Vertebrate genomes exhibit global methylation of cytosine residues where they occur in a cytosine-guanine dinucleotide (CpG) context and this epigenetic mark is generally thought to be repressive to transcription. Punctuating this pervasive DNA methylation landscape are short, contiguous regions of non-methylated DNA which are found at two thirds of mammalian gene promoters. These non-methylated regions exhibit CpG content close to expected levels as they escape the depletion of CpGs observed across the methylated fraction of the genome. The unique nucleotide properties of these CpG island (CGI) regions enable their identification by computational prediction in mammalian genomes. Owing to a lack of high-resolution genome-wide DNA methylation profiles in non-mammalian species, these CGI predictions have often been used as a proxy for non-methylated DNA in these organisms. In contrast to mammals, CGI predictions in cold-blooded vertebrates rarely coincide with gene promoters, leading to the belief that CGls are significantly divergent between vertebrate species, and that unique promoter-associated features may have been acquired during warmblooded vertebrate evolution. This thesis is primarily concerned with the location, establishment and biological function of non-methylated islands of DNA in vertebrate genomes. To experimentally determine genome-wide profiles of non-methylated DNA, a novel biochemical technique was established called biotinylated ZF-CxxC affinity purification (Bio-CAP), and development of this method is discussed in Chapter 3. Experimental analysis of non-methylated DNA profiles in this thesis initially addresses two main questions: (1) 'How does the non-methylated DNA landscape compare genome-wide for seven vertebrates considering distinct tissue types and developmental stages?' (2) 'How are vertebrate non-methylated regions of DNA defined and interpreted in the nuclear environment?' To address the first question, non-methylated DNA was profiled by Bio-CAP sequencing across the genomes of seven diverse vertebrate species, representing all major branch points of vertebrate evolution, and the results are discussed in Chapters 4 and S. Contrary to previously held dogma, experimentally determined nonmethylated islands of DNA (NMls) constitute an ancient epigenetic feature of vertebrate gene regulatory elements. However, despite having numerous high-resolution maps of vertebrate non-methylated DNA, the means by which NMls are identified and maintained in the nuclear environment remains poorly understood. To address the second question and identify features which determine the methylation state of DNA, exogenous DNA sequences were introduced into mouse embryonic stem (ES) c~.II~. Non-methylated DNA was profiled by Bio-CAP sequencing to investigate how different features, such as sequence-specific binding motifs, chromatin architecture and nucleotide composition of a given DNA sequence impact local DNA methylation patterns. Interestingly, the majority of exogenous promoters were appropriately non-methylated in mouse ES cells, germline and somatic cells suggesting that gene promoters have retained strong signals for the nonmethylated state across millions of years of evolution (discussed in Chapter 6). During mouse embryogenesis, genome-scale DNA demethylation and remethylation events occur to remodel the epigenetic landscape and loss of DNA methylation during this time leads to embryonic lethality. To investigate the biological function of non-methylated DNA, the third question addressed in this thesis is (3) 'What is the developmental importance of non-methylated islands of DNA during vertebrate embryogenesis?' To investigate this, members of the ZF-CxxC domain-containing family of chromatin modifiers were ablated in zebrafish embryos to perturb the chromatin landscape at NMls, and therefore interfere with their function during early development (Chapter 7). Early embryonic development and patterning was disrupted in knockdown embryos, suggesting that interpretation of non-methylated DNA and placement of chromatin modifications at NMls is essential for normal zebrafish embryogenesis. Together this work sheds light on the evolutionary origins of NMls, the mechanisms involved in the recognition and establishment of nonmethylated loci and provides an insight into the function of non-methylated DNA during early embryonic development.

