Chez l'homme, l'épissage alternatif (EA) affecte presque tous les gènes permettant de générer de vastes répertoires d'ARN et de protéines. L'épissage est un processus hautement régulé qui s'effectue principalement lorsque l'ARN est en cours de synthèse sur la chromatine. Beaucoup d'études suggèrent que la chromatine et ses marques épigénétiques influencent les décisions d'épissage au locus correspondant. A l'inverse, d'autres données laissent penser que l'épissage peut moduler les marques épigénétiques. Au cours de ma thèse, j'ai étudié différentes voies de couplage entre l'épissage et la chromatine. D'une part, j'ai exploré l'impact de la méthylation de l'ADN sur la régulation de l'épissage. J'ai montré que les enzymes qui méthylent l'ADN ont un effet global sur l'épissage d'exons enrichis en méthylation. Mes données suggèrent que les protéines qui lient la méthylation de l'ADN sont impliquées dans cette régulation. D'autre part, j'ai exploré les conséquences de l'EA sur la régulation de la chromatine en étudiant son impact de deux histones-methyltransferases (HMTase) : G9A et SUV39H2 dont les gènes génèrent des transcrits alternatifs. Tous les transcrits variants codent pour des protéines. La conservation des variants d'épissage de G9A dans des espèces et l'absence de différences dans leur activité HMTase, nous amènent à proposer que l'EA est associé à une fonction non liée aux histones. A l'inverse, les isoformes de SUV39H2 exhibent des activités HMTases différentes et régulent l'expression de gènes cibles différents. Ensemble, nos résultats apportent de nouvelles connexions dans le couplage épissage-chromatine et supporte un modèle où ces derniers s'auto-influencent. / In humans, alternative splicing affects almost all genes in the genome and generates extensive repertoires of RNAs and proteins. Splicing is a highly regulated process which occurs primarily when the RNA is being synthesized on chromatin. Many studies suggest that chromatin and epigenetic marks influence splicing choices to the corresponding locus. Conversely, other data suggest that splicing can modulate epigenetic marks. During my thesis, I studied different ways of crosstalk between splicing and chromatin. First, I investigated the effect of DNA methylation on splicing regulation. I have shown that the enzymes that methylate DNA have an overall effect on the splicing of exons with enriched methylation. My data suggest that proteins which bind to methylated DNA are involved in this regulation. On the other hand, I explored the impact of alternative splicing on chromatin regulation studying its impact on the expression and activity of both histone methyltransferases (HMTase): SUV39H2 and G9A. G9A and SUV39H2 generate variants transcripts whose expression is regulated according to tissues. All variants transcripts encode proteins. Conservation of G9A splice variants in species and no differences in their HMTase activity, lead us to propose that G9A alternative splicing is associated with a non-histone function. Conversely, SUV39H2 isoforms exhibit different HMTases activities, and regulate the expression of different target genes. All our results provide new connections in chromatin - splicing coupling and support a model in which they harbor self-influence.

