Molecular and biochemical characterisation of a Fugu nitric oxide synthase

A neuronal nitric oxide synthase (NOSl) gene was isolated from the the model vertebrate genome of the Japanese pufferfish Fugu rubripes. The Fugu NOSl gene was cloned by screening of a genomic cosmid library and PCR of genomic DNA. It was sequenced multiple times on both strands and conserved co-factor/substrate binding sites for haem, L-arginine, Ca2+/Calmodulin, FAD, FMN and NADPH were identifed. In addition, a CaM inhibitory sequence present only in constitutive isoforms was identified along with a PDZ domain specific to nNOS isoforms. At 22,203 bp the Fugu NOSl gene shows a reduction in size of -12 times when compared to the human NOSl gene. Full-length Fugu NOSl cDNA (fNOS) was isolated from the brain of another species of Japanese pufferfish, Takifugu poecilonotus, by 5' and 3' RACE and PCR. fNOS was cloned into the baculovirus-transfer vector pVL1393, sequenced and transfected into Spodoptera frugiperda clone 21 cells (Sf21) for expression studies. fNOS showed the highest amino acid identity to the mammalian and Xenopus laevis nNOS isoforms (74–75%). Amino acid identity dropped to 58% when fNOS was compared to eNOS isoforms, 54% for iNOS isoforms and 47–52% for the reported invertebrate NOS isoforms. Expression of the recombinant Fugu NOSl protein (FNOS) by pVLfNOS- infected Sf21 cells was detected by western blotting and immunocytochemical staining with a monoclonal anti-nNOS antibody. Expression of functional FNOS was greatest after 24 hours as measured by the spectrophometric conversion of oxyhaemoglobin to methaemoglobin by NO on a dual-wavelength spectrophotometer. In the presence of FAD, NADPH, and BH4, FNOS activity was dependent on the addition of L-arginine and was inhibitable by the NOS inhibitors L-NMMA, L-Thiocitrulline and 1400W. Partial purification of FNOS was achieved using a 2'5' ADP sepharose column and lOmM NADPH for elution

Comparative and molecular characterisation of a schizophrenia susceptibility locus

A substantial genetic contribution to the aetiology of schizophrenia and other major mental illnesses has been convincingly and repeatedly established by family, twin and adoption studies. However, phenotypic and genetic heterogeneity have severely hampered linkage and association studies, and consequently the molecular basis of the genetic contribution remains undefined. The use of cytogenetic abnormalities to identify disease loci is a well established technique that overcomes many of the problems of linkage and association studies. A balanced t(l;l I)(q42;q14) translocation segregates in a large Scottish family (LOD = 7.1) with schizophrenia and related psychiatric disorders. At least three independent studies have also identified the 1q42 region of the genome as a susceptibility locus for major mental illness. The chromosome 1 breakpoint region now represents one of the best-supported loci for susceptibility to major mental illness. Two novel genes are directly disrupted by the chromosome 1 breakpoint, Disrupted-In-Schizophrenia 1 and 2 (DISCI and DISC2). The central hypothesis of this work is that genes directly disrupted by, or near to the chromosome 1 breakpoint contribute a significant susceptibility to major mental illness. This thesis set out to characterise DISCI, DISC2 and neighboring genes through comparative sequence analysis. Specifically, the research aimed to better define the locus, the genes, their functions and regulatory sequences, to evaluate the functional consequences of the translocation and how these may relate to the t(1;11) phenotype.Human genomic sequence over the breakpoint region was assembled. The DISCI region of the Fugu rubripes genome was cloned and 45 kb of contiguous genomic sequence generated. The orthologous region of the mouse and chicken genomes was identified and characterised. A pipeline for preliminary genomic annotation and subsequent comparative genomic analysis was developed using the cystic fibrosis locus as a model, and subsequently applied to the DISCI locus. The method of "annotation anchored global sequence alignment" substantially increased the sensitivity in detection of biologically relevant conserved sequence motifs. Comparative genomic analysis, RT-PCR and cDNA clone identification were used to construct a transcriptional map of the Fugu genomic region and refine the human transcription map. Conservation of synteny between 0.7 Mb of the human genome and 45 kb of the Fugu genome was demonstrated, with one boundary of synteny being clearly defined. The region of conserved synteny contained the genes Egg Laying Nine-1 (EGLN1), Translin Associated factor X (TRAX) and DISCI in both species.EGLN1 was found to be a member of a previously undescribed gene family. The mouse and human members were identified and characterised. In addition, evolutionary evidence for a novel mechanism of host - pathogen interactions was discovered. TRAX and its homologue Translin were tentatively identified as members of a nucleic acid helicase family of proteins, providing a mechanistic basis for their known biological roles, and suggesting previously undescribed functional aspects of these proteins. DISCI was found to be rapidly evolving in both genomic structure and protein sequence, although three N-terminal motifs and blocks of coiled coil forming potential in the C-terminal half of the protein are conserved features, suggesting a general structure and function for the protein. Neither the antisense transcript DISC2 nor the intergenic splicing of TRAX to DISCI are conserved in Fugu.The work presented in this thesis has substantially enhanced understanding of the chromosome 1 breakpoint locus both at the genomic and encoded protein level. Two novel gene families have been defined and characterised, allowing a more complete evaluation of their functional candidacy in the aetiology of major mental illness. The sequence and clone resources resulting from this work also form the basis for protein functional studies and future characterisation of the locus in animal models

A novel approach to identifying regulatory motifs in distantly related genomes

Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applying phylogenetic footprinting to distantly related organisms, we developed a two-step procedure that combines the advantages of sequence alignment and motif detection approaches. The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size

Caractérisation du locus 12p12.3 impliqué dans la leucémie lymphoblastique aiguë

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Identification and characterization of conserved regulatory elements by comparative genomics

Ph.DDOCTOR OF PHILOSOPH

When needles look like hay: How to find tissue-specific enhancers in model organism genomes

AbstractA major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found.Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project

Identification and characterisation of the Cdx1 and Apc1 cis-regulatory elements in mouse and Fugu rubripes

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Transcriptional regulation of Hox genes during hindbrain development.

Hox genes play a crucial role in patterning the anteroposterior axis. Therefore, it is important to understand the mechanisms regulating their expression. One way of identifying regulatory regions is to compare related genomic sequences in order to find conserved elements. Previous work in transgenic mice has defined the elements required to recapitulate Hoxa2 expression in rhombomeres 3 and 5. However, the mechanisms regulating expression of Hoxa2 in rhombomeres 2 and 4 were unknown. In this study, I demonstrate that a highly conserved region in the intron of Hoxa2 contains the control elements directing rhombomere 4 expression. Further, I show that the rhombomere 2 enhancer is located in the second exon of Hoxa2. Due to genome-wide duplication events, the number of Hox genes increased during vertebrate evolution. In the pufferfish, this led to the presence of two Hoxa2 genes, Hoxa2(a) and Hoxa2(b). The two co-paralogous genes show differential expression. I compared the control regions of these two genes and identified subtle changes in their cw-regulatory regions. Using chick electroporation, I show that several changes in these elements are responsible for the differential expression. Hoxbl has a broad expression pattern in the hindbrain at early stages. This expression becomes restricted to rhombomere 4 during later development. I show that Krox20 binds to a highly conserved repressor region and that removal of this element in transgenic constructs leads to an expansion of reporter expression into rhombomeres 3 and 5. Finally, I show that Hoxbl expression in the second branchial arch is repressed by a mammalian-specific repressor element. This work has shed important insight into the mechanisms and factors that modulte expression of Hoxa2 and Hoxbl during hindbrain development