L’objectif de cette thèse est de déterminer l’étendue de la variabilité épigénétique, plus particulièrement du polymorphisme de méthylation de l’ADN, non liée à la variabilité génétique dans les populations asexuées en milieu naturel. Cette évaluation nous a permis de mieux cerner l’importance que peuvent avoir les processus épigénétiques en écologie et en évolution. Le modèle biologique utilisé est l’hybride clonal du complexe gynogénétique Chrosomus eos-neogaeus. Malgré une homogénéité génétique, une importante variabilité phénotypique est observée entre les hybrides d’une même lignée clonale mais retrouvés dans des environnements différents. L’influence des processus épigénétiques apporte une explication sur ce paradoxe. L’épigénétique se définit comme une modification de l’expression des gènes sans changement de la séquence d’ADN. La diversité des phénotypes peut entre autre s’expliquer par des patrons de méthylation différentiels des gènes et/ou des allèles des gènes entre les hybrides génétiquement identiques. La diversité des lignées épiclonales peut quant à elle s’expliquer par la colonisation de plusieurs lignées épiclonales, s’établir en réponse à l’environnement ou de façon aléatoire. Plusieurs méthodes seront utilisées afin de survoler le génome des hybrides clonaux pour mettre en évidence le polymorphisme de méthylation de l’ADN à l’échelle de l’individu et entre les individus de différentes populations. / The aim of the thesis is to determine the extent of epigenetic variation, more specifically DNA methylation polymorphism, not linked to genetic variation in natural populations of an asexual vertebrate. This evaluation enables to better understand the importance that plays epigenetics processes in ecology and evolution. The biological model used is the clonal hybrid of the gynogenetic Chrosomus eos-neogaeus complex. Even in absence of genetic difference, an important phenotypic variability is observed among hybrids of the same clonal lineage living in different environments. Epigenetics, a modification of genes expression without a change at the DNA sequence, provides an explanation to this paradox. The diversity of phenotypes may be explained by differential methylation patterns of genes and/or alleles among genetically identical hybrids. The diversity of epiclonal lineages may be explained by the colonisation of many epiclonal lineages, established in response to the environment or stochastically. Many methods were used for screening the genome of clonal hybrids in order to highlight DNA methylation polymophism at the scale of an individual and among individuals of different populations.

Sabe-se que algumas alterações nutricionais maternas durante o período perinatal estão associadas com doenças metabólicas na vida adulta das proles, tais como diabetes melito tipo 2, resistência à insulina, obesidade e hipertensão arterial. O período da gestação em que estas alterações nutricionais influenciam a prole na idade adulta ainda não está elucidado. Modificações epigenéticas têm sido propostas como mecanismos responsáveis por estas desordens metabólicas. Ratas Wistar de doze semanas de idade foram alimentadas com dieta com conteúdo baixo (HO - 0,15% NaCl) ou normal (NR - 1,3% NaCl) de sódio desde o primeiro dia de gestação até o nascimento da prole ou HO durante a primeira (HO10) ou segunda (HO20) metade da gestação. O peso corpóreo e a ingestão de água e ração foram avaliados semanalmente durante a gestação. Teste de tolerância à insulina (ITT) e à glicose (GTT) e HOMA-IR foram realizados nas proles adultas. Expressão gênica por qRT-PCR e metilação do DNA na região promotora dos genes foram mapeadas utilizando tratamento com bissulfito de sódio e avaliadas por pirosequenciamento. O ganho de peso materno foi menor no HO e HO20 na terceira semana de gestação em comparação com NR e HO10. O peso ao nascimento da prole foi menor em machos e fêmeas dos grupos HO e HO20 em relação ao NR e HO10. O HOMA-IR foi maior nos machos com 12 semanas de idade do grupo HO em comparação com NR e com 20 semanas de idade do grupo HO10 em comparação com NR e HO20. Nas fêmeas com 12 semanas de idade o HOMA-IR foi maior no HO10 comparado com HO. Os níveis de insulina no soro foram maiores tanto nos machos com 20 semanas de idade do grupo HO10 comparado com NR quanto nas fêmeas com 12 semanas de idade do grupo HO10 comparado com HO. A área sob a curva do GTT indicou intolerância à glicose nos machos do grupo HO. A porcentagem de metilação das ilhas CpG no promotor dos genes de Igf1, Igf1r, Ins1, Ins2 e Insr no fígado de machos e fêmeas neonatais