A Leucemia Linfóide Aguda (LLA) é uma doença heterogênea em relação à biologia e ao prognóstico. Além de alterações genéticas, anormalidades epigenéticas, estão estreitamente relacionadas ao processo de carcinogênese e entre os mecanismos epigenéticos, a acetilação das histonas é um componente essencial para a regulação da estrutura da cromatina e atividade transcricional. Esse processo é mediado pelas histonas acetiltransferases (HATs). Por outro lado, a desacetilação, por meio das histonas desacetilases (HDACs), está relacionada à condensação da cromatina e repressão transcricional. A expressão anormal das HDACs tem sido associada ao processo de leucemogênese, revelando ser uma área promissora na caracterização de grupos de risco e tratamento do câncer. Os objetivos deste trabalho foram avaliar a expressão dos genes da classe I de HDACs (HDAC 1, 2, 3 e 8), correlacionar os resultados com as características clínicas e de prognóstico (idade, gênero, grupo de risco, contagem inicial de blastos, imunofenótipo, resposta ao tratamento, doença residual mínima nos dias 14 e 18 e a sobrevida livre de eventos) em 46 amostras consecutivas de medula óssea de crianças e adolescentes portadores de LLA; comparar e correlacionar a expressão dos genes estudados entre as amostras de pacientes portadores LLA e 10 amostras de medula óssea sem doença hematológica. A análise da expressão gênica foi realizada através da técnica de PCR em Tempo Real pelo método TaqMan®. Foi observado um aumento da expressão do gene HDAC1 nas amostras dos pacientes bons respondedores ao ix tratamento. O gene HDAC2 foi mais expresso no grupo de pacientes do gênero masculino (p=0,038). Esse gene também mostrou uma expressão aumentada nos pacientes de alto risco (p=0,060) e com sobrevida menor (p=0,065), entretanto os valores encontrados não foram estatisticamente significativos. Além disso, foi observada uma expressão aumentada dos genes HDAC2 (p=0,007), HDAC3 (p=0,014) e HDAC8 (p=0,002) em amostras de pacientes com LLA quando comparadas às amostras de medula óssea sem doença hematológica. Houve correlação entre a expressão de todos os genes de classe I das HDACs, exceto entre HDAC1 e HDAC8. Os resultados obtidos nesse trabalho sugerem que as HDACs de classe I, podem representar importantes alvos para futuros estudos em LLA, no entanto são necessários de testes funcionais para confirmar estes resultados. / Acute Lymphoblastic Leukemia (ALL) is a heterogeneous disease with distinct biologic and prognostic groups. In addition to genetic alterations, epigenetic processes play an important role in carcinogenesis, among which histone acetylation/deacetylation is crucial for chromatin modulation structure and transcriptional activity. Histone acetylation is regulated by the enzyme histone acetyl transferases (HATs). On the other hand, the deacetylation process is regulated by histone deacetylases (HDACs) enzymes, which is associated with the chromatin condensation and transcriptional repression. Abnormal expression of HDACs is a common feature of cancer and has revealed a promising field to stratify cancer treatment and risk classification. The investigation of these expression profiles may represent an important clinical factor for diagnosis and management of hematological malignances. The objectives of the present study were to analyze the expression profile of the class 1 HDACs (HDAC1, 2, 3 and 8) genes in bone marrow samples obtained from 46 childhood ALL samples, to correlate the results with prognostic and clinical features (age, gender, risk group, immunophenotype, treatment response, minimal residual disease and event free survival) of the patients; to evaluated differences in gene expression between ALL samples and 10 bone marrow samples without hematological disease and to verify the correlation of these genes. The gene expression analysis were made using xi TaqMan real-time polymerase chain reaction. A higher expression of HDAC1 in patients with better treatment response was observed. The HDAC2 showed a higher expression in male gender (p=0,038). HDAC2 also showed a higher expression for higher risk (p=0,060) and lower survival patients (p=0,065), however the statistical analysis did not show significant results. Furthermore, there was a higher expression of HDAC2 (p=0,007), HDAC3 (p=0,014) and HDAC8 (p=0,002) in ALL samples when compared to healthy donors. Class I HDACs showed correlation in gene expression, except for HDAC1 and HDAC8. These results suggest that class I HDACs can represent important targets for ALL research; however, it is necessary to perform functional investigation to confirm these results.

