a maintenance role in the Purkinje cell in the mouse cerebellum. Nevertheless, the role of foxp4 in CNS development was still unclear. / In this study, we used zebrafish as a model to study the expression pattern and functional study of foxp4 in the developing CNS. RT-PCR analysis showed that foxp4 transcript was expressed at the bud stage and maintained in the later embryonic stages. Whole-mount in-situ hybridization showed that foxp4 expressed in the cephalic region during embryonic development. In adult zebrafish, foxp4 expresses in different tissues and organs including brain, eye and heart. Sectioned in-situ hybridization of the adult zebrafish brain showed that foxp4 was specifically expressed in the Purkinje cell and the periventricular gray zone of optic tectum. / To further investigate the function of foxp4 during embryonic development, we injected antisense morpholino, MO1 into the zebrafish embryo to knockdown foxp4. By 48 hour post fertilization (hpf), MO1-injected embryos displayed hydrocephalus in the 4th ventricle. Histological analysis revealed that the medulla oblongata below the 4th ventricle was compressed by the edema resulting in abnormal morphology of medulla oblongata in the MO1-injected morphant. In addition, a mild malformation of the mid-hindbrain boundary, disrupted hindbrain patterning was observed in MO1-injected morphant. / Our findings provide new insight into the function of foxp4 in embryonic CNS development. We suggested that foxp4 may be essential in regulating the brain ventricle development while the molecular mechanism underlying the functional role of foxp4 requires further investigation. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Wong, Wai Kei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 92-102). / Abstracts also in Chinese. / Abstract --- p.iii / 摘要 --- p.v / Acknowledgement --- p.vii / Figure and table list --- p.xi / Abbreviation --- p.xii / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Zebrafish as a developmental model --- p.1 / Chapter 1.2 --- Zebrafish development with highlights --- p.3 / Chapter 1.2.1 --- CNS development --- p.3 / Chapter 1.3 --- Forkhead domain gene in development --- p.5 / Chapter 1.3.1 --- History of forkhead domain gene --- p.5 / Chapter 1.3.2 --- Functional roles of forkhead domain genes in development --- p.6 / Chapter 1.4 --- Foxp subfamily --- p.8 / Chapter 1.4.1 --- Diverse functions of Foxp1, 2, 3 and 4 --- p.8 / Chapter 1.4.2 --- Relationship between Foxp subfamily members --- p.10 / Chapter 1.5 --- Foxp4 --- p.11 / Chapter 1.5.1 --- Genomic organization and protein structure of mFoxp4 --- p.11 / Chapter 1.5.2 --- Previous studies of mFoxp4 --- p.14 / Chapter 1.5.3 --- Foxp4 studies in other model organisms --- p.14 / Chapter 1.5.3.1 --- Rat --- p.15 / Chapter 1.5.3.2 --- Xenopus --- p.16 / Chapter 1.5.3.3 --- C. elegans --- p.16 / Chapter 1.5.4 --- Zebrafish foxp4 --- p.17 / Chapter 1.5.5.1 --- Genomic organization and protein structure of foxp4 --- p.17 / Chapter 1.5.5.2 --- Sequence alignment of foxp4 with other models --- p.19 / Chapter 1.6 --- Hypothesis, aim and strategy of the study --- p.22 / Chapter Chapter 2 --- Expression of foxp4 in zebrafish embryo and adult zebrafish brain / Chapter 2.1 --- Introduction --- p.24 / Chapter 2.2 --- Materials and methods --- p.25 / Chapter 2.2.1 --- Animals --- p.25 / Chapter 2.2.2 --- Materials --- p.26 / Chapter 2.2.3 --- Semi-quantitative PCR --- p.35 / Chapter 2.2.3.1 --- cDNA of zebrafish embryo --- p.35 / Chapter 2.2.3.2 --- Isolation of adult zebrafish organs --- p.36 / Chapter 2.2.3.3 --- RNA extraction and reverse transcription --- p.36 / Chapter 2.2.3.4 --- Polymerase chain reaction --- p.37 / Chapter 2.2.4 --- Subcloning of DNA fragment / Chapter 2.2.4.1 --- Preparation of cloning vectors --- p.40 / Chapter 2.2.4.2 --- Subcloning of DNA fragments --- p.40 / Chapter 2.2.4.3 --- Transformation of DNA into competent cells --- p.40 / Chapter 2.2.4.4 --- Preparation of recombinant plasmid DNA --- p.41 / Chapter 2.2.5 --- Whole mount in-situ hybridization of zebrafish embryo --- p.45 / Chapter 2.2.5.1 --- Preparation of equipment --- p.45 / Chapter 2.2.5.2 --- Preparation of zebrafish embryos --- p.45 / Chapter 2.2.5.3 --- Preparation of RNA probe --- p.46 / Chapter 2.2.5.4 --- Whole-mount in-situ hybridization --- p.48 / Chapter 2.2.6 --- Sectioned in-situ hybridization of adult zebrafish brain --- p.49 / Chapter 2.2.6.1 --- Histology of adult zebrafish brain --- p.49 / Chapter 2.2.6.2 --- Sectioned in-situ hybridization --- p.50 / Chapter 2.3 --- Results --- p.51 / Chapter 2.3.1 --- Expression profile of foxp4 in different stages of zebrafish embryo --- p.51 / Chapter 2.3.2 --- Expression