e no fígado, tecido adiposo branco e músculo em machos com 20 semanas de idade foi influenciada pela baixa ingestão de sal durante a gestação. Nenhuma destas alterações foi identificada nas fêmeas com 20 semanas de idade. Em conclusão, a baixa ingestão de sal na segunda metade da gestação é responsável pelo baixo peso ao nascimento em ambos os sexos. A intolerância à glicose observada na prole adulta ocorreu somente se a dieta hipossódica é dada durante a gestação inteira. Por outro lado, a resistência à insulina em resposta ao consumo de dieta hipossódica durante a gestação está relacionada com o momento em que ocorre este insulto e com o envelhecimento da prole. Também foi observado que alterações na metilação do promotor do gene Igf1 está correlacionado com o baixo peso ao nascimento em resposta a ingestão de dieta hipossódica durante a gestação / It is known that some maternal nutritional alterations during pregnancy are associated with metabolic disorders in adult offspring, such as insulin resistance, type 2 diabetes mellitus, obesity and arterial hypertension. The period of pregnancy in which these nutritional alterations influence adult offspring remains uncertain. Epigenetic changes are proposed to underlie these metabolic disorders. Twelve-week-old female Wistar rats were fed a low-salt (LS - 0.15% NaCl) or normal-salt (NS - 1.3% NaCl) diet since the first day of gestation until delivery or LS during the first (LS10) or second (LS20) half of gestation. Body weight, food and water intake were weekly evaluated during gestation. Blood glucose, insulin (ITT) and glucose (GTT) tolerance tests, HOMA-IR were performed in adult offspring. Gene expression and DNA methylation were mapped using bisulfite treatment evaluated by pyrosequencing in the male and female neonates and adult offspring. Weight gain was lower in LS and LS20 dams than in NS and LS10 dams in the third week of pregnancy. Birth weights were lower in male and female LS20 and LS rats compared with NS and LS10 neonates. HOMA-IR was higher in 12-week-old LS males compared with NS and in 20-week-old male LS10 rats compared with NS and LS20 rats. In 12-week-old LS10 females, HOMA-IR was higher than in LS. Serum insulin levels were higher in 20 week-old LS10 male compared with NS rats and in 12-week-old LS10 female compared to LS rats. The area under the curve of GTT indicated glucose intolerance in 12- and 20-week-old LS male. Methylation of CpG islands of the Insr, Igf1, Igf1r, Ins1 and Ins2 genes in liver in neonates male and female offspring and liver, white adipose tissue and muscle in 20-week-old male offspring were influenced by low-salt intake during pregnancy. None of these alterations was identified in 20-week-old females. In conclusion, low-salt diet consumption in the second half of pregnancy can result in low birth weights in the males and females offspring. Glucose intolerance observed in adult offspring occurred only if low salt intake was given throughout pregnancy. However, insulin resistance in response to low salt intake during pregnancy is related to the time at which this insult occurs and to the age of the offspring. Alterations in the DNA methylation of Igf1 were observed to be correlated with low birth weight in response to low salt feeding during pregnancy

O câncer de mama é a principal causa de mortalidade por câncer entre as mulheres. Alguns biomarcadores e características clínicas são utilizados para avaliar o prognóstico e prever a resposta a uma série de abordagens terapêuticas. A Homocisteína é conhecida como um fator de risco para doença vascular aterosclerótica, mas sua participação na biologia do câncer ainda é incerta. Cisteína é o aminoácido sulfurado derivado da Homocisteína no ciclo da Metionina. Este ciclo metabólico origina as bases nitrogenadas e também determina o nível de metilação da molécula de DNA. É atualmente reconhecido que a hipometilação global do genoma é um evento chave na transformação maligna das células. O objetivo deste estudo foi avaliar os níveis séricos de homocisteína e cisteína como biomarcadores de sobrevida e de progressão da doença em câncer de mama. Também foi avaliado o efeito de um curso de curta duração (um mês) de tratamento hormonal sobre os níveis de Homocisteína, Cisteína e metilação do DNA. Amostras de sangue foram obtidos por ocasião da biópsia inicial (pré-tratamento) em todas as pacientes e, de tumor e de tecido normal adjacente, ao diagnóstico eem um mês após, para as pacientes que receberam o regime hormonal neo-adjuvante (pré-operatório). Todas as pacientes eram mulheres na pós-menopausa, com