Introdução: A formação da memória envolve mudanças na expressão de genes neuronais. Remodelações epigenéticas da cromatina e modificações pós-traducionais reversíveis no DNA ou nas proteínas histonas representam mecanismos centrais na regulação da expressão gênica durante o desenvolvimento do cérebro e a aprendizagem inicial ou recuperação da memória. Desequilíbrios nos níveis de acetilação de histonas estão associados à uma ampla variedade de desordens cerebrais. Histonas deacetilases (HDACs) desempenham um papel fundamental na homeostase da acetilação de histonas e na regulação de atividades celulares fundamentais como a transcrição, tornando-as um foco de estudo. Evidências mostram que a administração de inibidores de histonas deacetilases (HDACis) restauram a memória associada à regulação da expressão gênica e melhora a memória em ratos. Estudos em modelos animais têm mostrado que a formação da memória envolve uma série de alterações bioquímicas em várias áreas do sistema nervoso central, entre as quais se destacam o hipocampo e a amígdala basolateral (BLA). Neste contexto, fármacos experimentais, como a tricostatina A (TSA), que atuam sobre mecanismos epigenéticos, têm sido recentemente propostos como potenciais terapias para o tratamento de disfunção cognitiva e memória associados a doenças neurológicas e psiquiátricas. Objetivo: Neste trabalho objetivamos compreender e elucidar o papel da acetilação de histonas em processos envolvidos na modulação da memória utilizando o fármaco TSA e se baseia na hipótese de que a atividade de HDACs é essencial para a modulação das respostas de aprendizado na tarefa de esquiva inibitória (IA). Métodos: Ratos Wistar foram canulados bilateralmente na amígdala. Os efeitos das micro-infusões intra-amigdalares de TSA foram observados na consolidação e na extinção da memória após o treino na tarefa de esquiva inibitória e nos níveis do fator neurotrófico derivado do cérebro (BDNF) na BLA e no hipocampo referentes à consolidação da memória. Resultados: Os resultados demonstraram que a infusão intra-amigdalar de TSA 1.5 h, 3 h e 6 h após o treino na tarefa de esquiva inibitória resulta na melhora da memória de longa duração (LTM). TSA acelerou a extinção da memória quando infundido imediatamente pós-teste. Além disso, aumentou os níveis de BDNF no hipocampo. Conclusão: Estes resultados indicam que eventos epigenéticos possuem um papel importante no aprendizado e na memória através da atividade de HDACs. / Introduction: Memory formation involves changes in the expression of neuronal genes. Epigenetic remodeling of chromatin and reversible post-translational modifications in the DNA or in the histone proteins represent central mechanisms in the regulation of gene expression during brain development and early learning or memory retrieval. Imbalances in the levels of histone acetylation are associated with a wide variety of brain disorders. Histone deacetylases (HDACs) play a key role in homeostasis of histone acetylation and regulation of fundamental cellular activities, such as transcription, making them a focus of study. Evidences shows that the administration of histone deacetylases inhibitors (HDACis) restore the memory associated with the regulation of gene expression and improves memory in rats. Studies in animal models have shown that memory formation involves a series of biochemical changes in several areas of the central nervous system, which the hippocampus and basolateral amygdala (BLA) are the most highlighted. In this context, experimental drugs, such as trichostatin A (TSA), that act on epigenetic mechanisms, have recently been proposed as potential therapies for the treatment of memory and cognitive dysfunction associated with psychiatric and neurological disorders. Objective: In this work we aimed to understand and elucidate the role of histone acetylation in processes involved in memory modulation using the drug TSA and is based on the hypothesis that HDACs activity is essential for the modulation of learning answers in the inhibitory avoidance (IA) task. Methods: Wistar rats were cannulated bilaterally in the amygdala. The effects of TSA micro-infusions into the BLA were observed in the consolidation and extinction of memory after training in the inhibitory avoidance task and the levels of brain-derived neurotrophic factor (BDNF) in the BLA and hippocampus related to memory consolidation. Results: The results demonstrated that the TSA infusion into BLA 1.5 h , 3 h and 6 h posttraining in the inhibitory avoidance task results in improved long-term memory (LTM). TSA accelerated the extinction of memory when infused immediately post-test. In addition, increased levels of BDNF in the hippocampus. Conclusion: These results indicate that epigenetic events play an important role in learning and memory by HDAC activity.

Les ARNnc sont impliqués dans la régulation de l’expression de gènes chez les Procaryotes, les Archées et les Eucaryotes. Cette régulation peut être effectuée au niveau transcriptionnel ou post-transcriptionnel. Elle fait parfois intervenir des modifications des histones comme la méthylation ou l’acétylation. J’ai étudié le gène TIR1 dont l’expression est fortement réduite lorsqu’un ARNnc codant antisens nommé TIR1axut est stabilisé. J’ai montré que cette régulation est dépendante de l’histone déacétylase Hda1. De plus, j’ai montré que l’acétylation de H3K14 et H3K18 ne sont pas directement impliquées dans la régulation de TIR1 mais qu’un résidu polaire est nécessaire pour la répression de TIR1 en présence de l’ARNnc antisens. En outre, j’ai mis en évidence que la répression de TIR1 par son XUT est en parti post-transcriptionnel, mais ne fait pas varier la stabilité de l’ARNm. Finalement, j’ai tenté en vain de comprendre le ciblage de l’activité histone déacétylase de Hda1 le long de TIR1 en cherchant la présence d’hybride ARN/ADN grâce à un anticorps reconnaissant ce type de structure. / NcRNAs are involved in gene regulation in Prokaryotes, Eukaryotes and Archaea. This regulation could be transcriptional or post-transcriptional. Histone modifications could be involved such as methylation or acetylation. I studied TIR1 gene whose expression is highly reduced when an antisense ncRNA called TIR1axut is stabilized. I showed that this regulation is Hda1-dependant. In addition to that, I showed that H3K14ac and H3K18ac are not directly responsible for TIR1 repression but a polar residue is required for a proper silencing of TIR1 in a XUT depending manner. Moreover, I showed that TIR1 repression is due to a post-transcriptional effect but does not affect mRNA stability. Finally, I tried in vain to understand Hda1 targeting on TIR1 searching for RNA/DNA hybrids using an antibody that recognizes such structures.

