Entre as modificações sofridas pelo transcrito primário de RNA de eucariontes, o splicing é responsável pela colocação lado a lado das sequências expressas alinhando a região codificadora no RNAm. Este mecanismo, descrito na década de 1970, como o responsável pela remoção dos íntrons e junção dos éxons consecutivos, é efetuado por um complexo ribonucleoprotéico conhecido como spliceossomo. O reconhecimento por este complexo dos segmentos definidos como éxons e íntrons depende de diversas sequências presentes no RNA e reconhecidas por ligantes protéicos. A modulação desta interação resulta na geração de diferentes transcritos maduros a partir de um mesmo gene, evento conhecido como splicing alternativo, comum a maioria dos genes humanos e um dos grandes responsáveis pela geração de variabilidade proteômica dos eucariotos e sua complexidade morfo-fisiológica. O splicing alternativo é um importante gerador de diversidade funcional no sistema nervoso central, onde participa da geração de variantes para mais de 80% dos genes. Entre estes está o gene do Retardo Mental do X Frágil (FMR1), cujo transcrito primário pode sofrer splicing alternativo de quatro éxons, produzindo até vinte isoformas diferentes da FMRP. Os objetivos gerais deste projeto foram (i) a análise da expressão do éxon 12 do Fmr1 em córtex cerebral frontal, hipocampo e cerebelo de ratos em E19 e P2; e (ii) a busca por elementos em cis reguladores do splicing do éxon 12 do Fmr1 de rato. Para averiguar os níveis da expressão do éxon 12 do Fmr1, no final do período embrionário e início do pós-natal de rato, foi realizada RT-PCR em tempo real com os tecidos citados acima, em E19 e P2. Observamos significativa inclusão do éxon 12 nos transcritos do Fmr1 no córtex frontal em P2 quando comparado a E19, o que não se relacionou ao aumento geral da expressão do Fmr1. No hipocampo, houve aumento da expressão do conjunto de mensagens do Fmr1 e tendência à exclusão do éxon 12 em P2, quando comparado a E19. Estes dados revelam o córtex cerebral como fonte de proteínas ativadoras do splicing do éxon 12 do Fmr1 e onde se deve buscar pela relevância funcional das isoformas da FMRP expressando este éxon. A busca por elementos reguladores do splicing do éxon 12 se baseiou na avaliação da expressão por RT-PCR de mini-gene de segmento genômico do gene Fmr1 usado para transfectar células C6 (glioma de rato). Estas células demonstraram inclusão preferencial do éxon 12 em seus transcritos superexpressos. Um segundo clone foi gerado com uma deleção a partir do clone original, na região 5 do íntron 12, na qual observamos in silico, elementos ricos em U e C, candidatos a acentuadores da inclusão do éxon 12. A superexpressão deste clone em C6 revelou exclusão preferencial do éxon 12, um padrão invertido em relação ao anteriormente observado. Estes dados indicam o elemento rico em U e C como um forte candidato a acentuar a inclusão do éxon 12 no RNAm do Fmr1. / Splicing is an important hnRNA processing mechanism in eukaryotes, aligning exons in the mRNA. First described in the 1970s, it is performed by a molecular complex named spliceosome, which recognizes RNA sequences in the boundaries between exons and introns. Interaction modulation in the spliceosome results in mature transcripts with varying sizes, a process known as alternative splicing, common to most human genes and the major mechanism leading to proteomic diversity and morphological and functional complexity in eukaryotes. Alternative splicing is very important in generating functional diversity in the central nervous system (CNS), where it takes part in more than 80% of primary transcript processing. Among these is the Fragile Mental Retardation 1 gene (FMR1), which undergoes alternative splicing of four exons creating the possibility of 20 non-redundant FMRP isoforms. The aims of this project were (i) to analyze the expression of rat Fmr1 exon 12 in frontal cerebral cortex, hippocampus, and cerebellum at E19 and P2 days; and (ii) to search for cis-acting elements regulating exon 12 splicing. We performed real-time RT-PCR to examine Fmr1 exon 12 expression, in