tumores de mama ressecáveis, acompanhadas em dois hospitais públicos, que consentiram em participar de outros dois protocolos de pesquisa prévios. Homocisteína e Cisteína foram analisadas por HPLC e a metilação global do DNA do tecido foi determinada por meio da técnica de MSRE (Methylation-Sensitive Restriction Enzyme). Foi observada uma diferença significativa entre os níveis pré e póstratamento de Homocisteína e Cisteína em tumores avançados, sugerindo um papel prognóstico em pacientes com características clínicas reservadas. As variações nos níveis de Homocisteína se mostraram significativamente correlacionadas com a sobrevida livre de doença. O modelo de risco proporcional de Cox demonstrou que os níveis de homocisteína e o status dos linfonodos representaram fatores prognósticos independentes em termos de sobrevida livre de doença. Embora mais estudos sejam necessários para confirmar estes resultados, nossa pesquisa sugere que a Homocisteína pode ser usada como um biomarcador de prognóstico para câncer de mama / Breast cancer is the leading cause of cancer mortality among women. Some biomarkers and clinical features are used to evaluate prognosis and to predict response to a range of therapeutic approaches. Homocysteine is well known as a risk factor in atherosclerotic vascular diseases, but its participation in cancer biology is still unclear. Cysteine is a sulfur amino acid derived from Homocysteine in the Methionine cycle. This metabolic cycle originates the nitrogenous bases and determines the methylation level of the DNA molecule as well. It is currently recognized that the global hipomethylation of the genome is a key event in the malign transformation of cells. The aim of this study was to evaluate serum Homocysteine and Cysteine as biomarkers of survival and disease progression in breast tumor, as well as the methylation status of tumor and normal tissues. The effect of a short course (one month) of hormonal treatment on Homocysteine, Cysteine and DNA methylation levels was also evaluated. Blood samples were collected during the initial biopsy (pretreatment) in all patients and, tumor samples and normal adjacent tissue, at diagnosis and one month after, for the patients that received neo-adjuvant hormonal regimen (pre-treatment). All patients were post-menopausal women, with resectable breast tumors, followed at two public hospitals, and that had consented to participate in two previous research protocols related to their disease. Serum Homocysteine and Cysteine were analyzed by HPLC and tissue global DNA methylation was determined by the MSRE (Methylation- Sensitive Restriction Enzyme) technique. A significant difference was observed between pre- and post-treatment levels of Homocysteine and Cysteine in advanced tumors, suggesting a prognostic role in patients with poor clinical characteristics. Variations in Homocysteine levels were significantly correlated with disease free survival. Cox proportional risk model demonstrated that nodal status and Homocysteine levels were independent prognostic factors for Disease Free Survival. Although more studies are needed to confirm these results, our research suggests that Homocysteine might be used as a prognostic biomarker for breast cancer

Introdução: Os linfomas não-Hodgkin de células T periféricas (LCTP) são neoplasias raras caracterizadas pela proliferação monoclonal de linfócitos T maduros. Correspondem a 15% das malignidades linfoides e têm distribuição geográfica peculiar. Compreendem 22 entidades clínico-patológicas distintas, heterogêneas do ponto de vista clínico-epidemiológico, morfológico, fenotípico e molecular. O grupo de apresentação predominantemente nodal compreende as variantes histológicas LGCA/ALK+, LGCA/ALK-, LCTA e LCTP/SOE. Sua terapêutica se baseia em poliquimioterápicos à base de antraciclina e consolidação com transplante de células tronco hematopoiéticas autólogas (TCTH). Com exceção do LGCA/ALK+, apresentam sobrevida global em cinco anos de 30% a 40%. Devido aos desfechos desfavoráveis, estudos de perfil de expressão gênica e de metilação de genes supressores tumorais têm emergido nos últimos anos para refinar o diagnóstico destas neoplasias, melhorar o conhecimento fisiopatológico e o prognóstico e estabelecer possíveis alvos terapêuticos. Estudos preliminares com LCTP nodais indicam valor prognóstico favorável da hiperexpressão de genes de padrão inflamatório NFkB1 e IKBkB e desfavorável nos casos de supraregulação de genes de padrão proliferativo como CCNA2, TOP2A e CHEK1 e do fenótipo metilado de p15INK4b e p16INK4a. Objetivo:Avaliar o