pattern of foxp4 in different stages of zebrafish embryo --- p.54 / Chapter 2.3.3 --- Expression profile of foxp4 in different zebrafish organs and tissues --- p.57 / Chapter 2.3.4 --- Expression pattern of foxp4 in adult zebrafish brain --- p.59 / Chapter 3.4 --- Discussion --- p.61 / Chapter Chapter 3 --- Functional analysis of foxp4 in zebrafish embryonic development / Chapter 3.1 --- Introduction --- p.63 / Chapter 3.2 --- Materials and methods --- p.64 / Chapter 3.2.1 --- Materials --- p.64 / Chapter 3.2.2 --- Design of morpholino --- p.68 / Chapter 3.2.3 --- Sequencing of morpholino target regions of foxp4 --- p.70 / Chapter 3.2.4 --- Microinjection --- p.70 / Chapter 3.2.4.1 --- Preparation of materials and equipment --- p.70 / Chapter 3.2.4.2 --- Preparation of injection needle --- p.70 / Chapter 3.2.4.3 --- Preparation of morpholinos --- p.70 / Chapter 3.2.4.4 --- Calibration of injection volume --- p.71 / Chapter 3.2.4.5 --- Microinjection of zebrafish embryo --- p.71 / Chapter 3.2.5 --- Western blotting to assay foxp4 translation inhibition --- p.72 / Chapter 3.2.5.1 --- Preparation of protein extracts --- p.72 / Chapter 3.2.5.2 --- Coomassie blue staining --- p.73 / Chapter 3.2.5.3 --- Western blotting --- p.74 / Chapter 3.2.6 --- Whole mount in-situ hybridization --- p.74 / Chapter 3.3 --- Results --- p.75 / Chapter 3.3.1 --- MO1 knockdown efficiency assayed by Western blotting --- p.75 / Chapter 3.3.2 --- General morphology of morphants --- p.77 / Chapter 3.3.3 --- Histology at the hindbrain region showing the phenotype --- p.79 / Chapter 3.3.4 --- Whole mount in-situ hybridization of different molecular markers --- p.81 / Chapter 3.4 --- Discussion --- p.85 / Chapter Chapter 4 --- Future directions and conclusion / Chapter 4.1 --- Future directions --- p.89 / Chapter 4.2 --- Conclusion --- p.91 / Reference --- p.92

Genome stability has great importance in maintaining cell viability and optimal functionality of cellular processes. Loss of genome stability can lead to cell death in the simplest organisms and to deregulation of the cell proliferation machinery in higher organisms, potentially causing cancer or morbid states. The Single Stranded DNA Binding (SSB) protein of Escherichia coli is an essential protein that binds and stabilises ssDNA stretches. Its role is particularly crucial during DNA replication, recombination and repair processes and it has therefore been predicted to play a prominent role in the maintenance of genome stability. The role of SSB in genome instability was investigated using an E. coli strain in which, the expression of the ssb gene was placed under the control of the arabinose promoter. The level of SSB protein present in the cell could therefore be tuned by varying the arabinose concentration in the medium. A wide characterisation of the behaviour of the strain at low SSB level was carried out. Viability and growth tests showed that a threshold level of protein is required to allow normal growth. Microscopy analyses were carried out to follow cell division, nucleoid morphology and SOS response activation. Cells grown at low SSB level, showed a phenotype consistent with impaired cell division and altered nucleoid morphology. The SOS response was activated at low SSB levels and cell elongation was detected. Lowering the arabinose concentration in solid medium allowed the selection of suppressor strains that could form colonies under the new conditions. Sequencing of the entire genome of one such suppressor strain was carried out revealing a possible candidate for the phenotype change. The stability of a 105bp and of a 246bp DNA imperfect palindromes and the stability of CAG·CTG trinucleotide repeat arrays, inserted in the E. coli chromosome, were investigated in correlation to the SSB cellular level. Lowering the SSB level in cells grown on solid medium, increased the instability of the 105bp palindrome presumably by increasing the number of slippage events. On the other hand, SSB overexpression did not have an effect on the stability of the 246bp palindrome. The stability of a leading strand (CAG)75 repeat array was highly increased by overexpressing SSB, while the same effect was not observed for a leading strand (CTG)137 repeat array. Furthermore, excess SSB caused a change in the deletion size distribution profile for the leading strand (CAG)75 strain, lowering the bias towards big deletions. This is consistent with SSB being able to preferentially impede the formation of big DNA hairpins. Also, SbcCD nuclease was shown to have an effect on the deletion size distribution profile of the leading strand (CTG)137 strain. The lack of SbcCD led to a slight reduction of the number of big deletions.