the above-mentioned CNS structures, between the end of embryonic period and the second postnatal day. We observed significant inclusion of exon 12 in Fmr1 mRNA in frontal cortex at P2 as compared to E19, which was unrelated to general Fmr1 expression increase. At P2 hippocampus there was a significant increase at the expression levels of Fmr1, and a trend to exclude exon 12 from the primary transcript. This data indicates that cerebral cortex is an important source of proteins activating exon 12 splicing, and also a tissue where the functional relevance of FMRP isoforms expressing exon 12 should be regarded. We adopted the mini-gene approach to search for cis elements regulating Fmr1 exon 12 splicing. RTPCR was performed to evaluate C6 (rat glioma) cells overexpressing a clone containing a genomic Fmr1 segment. Transfected cells revealed preferential inclusion of Fmr1 exon 12. A deletion construct lacking the initial bases of intron 12 was generated. The deleted segment harbor U- and C-rich sequences that had been identified in silico in a search for intronic splicing enhancers. Overexpression of the deletion construct in C6 yielded to preferential exclusion of exon 12, as opposed to the expression pattern previously observed in the original clone. Therefore, the U- and C-rich elements at Fmr1 intron 12 are strong candidates to enhance Fmr1 exon 12 splicing.

Valproic acid (2-propylpentanoic acid, VPA) is a clinically used anti-epileptic drug and an effective mood stabilizer. VPA is also a histone deacetylase inhibitor and can induce embryonic malformations in both humans and mice. The mechanism(s) of VPA-induced teratogenicity are not well characterized. The objectives of my study were three fold, to: (i) investigate the effect of VPA on mouse embryonic development, (ii) characterize the putative mechanism(s) of VPA-induced teratogenicity and, (iii) investigate VPA associated epigenetic regulation of Hoxa2 gene in cell lines and in developing embryos. Whole mouse embryo cultures were treated with VPA at doses of 0, 50 (0.35 mM), 100 (0.70 mM), 200 (1.4 mM), and 400 µg/mL (2.8 mM), encompassing the therapeutic range of 0.35 mM to 0.70 mM. Van Maele-Fabry’s morphologic scoring system was used to quantitatively assess embryonic organ differentiation and development. Hoxa2 gene expression was measured by quantitative real-time RT-PCR (Reverse Transcriptase-Polymerase Chain Reaction). To assess epigenetic changes on the Hoxa2 gene promoter, DNA methylation was determined by bisulfite (BSP) sequencing and pyrosequencing. Histone “bivalent domains” H3K4me3 (histone 3 lysine 4 trimethylation) and H3K27me3 (histone 3 lysine 27 trimethylation) associated with gene activation repression, respectively, analyzed qChIP-PCR (quantitative chromatin immunoprecipitation-PCR). Telomere length and telomerase activity were analyzed in mouse embryos and in NIH3T3 cell line treated with VPA. Results indicate significantly increased incidence of dysmorphogenesis in embryos (11.8%, 35.3%, 47.0% and 88.3%) exposed to increasing doses of VPA (0.35 mM, 0.70 mM, 1.4 mM and 2.8 mM respectively). Van Maele-Fabry’s quantitative differentiation assessment of developing embryos demonstrated a significantly lower score for the circulation system, central nervous system, craniofacial development and limb development in VPA treated embryos (0.35 mM to 2.8 mM) compared to the untreated control group. Glutathione homeostasis was altered as indicated by decreased total glutathione content and increased GSSG/GSH ratio in all VPA treatment groups. In addition, a dose-dependent inhibition of Hoxa2 gene expression was observed in embryos and in the NIH3T3 cell line exposed to VPA. Pre-treatment with ascorbic acid [1000 µg/mL (5 mM)] restored glutathione level and normalized Hoxa2 gene expression in embryos exposed to VPA. DNA methylation status was characterized on the Hoxa2 gene promoter at the three CpG islands; CpG island 1 (-277 to -620 bp), CpG island 2 (-919 to -1133 bp), and CpG island 3 (-1176 to -1301 bp) in the two cells lines (NIH3T3 and EG7) and in developing embryos. CpG sites