impacto da expressão relativa dos genes CCNA2, TOP2A, CHEK1, NFkB1, IKBkB e VEGF1 e da metilação dos genes p15 e p16 em população brasileira com LCTP nodais tratados com quimioterapia CHOP-símile para os desfechos de sobrevida global, sobrevida livre de progressão e sobrevida livre de doença. Métodos: A expressão gênica foi avaliada por qtPCR de amostras fixadas em formol e incluídas em parafina de 63 pacientes. A mediana de expressão dos genes foi comparada com variáveis clínicas e desfechos. PCR qualitativa metilação-específico foi usada avaliar a metilação de p15 e p16. Resultados: Com mediana de seguimento de vinte meses, as SG, SLP e SLD foram, respectivamente, 45,6%, 34,3% e 63,0% e a resposta completa de 46,0%. Em análise multivariada, ECOG >= 2 e a hiperexpressão do gene CCNA2 foram associadas à pior SG em cinco anos, nos LCTP nodais (p=0,008 e p=0,002). Em análise univariada os genes CCNA2, TOP2A e CHEK1 foram associados ao pior prognóstico nos LCTP/SOE e melhor nos LGCA/ALK-. A hiperexpressão do gene VEGF1 se associou ao pior prognóstico no LGCA/ALK- e LCTA. Metilação de p15INK4b não foi encontrada nos LGCA/ALK+ e em análise multivariada foi associada a pior SLP em 5 anos nos LCTP não-ALK+ (HR: 9,88; p=0,03). O painel gênico testado não apresentou poder para discriminar as diferentes variantes histopatólogicas de LCTP nodais, porém demonstrou-se associação direta entre a intensidade de mediana de expressão desses genes e agressividade biológica nesse grupo heterogêneo de neoplasias. O significado prognóstico de imunoexpressão da proteína ALK sofreu influência das variáveis constituintes do IPI nessa coorte. Conclusão: A hiperexpressao dos genes CCNA2, TOP2A e CHEK1 foram associadas a prognóstico desfavorável nos LCTP/SOE e favorável nos LGCA/ALK-. Fenótipo hipermetilado de p15INK4b não foi evento observado em LGCA/ALK+, porém foi associado a pior prognóstico nos LCTP nodais não-ALK+ / Background: Peripheral T-cell non-Hodgkin\'s lymphomas (PTCL) are rare tumors characterized by monoclonal proliferation of mature T lymphocytes; they correspond to 15% of lymphoid malignancies and have specific geographic distribution. PTCL comprise 22 distinct clinicopathologic entities, heterogeneous from the clinical and epidemiological perspective, as well as morphologic, phenotypic and molecular. The group of presentation predominantly nodal comprises the histological variants ALCL/ALK+, ALCL/ALK-, AITL and PTCL/NOS. Its treatment is based on polychemotherapy with anthracycline and consolidation with autologous hematopoietic stem cell transplantation (ASCT). With the exception of ALCL/ALK+, these tumors show overall survival at 5 years from 30% to 40%. Due to unfavorable outcomes, gene expression profile studies, as well as studies of methylation of tumor suppressor genes, have emerged in recent years in order to refine the pathological diagnosis of these cancers, improve the pathophysiological knowledge and prognosis, and establish possible therapeutic targets. Preliminary studies with nodal PTCLs indicate favorable prognostic value of overexpression of inflammatory pattern genes like NFkB1 e IKBkB, and unfavorable in the case of proliferative genes as CCNA2, TOP2A, CHEK1 and the methylated phenotype of suppressor genes p15INK4b e p16INK4a. Objectives: Assess the impact of relative expression of genes CCNA2, TOP2A, CHEK1, NFkB, IKBkB and VEGF1 and the methylation of the genes p15 and p16 in Brazilian population with nodal PTCLs treated with CHOP-like chemotherapy for the outcomes of overall survival, progression-free survival and disease-free survival. Methods: Gene expression was assessed by qtPCR of paraffin samples of 63 patients. The median gene expression was compared with clinical variables and outcomes. Qualitative methylation-specific PCR was used to assess the methylation of p15 and p16. Results: With a segment median of 20 months, the OS, PFS and DFS were, respectively, 45,6%, 34,3% and 63,0% and the complete response (CR) was 46,0%. In multivariate analysis, ECOG >= 2 and overexpression of the gene CCNA2 were associated with worse OS at 5 years in nodal PTCLs (p = 0,008 and p = 0,002). In univariate analysis, the genes CCNA2, TOP2A and CHEK1 were associated with worse prognosis in PTCL/NOS and better in ALCL/ALK negative. The overexpression of the gene VEGF1 was associated with worse prognosis in the variants AITL and ALCL/ALK negative. Methylation of the gene p15INK4b was not found in ALCL/ALK+ group, and in multivariate analysis was associated with worse 5-years PFS in the group of PTCL non-ALK+ (HR: 9,88 and p = 0,03). The gene panel tested showed no power to discriminate the different histopathology of nodal PTCL, but it showed a direct association between the median intensity of expression of these genes and biological aggressiveness in this heterogeneous group of neoplasms. The prognostic significance of immunostaining of ALK protein was influenced by IPI constituents variables in this cohort. Conclusion: The overexpression of genes CCNA2, TOP2A e CHEK1 were associated with poor prognosis in PTCL/NOS and favorable in ALCL/ALK negative. Hypermethylated phenotype of gene p15INK4b was not an observed event in ALCL/ALK+, but it was associated with poor prognosis in nodal PTCL non-ALK+