DNA-binding proteins bind to specific sequences to direct their activity to defined loci in the genome. Regulation of gene expression, for example, is dependent on the recognition of specific DNA sequences by transcription factors (TFs). These TFs receive input from cellular signals to control panels of genes to meet the needs of the cells. Critical to this function is the recognition and binding of TFs to the correct DNA sequence. The main focus of this thesis is to quantitatively determine how proteins, including TFs, distinguish DNA sequences, and to understand how DNA sequence affect their function. Primarily using the Glucocorticoid receptor (GR) as the model TF, I developed novel methods to measure the DNA binding specificity over long binding sites. These methods: 1) Distinguished the sequence specificity of GR and closely related androgen receptor (AR), which helped to both account for differential genomic localization between the two factors, and explained how GR can functionally substitute for AR in castration-resistant prostate cancer (Chapter II); 2) Explored the effect of DNA sequence on GR-regulated transcription through the specification of monomeric versus dimeric binding. Sequence motifs that bias GR binding toward the monomeric state were discovered (Chapter III); 3) Demonstrated a conserved role of intrinsic specificity in directing the degree of GR genomic occupancy in vivo in a fixed chromatin context (Chapter V); 4) Quantitatively modeled and decoupled the DNA binding and cleavage specificities of CRISPR-Cas9 system, providing a rapid pipeline to characterize the genome-editing reagents (Chapter IV). In summary, we showed here that DNA binding specificity is only the initial step in directing the activity of the bound protein. Beyond the affinity-based recruitment, DNA sequences can regulate the protein activity through alternative mechanisms, such as modulating the binding cooperativity, or directly serving as an allosteric ligand for protein function that is independent of DNA binding affinity.

Doctor of Philosophy(PhD) / The present study deals with the synthesis and characterization of six tri-palladium complexes code named MH3, MH4, MH5, MH6, MH7 and MH8 that contained two planaramine ligands bound to the central or each of the terminal metal ions. The activity of the compounds against human cancer cell lines: A2780, A2780cisR and A2780ZD0473R, cell uptake, levels of DNA-binding and nature of interaction with salmon sperm and pBR322 plasmid DNA have also been determined. Whereas cisplatin binds with DNA forming mainly intrastrand GG adduct that causes local bending of a DNA strand, the tri-palladium complexes are expected to bind with DNA forming a number of long-range interstrand GG adducts that would cause a global change in DNA conformation. Among the designed complexes, MH6 that has two 2-hydroxypyridine ligands bound to each of the two terminal palladium ions is found to be most active. The compound also has the highest cell uptake and Pd-DNA binding levels. In contrast, MH8 which has two 4-hydroxypyridine ligands bound to each of the two terminal palladium ions is found to be least active. The results indicate that, as applied to the terminal metal centres, 2-hydroxypyridine would be more activating than 4-hydroxypyridine perhaps because of greater protection provided to the terminal centres from coming in contact with the solvent molecules. In contrast, when bound to the central metal centre, 4-hydroxypyridine appears to play a slightly greater activating role than 2-hydroxypyridine or 3-hydroxypyridine, suggesting that non-covalent interactions such as hydrogen bonding associated with the ligand rather than its steric effect may be a more important determinant of antitumour property. The results illustrate structure-activity relationships and suggest that the tri-palladium complex containing two 2-hydroxypyridine ligands bound to each of the three metal centres or the compound that contains two 2-hydroxypyridine ligands bound to each of the two terminal metal centres and two 4-hydroxypyridine ligands bound to the central metal centre, may be much more active than any of the designed complexes.