remained unmethylated on the Hoxa2 gene promoter in the NIH3T3 cell line which expresses the Hoxa2 gene, whereas these same CpG sites were methylated in EG7 cells that did not express Hoxa2. CpG island 1 is closest to Hoxa2 transcription start site and its methylation status was most affected. In developing embryos, CpG island 1 was found to be highly methylated at E6.5 when Hoxa2 is not expressed, whereas the methylation status of CpG sites on the CpG island 1 declined between E8.5 and E10.5 when Hoxa2 expression is present. VPA induced methylation of several CpG sites on CpG island 1 in NIH3T3 cell line and in E10.5 embryos when Hoxa2 expression was down regulated following VPA exposure. In addition, embryos and the NIH3T3 cell line treated with VPA impacted the “bivalent domains” resulting in increased H3K27me3 enrichment and decreased H3K4me3 enrichment on Hoxa2 promoter. Pre-treatment with ascorbic acid normalized Hoxa2 expression and histone bivalent domain changes and prevented increased DNA methylation following VPA exposure. Moreover, the telomerase activity and telomere length were both impacted by changes in glutathione redox potential induced by VPA. Oxidative stress following VPA treatment reduced telomerase activity and accelerated telomere shortening. These results are the first to demonstrate: (i) a correlation between VPA dose and total morphologic score in the developing mouse embryos. VPA impacted embryonic tissue differentiation and neural system development in the dose range of 0.35 mM to 2.8 mM; (ii) VPA altered glutathione homeostasis in cultured mouse embryos and inhibited Hoxa2 gene expression; (iii) Histone bivalent domains of H3K27 and H3K4 trimethylation and DNA methylation status at the Hoxa2 gene promoter region were altered following treatment with VPA. This appears to be the epigenetic event in transcriptional silencing of Hoxa2 gene expression after VPA exposure; and (iv) Ascorbic acid normalizes glutathione homeostasis, H3K27 and H3K4 trimethylation and DNA methylation status, restoring Hoxa2 gene expression following VPA exposure. Taken together our results show VPA- induced altered glutathione homeostasis, telomere shortening and telomerase dysfunction, and an inhibition of Hoxa2 gene expression leads to developmental abnormalities. Exposure to ascorbic acid had a protective effect on developing embryos exposed to VPA.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 78-94).

Entre as modificações sofridas pelo transcrito primário de RNA de eucariontes, o splicing é responsável pela colocação lado a lado das sequências expressas alinhando a região codificadora no RNAm. Este mecanismo, descrito na década de 1970, como o responsável pela remoção dos íntrons e junção dos éxons consecutivos, é efetuado por um complexo ribonucleoprotéico conhecido como spliceossomo. O reconhecimento por este complexo dos segmentos definidos como éxons e íntrons depende de diversas sequências presentes no RNA e reconhecidas por ligantes protéicos. A modulação desta interação resulta na geração de diferentes transcritos maduros a partir de um mesmo gene, evento conhecido como splicing alternativo, comum a maioria dos genes humanos e um dos grandes responsáveis pela geração de variabilidade proteômica dos eucariotos e sua complexidade morfo-fisiológica. O splicing alternativo é um importante gerador de diversidade funcional no sistema nervoso central, onde participa da geração de variantes para mais de 80% dos genes. Entre estes está o gene do Retardo Mental do X Frágil (FMR1), cujo transcrito primário pode sofrer splicing alternativo de quatro éxons, produzindo até vinte isoformas diferentes da FMRP. Os objetivos gerais deste projeto foram (i) a análise da expressão do éxon 12 do Fmr1 em córtex cerebral frontal, hipocampo e cerebelo de ratos em E19 e P2; e (ii) a busca por elementos em cis reguladores do splicing do éxon 12 do Fmr1 de rato. Para averiguar os níveis da expressão do éxon 12 do Fmr1, no final do período embrionário e início do pós-natal de rato, foi realizada RT-PCR em tempo real com os tecidos citados acima, em E19 e