Alterações epigenéticas, como metilação do DNA e modificações pós traducionais em histonas, tem importante papel na carcinogênese mamária. A modulação de eventos epigenéticos constitui relevante alvo terapêutico, devido ao seu caráter reversível. Experimentalmente, o ácido docosahexaenoico (DHA), um membro da família dos ácidos graxos ômega-3, é capaz de diminuir proliferação, induzir morte celular e diminuir o potencial invasivo de células tumorais de mama. No entanto, os mecanismos antitumorais do DHA e sua capacidade de modular eventos epigenéticos ainda não estão totalmente elucidados. Nosso objetivo foi verificar, in vitro, a ação do DHA em eventos epigenéticos em diferentes linhagens de carcinoma mamário humano. Três linhagens celulares de câncer de mama (MDA-MB-231, SKBR-3 e MCF-7) foram tratadas durante 72 horas com 100 ?M de DHA ou etanol (controle). As modificações pós traducionais em histonas, acetilação no resíduo de lisina 9 da histona 3 (H3K9ac) e no resíduo 16 da histona 4 (H4K16ac), bem como trimetilação no resíduo de lisina 9 da histona 3 (H3K9me3) e no resíduo de lisina 27 da histona 3 (H3K27me3) foram avaliadas pela técnica de western blot. A análise da expressão do genes RASSF1A, DNMT1, DNMT3A e DNMT3B foi feita pela técnica da reação em cadeia da polimerase quantitativa via transcriptase reversa (RT-qPCR). A avaliação do padrão de metilação de região promotora do gene RASSF1A foi realizada pela técnica de reação em cadeia da polimerase metilação específica (MS-PCR). Foram também analisadas as fases do ciclo celular por citometria de fluxo. Comparado ao controle, o DHA induziu a acetilação no resíduo 16 da histona 4 (H4K16ac) nas linhagens MCF7 (p = 0,04) e MDA-MB-231 (p = 0,03). Observamos que a H3K9me3 foi parcialmente inibida nas linhagens MDA-MB-231 e SKBR-3, após o tratamento com DHA, mas sem alcançar valor estatisticamente significante. Encontramos também diminuição dos níveis de H3K27me3 após o tratamento com DHA nas três linhagens estudadas, porém não foi estatisticamente significativo. O DHA aumentou a expressão do gene RASSF1A na linhagem MCF-7 (1,98 vezes, p = 0,03), mas não nas linhagens MDA-MB-231 e SKBR-3. Não houve mudanças estatisticamente significativas na expressão dos genes DNMT1, DNMT3A e DNMT3B. As análises qualitativas da metilação demonstraram que a região promotora analisada do gene RASSF1A apresentou-se hipermetilada nas três linhagens celulares. Após o tratamento com DHA, houve tendência de desmetilação na região promotora do RASSF1A na linhagem MCF-7 e SKBR3, mas não na linhagem MDA-MB-231. Não houve diferença significativa na porcentagem de morte e distribuição das células MDA-MB-231, SKBR-3 e MCF-7 nas diferentes fases do ciclo celular após tratamento com DHA. Em conclusão, o DHA pode atuar em mecanismos epigenéticos e, ainda, reativar o gene supressor de tumor, como RASSF1A, anteriormente silenciado por hipermetilação, em células MCF-7. Espera-se que esses resultados contribuam para melhor compreensão do potencial papel anticâncer do DHA no câncer de mama / Epigenetic changes, such as DNA methylation and post-translational histone modifications, play an important role in mammary tumorigenesis. Epigenetic events are important as therapeutic targets, because of its reversible nature. Experimentally, docosahexaenoic acid (DHA), a member of the omega-3 fatty acids family, can reduce proliferation, induce apoptosis and decrease the invasive potential of breast tumor cells. However, the antitumor mechanism of DHA and its ability to modulate epigenetic events are not completely understood. Our objective was to verify, in vitro, the action of DHA in epigenetic events related to transcriptional reactivation of tumor suppressor gene, such as RASSF1A, in different human breast cancer cell lines. Three breast cancer cell lines (MCF-7, MDA-MB-231, SKBR-3) were treated with DHA (100 ?M) or vehicle (ethanol) for 72 hours. Western