Triazoles have been widely used as amide bond isosteres in chemical biology as linkers and to enhance proteolytic stability. The use of triazoles has grown exponentially since the discovery of the copper (I) catalysed alkyne azide cycloaddition reaction in 2002 as the reaction is solvent and functional group tolerant, and usually high yielding. The reaction is also orthogonal to reactions used in nature, meaning it has become a powerful coupling tool. In post-translational modification (PTM), proteins are modified by covalent attachment of functional groups to amino acid side chains. These PTM processes are generally thought to be dynamic and highly regulated by cell machinery, controlling protein function in response to stimuli. The ability to control function post protein synthesis allows organisms to have a smaller genome, which is advantageous as it reduces the energy required for DNA replication and repair. Research into the function of PTMs has been limited by the difficulty in generating recombinant proteins that bear a single PTM in a specific location. Although many elegant methods have been proposed that solve this problem, to date cysteine alkylation is one of the most successful techniques. For lysine PTMs, thia-lysine II (sLys) derivatives have been shown to be excellent mimics of lysine, where the only perturbation between the native lysine-containing analogue is the switch of a CH2 for S in the side chain. Biotin is a well-known PTM in biotin dependent carboxylases, where biotin is involved in CO2 transfer. Recently biotinylation has also been shown to be a PTM on many other proteins, however the role of biotinylation is not well understood. Biotin triazole III has been shown to be a good mimic of the biotin amide bond and retains excellent affinity to Avidin (Av). In Chapter 1 the effects of modification to the valeryl side chain, and orientation of the biotin triazole bond affect affinity to Av using ITC are investigated. Compounds III, V and VI are shown to have a KD < 120 pM, but further information on the binding affinity of these compounds could not be assessed by ITC. Biotin triazoles III-VI were also shown to be resistant to hydrolysis in serum, unlike the native biotin amide bond, which is hydrolysed by the enzyme biotinidase (BTD). Generation of amide sLys derivatives has been shown to be synthetically challenging. In Chapter 2, the synthesis and applications of chloromethyl-triazole biotin as a sulfhydryl selective alkylation reagent are investigated. The electron withdrawing nature of the triazole was proposed to give a ‘pseudo-benzylic’ halide α to the triazole, thus increasing reactivity. The controlled alkylation of peptides and proteins has shown that chloromethyl-triazole biotin shows enhanced reactivity over many commercial alkylation reagents and also gives good selectivity for cysteine. Alkylation of histone H4K12C gave the singly alkylated product, accompanied by low amounts of double alkylation. Biotinylation was confirmed by Western blot with anti-biotin. Due to the wide range of readily available functional azides, it was envisaged that halomethyltriazoles could be incorporated into other PTM mimics. In Chapter 3, efforts to expand the range of PTMs accessible using halomethyl-triazoles and further enhance the reactivity of chloromethyl triazoles by preparation of bromo- and iodomethyl triazoles are detailed. Synthesis of reagents to mimic malonylation, succinylation and GlcNAcylation PTMs is described and the reactivity of these halomethyl-triazole reagents is assessed. An alternate approach to the development of PTM mimics through cysteine propargylation and subsequent CuAAC coupling is also described in chapter 3. In conclusion, a series of new reagents have been developed to mimic protein PTMs through alkylation of cysteine. The reagents, which include biotin, GlcNAc, succinyl and malonyl mimics, are based on a halomethyl-triazole scaffold and have been successfully reacted with cysteine containing peptides and proteins.