P2. Observamos significativa inclusão do éxon 12 nos transcritos do Fmr1 no córtex frontal em P2 quando comparado a E19, o que não se relacionou ao aumento geral da expressão do Fmr1. No hipocampo, houve aumento da expressão do conjunto de mensagens do Fmr1 e tendência à exclusão do éxon 12 em P2, quando comparado a E19. Estes dados revelam o córtex cerebral como fonte de proteínas ativadoras do splicing do éxon 12 do Fmr1 e onde se deve buscar pela relevância funcional das isoformas da FMRP expressando este éxon. A busca por elementos reguladores do splicing do éxon 12 se baseiou na avaliação da expressão por RT-PCR de mini-gene de segmento genômico do gene Fmr1 usado para transfectar células C6 (glioma de rato). Estas células demonstraram inclusão preferencial do éxon 12 em seus transcritos superexpressos. Um segundo clone foi gerado com uma deleção a partir do clone original, na região 5 do íntron 12, na qual observamos in silico, elementos ricos em U e C, candidatos a acentuadores da inclusão do éxon 12. A superexpressão deste clone em C6 revelou exclusão preferencial do éxon 12, um padrão invertido em relação ao anteriormente observado. Estes dados indicam o elemento rico em U e C como um forte candidato a acentuar a inclusão do éxon 12 no RNAm do Fmr1. / Splicing is an important hnRNA processing mechanism in eukaryotes, aligning exons in the mRNA. First described in the 1970s, it is performed by a molecular complex named spliceosome, which recognizes RNA sequences in the boundaries between exons and introns. Interaction modulation in the spliceosome results in mature transcripts with varying sizes, a process known as alternative splicing, common to most human genes and the major mechanism leading to proteomic diversity and morphological and functional complexity in eukaryotes. Alternative splicing is very important in generating functional diversity in the central nervous system (CNS), where it takes part in more than 80% of primary transcript processing. Among these is the Fragile Mental Retardation 1 gene (FMR1), which undergoes alternative splicing of four exons creating the possibility of 20 non-redundant FMRP isoforms. The aims of this project were (i) to analyze the expression of rat Fmr1 exon 12 in frontal cerebral cortex, hippocampus, and cerebellum at E19 and P2 days; and (ii) to search for cis-acting elements regulating exon 12 splicing. We performed real-time RT-PCR to examine Fmr1 exon 12 expression, in the above-mentioned CNS structures, between the end of embryonic period and the second postnatal day. We observed significant inclusion of exon 12 in Fmr1 mRNA in frontal cortex at P2 as compared to E19, which was unrelated to general Fmr1 expression increase. At P2 hippocampus there was a significant increase at the expression levels of Fmr1, and a trend to exclude exon 12 from the primary transcript. This data indicates that cerebral cortex is an important source of proteins activating exon 12 splicing, and also a tissue where the functional relevance of FMRP isoforms expressing exon 12 should be regarded. We adopted the mini-gene approach to search for cis elements regulating Fmr1 exon 12 splicing. RTPCR was performed to evaluate C6 (rat glioma) cells overexpressing a clone containing a genomic Fmr1 segment. Transfected cells revealed preferential inclusion of Fmr1 exon 12. A deletion construct lacking the initial bases of intron 12 was generated. The deleted segment harbor U- and C-rich sequences that had been identified in silico in a search for intronic splicing enhancers. Overexpression of the deletion construct in C6 yielded to preferential exclusion of exon 12, as opposed to the expression pattern previously observed in the original clone. Therefore, the U- and C-rich elements at Fmr1 intron 12 are strong candidates to enhance Fmr1 exon 12 splicing.