blot was used to analyze histone modification, as histone H3 lysine 9 (H3K9ac) and histone H4 lysine 16 (H4K16ac) acetylation, H3K9 trimethylation (H3K9me3) and H3K27 trimethylation (H3K27me3). Real time quantitative PCR (RT-qPCR) was performed for gene expression quantification of RASSF1A, DNMT1, DNMT3A and DNMT3B. DNA methylation of the promoter region of RASSF1A was evaluated by methylation specific PCR (MS-PCR). Moreover, we evaluated the phases of the cell cycle by flow cytometry. Compared to control cells, DHA induced H4K16ac in MCF-7 (p=0.04) and MDA-MB-231 (p=0.03). We observed that H3K9me3 was partially inhibited in MDA-MB-231 and SKBR-3 cells, after treatment with DHA, but did not reach a statistically significant value. We also found decreased levels of H3K27me3 after treatment with DHA in the three cell lines studied, but not statistically significant. DHA increased RASSF1A expression on MCF-7 (1.98 fold; p=0.03), but not in MDA-MB-231 and in SKBR-3 cells. There were no statistically significant changes in expression of genes DNMT1, DNMT3A and DNMT3B. These three breast cancer cells lines show methylation in specific region of RASSF1A promoter. DHA treatment increased RASSF1A promoter region hypomethylation in MCF-7 and SKBR-3. No significant difference was observed in the percentage of cell death nor cell distribution of MDA-MB-231, SKBR-3 and MCF-7 at different stages of the cell cycle after treatment with DHA. In conclusion, we suggest that DHA may act beneficially in epigenetic mechanisms and reactivation of tumor suppressor gene, RASSF1A as previously silenced by hypermethylation. It is hoped that these results can contribute to better understanding of the anticancer role of DHA in breast cancer

Chez les végétaux supérieurs, lembryogenèse est une phase clé du développement au cours de laquelle lembryon établit les principales structures de la future plante. La compréhension des processus moléculaires et physiologiques menant à la formation de la graine est donc dun intérêt agronomique majeur. Chez Phaseolus la caractérisation moléculaire de lembryogenèse permet de mieux comprendre les mécanismes du développement embryonnaire et de son dysfonctionnement observé chez les hybrides interspécifiques. Cette thèse sinscrit dans ce cadre et vise à identifier et caractériser des gènes clés impliqués dans le développement de l'embryon chez Phaseolus. Des hybridations interspécifiques ont été réalisées entre lespèce P.vulgaris L. (cultivar NI637) utilisée comme parent mâle et lespèce P. coccineus L. (cultivar NI16) utilisée comme parent femelle. Des analyses ont aussi été effectuées sur un mutant obtenu par mutagenèse chimique à l'EMS (Ethyl Méthyl Sulfonate) de graines de la variété BAT93 de P.vulgaris. Une étude histologique comparative a permis de suivre la dynamique de lembryogenèse du haricot commun à partir dembryons prélevés 3 à 12 jours après la pollinisation et provenant de plantes normales et déficients dans la production de graines. Les embryons de P. vulgaris se développent plus rapidement par rapport à ceux issus du mutant EMS. Ces derniers présentent des anomalies au niveau de lembryon et du suspenseur. La caractérisation fonctionnelle de deux gènes candidats MIPS (myo-inositol phosphate synthase) et Sus (sucrose synthase) a été réalisée par RT-PCR quantitative et hybridation in situ suite à une étude spatio-temporelle dexpression de ces deux gènes candidats au cours de développement embryonnaire chez Phaseolus. Lanalyse du profil dexpression de ces deux gènes montre quils sont exprimés différemment au niveau des tissus de lembryon et du suspenseur. Lanalyse in silico nous a permis de sélectionner 22 gènes candidats dont nous avons vérifié l'expression au cours de développement de la graine chez Phaseolus. Des variations au niveau de la méthylation de lADN ont été déterminées chez les hybrides interspécifiques comparativement à leurs parents. La technique de lHSS a permis disoler des fragments dADNs complémentaires différemment exprimés au cours de développement de la graine chez Phaseolus. Lanalyse des séquences de ces ADNs complémentaires montre quils codent pour plusieurs protéines intervenant dans le développement cellulaire et embryonnaire, en particulier le "storage protein activator" (SPA), le "pentatricopeptide repeat-containing protein" (PPR) et lacetyl-CoA carboxylase (ACCase). La caractérisation de ces différents gènes exprimés au cours du développement de la graine, fournit de nouveaux outils susceptibles de mettre en évidence des mécanismes de dysfonctionnement embryonnaire chez le genre Phaseolus.