Rising temperatures all over the world has correlated with more frequent heat stroke related injuries and death. This statistic not only applies to humans, but to canines as well, who have similar body temperature thresholds. Recent studies have demonstrated that serum histones, released after cell death from heat stroke, play a role in heat stroke related injuries and death. This proposal aims to determine the severity of the effects caused by serum histone release after heat stroke by exposing selected canine cell lines to cell lysate and purified histones H2A, H2B, H3, and H4, which have been found to be associated with heat stroke injuries. Effectiveness of the histones will be determined by measuring the levels of apoptosis, NETosis, and necrosis in the cells, as well as the expression levels of heat shock proteins. Further research will also be done to determine whether toll-like receptors present on the cell surface are responsible for the mechanism utilized by serum histones to damage tissue in the body.

Résumé indisponible / Résumé indisponible

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 149-167).

Les modifications d'histones chez T. gondii représentent un des mécanismes majeurs pour contrôler la transcription des gènes et l'acétylation de certaines histones est impliquée dans le phénomène de différenciation parasitaire qu'est l'interconversion. Nous avons utilisé un inhibiteur d'histones déacétylases, FR235222, comme outil afin de clarifier l'implication de l'acétylation des histones chez T. gondii. Le séquençage d'un mutant résistant à la FR235222 a permis d'identifier TgHDAC3 comme cible préférentielle de cet iHDAC. Le domaine d'interaction est spécifique de la famille des Apicomplexa ce qui explique la sélectivité de cette molécule pour T. gondii et d'autres Apicomplexes dont Plasmodium sp. Sur tachyzoïtes traités, FR235222 augmente le taux d'acétylation des histones de certains gènes dont 1/3 est spécifique des stades sporozoïtes ou bradyzoïtes avec une surexpression de ces gènes après traitement par FR235222. L'activité antiparasitaire de différents iHDAC a été testée parallèlement sur les deux stades importants en pathologie humaine: le tachyzoïte et le kyste. Sur le tachyzoïte, seuls les tétrapeptides cycliques présentent une forte activité antiparasitaire avec des EC50 d'environ 10 nM. Les kystes ex-vivo traités avec FR235222, sont non infectants: absence de toxoplasmose chez la souris ré-inoculée avec ces kystes. En conclusion, FR235222 présente une activité dirigée contre l'HDAC3 de T. gondii et une spécificité envers les Apicomplexes. En interférant avec le cycle naturel du parasite, cette molécule induit la mort des tachyzoïtes in vitro et supprime le pouvoir infectant des kystes in vivo. Ce travail ouvre une voie prometteuse dans la stratégie thérapeutique des pathologies à Apicomplexes.

Dans ce manuscrit nous abordons les propriétés mécaniques de fibres de chromatine à l'échelle de la molécule unique. La chromatine est la structure nucléoprotéique qui contient le génome des cellules eucaryotes. À ce titre, cette fibre est soumise à de nombreuses contraintes mécaniques, telle la torsion, lors des processus de transcription, de réplication ou bien encore de réparation. Une revue des connaissances concernant la chromatine est présentée dans un premier chapitre. En particulier, nous introduisons l'influence d'une histone, appelée histone de liaison. Cette protéine permet à la fibre d'accéder à un niveau de compaction supérieur. Ensuite nous donnons les outils théoriques et expérimentaux d'étude du substrat chromatinien. Nous détaillons les propriétés topologiques de la chromatine. Le dispositif d'étude que nous avons utilisé, les pinces magnétiques, est décrit. Il permet d'exercer sur une fibre unique des contraintes mécaniques de tension et de torsion controlées. Enfin nous présentons les résultats obtenus sur des fibres de chromatine reconstituées en présence ou non de l'histone de liaison. À l'aide des pinces magnétiques, nous avons pu mettre en évidence le fait que l'histone de liaison ne modifie pas l'élasticité torsionnelle remarquable de la chromatine, même si la fibre est dans un état plus condensé. Sous forte déformation torsionnelle positive, le nucléosome subit une transition chirale qui permet de relâcher la contrainte topologique appliquée à la fibre. Nous avons pu montrer que ce changement conformationnel peut tout à fait se dérouler au sein des fibres contenant l'histone de liaison. Les implications biologiques de ces phénomènes sont examinées. La capacité propre à la chromatine à supporter la contrainte de torsion pourrait avoir un rôle dans le maintien de l'organisation chromatinienne lors du cycle cellulaire.