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-07-12T15:47:35Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Dissertação Gustavo Barbosa de Lima PPGG UFPE 2016.pdf: 2227933 bytes, checksum: 03616701d6dbf5994db493d4eb7b243c (MD5) / Made available in DSpace on 2017-07-12T15:47:35Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Dissertação Gustavo Barbosa de Lima PPGG UFPE 2016.pdf: 2227933 bytes, checksum: 03616701d6dbf5994db493d4eb7b243c (MD5) Previous issue date: 2016-03-09 / A família de protozoários tripanosomatídeos apresenta características moleculares diferenciadas dos demais eucariotos, onde a regulação da expressão gênica é feita principalmente em nível pós-transcricional. Como em outros eucariotos, acredita-se que a iniciação da tradução seja uma etapa crítica de controle pós-transcricional, onde atuam diferentes fatores de iniciação da tradução (eIFs). Nesta etapa os pontos centrais são o reconhecimento do mRNA maduro e o recrutamento do ribossomo para dar início ao processo, atividades realizadas pelo complexo eIF4F, formado por três subunidades: eIF4E, eIF4A e eIF4G. Nos tripanosomatídeos foram descritos seis homólogos de eIF4E, a proteína de ligação ao cap. Dois destes, EIF4E3 e EIF4E4, participam da formação de complexos envolvidos no processo de tradução e outros dois, EIF4E5 e EIF4E6, participam de novos complexos de função desconhecida. Destes quatro homólogos, o EIF4E4 já foi caracterizado, de forma que o presente trabalho visa contribuir para o entendimento da importância dos demais (EIF4E3, EIF4E5 e EIF4E6) na viabilidade e taxa de crescimento celular de Leishmania sp. Construções gênicas foram geradas de forma a permitir a deleção das duas cópias gênicas de cada proteína por meio da transfecção de Leishmania e seleção com antibióticos. As três proteínas, e mutantes do EIF4E3, foram ainda expressas em parasitas transgênicos para a realização de experimentos de complementação. Os resultados mostram que os baixos níveis de expressão de EF4E5 e EIF4E6 indicam que as três proteínas parecem ser importantes para a viabilidade celular com funções não sobrepostas. Sítios específicos no EIF4E3 foram também identificados de forma isolada como essenciais para a função da proteína e críticos para a sobrevivência do organismo. Os resultados obtidos neste trabalho mostram a importância do estudo do papel destes homólogos de eIF4E na síntese protéica, assim com seu papel na biologia celular de tripanossomatídeos. / The Trypanosomatid of protozoans display distinct molecular features not seen in other eukaryotes, where the regulation of gene expression is mainly performed at the post-transcriptional level. As in other eukaryotes, it is believed that the initiation of translation is a critical stage of post-transcriptional control, where different initiation factors (eIFs) are active. At this stage, critical steps are the recognition of the mature mRNA and the ribosome recruitment to start the process, activities of the eIF4F complex, consisting of three subunits: eIF4E, eIF4A and eIF4G. In trypanosomatids, six homologues of eIF4E, the cap binding protein, have been described. Two of these, EIF4E3 and EIF4E4, participate in the formation of complexes involved in the translation process and two others, EIF4E5 and EIF4E6, participate in new complexes of unknown function. Among these four homologues, EIF4E4 has been better characterized, so that the present work aims to contribute to the understanding of the remaining homologues (EIF4E3, EIF4E5 and EIF4E6) and study their importance for cell viability and growth rate of Leishmania species. Gene constructs were generated to allow deletion of the two gene copies of each protein by transfection of Leishmania cells and selection with antibiotics. The three proteins and EIF4E3 mutants were also expressed in transgenic parasites in order to carry out complementation experiments. The results show low levels of expression of EF4E5 and EIF4E6 and indicate that the three proteins appear to be important for cell viability with non-overlapping functions. EIF4E3 specific residues were also identified which are essential for the protein to the function and critical for the survival of the organism. The results of this study highlight the importance of the study on the role of eIF4E homologues in protein synthesis, as well as their role for the trypanosomatids cell biology.

is a functionally diverse large group of proteins sharing a jelly roll β-barrel fold. An enzymatic member 3-hydroxyanthranilate-3,4-dioxygenase (HAO) and a non-enzymatic member pirin, which is a human nuclear metalloprotein of unknown function present in all human tissues, were selected for structural and functional studies in this dissertation work. HAO is an important enzyme for tryptophan catabolism and for 2-nitrobenzoic acid biodegradation. In this work, seven catalytic intermediate were captured in HAO single crystals, enabling for the first time a nearly complete structural snapshot viewing of the entire molecular oxygen activation and insertion mechanism in an iron- and O2-depedent enzyme. The rapid catalytic turnover rate was found achieved in large part by protein dynamics that facilitates O2 binding to the catalytic iron, which is bound to the enzyme by a facile 2-His-1-carboxylate ligand motif. An iron storage and chaperon mechanism was also discovered in the bacterial source of this enzyme, which led to a proposed novel biological function of a mononuclear iron-sulfur center. Although human pirin protein shares the same structural fold with HAO, its iron ion is coordinated by a 3-His-1-carboxylate ligand motif. Pirin belongs to a subset of proteins whose members are playing regulatory functions in the superfamily. In this work, pirin is shown to act as a redox sensor for the NF-κB transcription factor, a critical mediator of intracellular signaling that has been linked to cellular responses to pro-inflammatory signals which controls the expression of a vast array of genes involved in immune and stress responses.

Gene expression underlies all important biological processes in a cell and mis-regulated gene expression plays a causal or contributory role in several diseases including cancers. Towards identifying molecular determinants that confer susceptibility and resistance to tumor promoter induced neoplastic transformation, we analyzed the gene expression profile differences among tumor promoter TPA treated and untreated mouse epidermal JB6 cells by means of cDNA microarray analyses. The expression patterns for several genes were validated by real time PCR analyses. Seventy-four genes belonging to six functional categories were found to be differentially expressed. Data from this study implicate pathways which mediate cell adhesion, migration and interferon signalling, tumor suppressors, apoptotic proteins and transcription factors and includes twenty-six genes whose involvement has not been previously implicated in cancer. In a second study we used a DNA affinity chromatography based assay to purify two proteins that bound specifically to the AP-1 DNA binding site. Analyses of the purified proteins by mass spectrometric sequencing determined the identities of these proteins as nucleolin and Y-box binding protein 1 (YB-1). We tested the hypothesis that these proteins regulate transactivation at the AP-1 site. Overexpression of nucleolin and YB-1, both alone or in combination, repressed AP-1 dependent gene transactivation. To understand the mechanism of transrepression, we analyzed whether nucleolin and/or YB-1 affected the levels and/or disrupted the intracellular localization of the AP-1 protein subunits. Western blot analyses of all the AP-1 subunits revealed that the levels of AP-1 were unaffected. Cell fractionation confirmed that the AP-1 levels were not altered in the nuclear or cytoplasmic compartments. We further tested the hypothesis that nucleolin and YB-1 repressed AP-1 transactivation by competing with AP-1 proteins for the AP-1 site. The results from this experiment were inconclusive and the precise mechanism of repression is currently under investigation.

is a functionally diverse large group of proteins sharing a jelly roll β-barrel fold. An enzymatic member 3-hydroxyanthranilate-3,4-dioxygenase (HAO) and a non-enzymatic member pirin, which is a human nuclear metalloprotein of unknown function present in all human tissues, were selected for structural and functional studies in this dissertation work. HAO is an important enzyme for tryptophan catabolism and for 2-nitrobenzoic acid biodegradation. In this work, seven catalytic intermediate were captured in HAO single crystals, enabling for the first time a nearly complete structural snapshot viewing of the entire molecular oxygen activation and insertion mechanism in an iron- and O2-depedent enzyme. The rapid catalytic turnover rate was found achieved in large part by protein dynamics that facilitates O2 binding to the catalytic iron, which is bound to the enzyme by a facile 2-His-1-carboxylate ligand motif. An iron storage and chaperon mechanism was also discovered in the bacterial source of this enzyme, which led to a proposed novel biological function of a mononuclear iron-sulfur center. Although human pirin protein shares the same structural fold with HAO, its iron ion is coordinated by a 3-His-1-carboxylate ligand motif. Pirin belongs to a subset of proteins whose members are playing regulatory functions in the superfamily. In this work, pirin is shown to act as a redox sensor for the NF-κB transcription factor, a critical mediator of intracellular signaling that has been linked to cellular responses to pro-inflammatory signals which controls the expression of a vast array of genes involved in immune and stress responses.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.