Mi trabajo ha estado enfocado en la implicación de los diferentes mecanismos epigenéticos de PML-RARa en la inducción de la leucemia promielocítica aguda (APL).En particular yo estudié el rol de MBD1, un miembro de la conservada familia de proteinas capaces de unirse al DNA metilado, demostrando que desempeña un papel importante en la progresión de la leucemia. De hecho, mostré que MBD1 es recruida por PML-RARa a sus promotores diana a través de los mecanismos mediados por HDAC3, participando por tanto en la represión transcripcional. Además, investigué hasta donde la metilación de la H3K27 mediada por Polycomb contribuye a la tumorgénesis mediada por PML-RARa. Demostré que PML-RARa dirige al PRC2 hacia el locus del tumor supresor causando la metilación de la H3K27. Fue interesante ser capaz de mostrar que tanto la metilación del DNA como la de las histonas era requerida para mantener el aberrante silencio génico. Esto apuntaba hacia una intercomunicación entre estos diferentes marcadores epigenéticos contribuyendo a la patología molecular de la leucemia. Resumiendo, estos resultados nos proporcionan elementos nuevos para comprender los mecanismos moleculares esenciales en la tumorgénesis y progresión de la APL. / My work was focused on the involvement of different epigenetic mechanisms in PML-RARa-induced acute promyelocytic leukemia (APL). In particular, I studied the role of MBD1, a member of a conserved family of proteins able to bind methylated DNA, demonstrating that has an important function in leukemia progression. Indeed, I showed that MBD1 is recruited by PML-RARa to its target promoters through an HDAC3-mediated mechanism, thus participating in transcriptional repression.. Furthermore, I investigated how far Polycomb-mediated H3K27 methylation contributes to PML-RARa mediated tumorigenesis. I demonstrated that PML-RARa targets the PRC2 to tumor suppressor loci causing H3K27 methylation. Interestingly, I was able to show that both DNA and histone methylation are required to maintain PML-RARa aberrant gene silencing, pointing towards a crosstalk among these different epigenetic layers that contributes to the molecular pathology of leukemia. In summary these results provide new insights into the molecular mechanisms underlying APL tumorigenesis and progression.

L’objectif de cette thèse est de déterminer l’étendue de la variabilité épigénétique, plus particulièrement du polymorphisme de méthylation de l’ADN, non liée à la variabilité génétique dans les populations asexuées en milieu naturel. Cette évaluation nous a permis de mieux cerner l’importance que peuvent avoir les processus épigénétiques en écologie et en évolution. Le modèle biologique utilisé est l’hybride clonal du complexe gynogénétique Chrosomus eos-neogaeus. Malgré une homogénéité génétique, une importante variabilité phénotypique est observée entre les hybrides d’une même lignée clonale mais retrouvés dans des environnements différents. L’influence des processus épigénétiques apporte une explication sur ce paradoxe. L’épigénétique se définit comme une modification de l’expression des gènes sans changement de la séquence d’ADN. La diversité des phénotypes peut entre autre s’expliquer par des patrons de méthylation différentiels des gènes et/ou des allèles des gènes entre les hybrides génétiquement identiques. La diversité des lignées épiclonales peut quant à elle s’expliquer par la colonisation de plusieurs lignées épiclonales, s’établir en réponse à l’environnement ou de façon aléatoire. Plusieurs méthodes seront utilisées afin de survoler le génome des hybrides clonaux pour mettre en évidence le polymorphisme de méthylation de l’ADN à l’échelle de l’individu et entre les individus de différentes populations. / The aim of the thesis is to determine the extent of epigenetic variation, more specifically DNA methylation polymorphism, not linked to genetic variation in natural populations of an asexual vertebrate. This evaluation enables to better understand the importance that plays epigenetics processes in ecology and evolution. The biological model used is the clonal hybrid of the gynogenetic Chrosomus eos-neogaeus complex. Even in absence of genetic difference, an important phenotypic variability is observed among hybrids of the same clonal lineage living in different environments. Epigenetics, a modification of genes expression without a change at the DNA sequence, provides an explanation to this paradox. The diversity of phenotypes may be explained by differential methylation patterns of genes and/or alleles among genetically identical hybrids. The diversity of epiclonal lineages may be explained by the colonisation of many epiclonal lineages, established in response to the environment or stochastically. Many methods were used for screening the genome of clonal hybrids in order to highlight DNA methylation polymophism at the scale of an individual and among individuals of different populations.

Mechanisms underlying congenital malformations are largely unknown despite its high incidence, affecting 2-3% of liveborn infants. A broader knowledge about the causes of birth defects would provide valuable information regarding the outcome and prognosis of the anomaly, the development and establishment of diagnostic protocols, the design of therapeutic strategies and genetic counseling to the family. Different approaches have been used in the present thesis regarding technologies and model diseases to elucidate the contribution of genetic and epigenetic alterations in the etiopathogenesis of congenital malformations. Copy number variations, methylation patterns, as well as point mutations have been explored. Moreover, a study to analyze genetic counseling in relation to one of the new molecular techniques used has been performed. Obtained data reveal a relevant role of genetic and epigenetic alterations in congenital malformations, in some cases as a unique cause to explain the disease and in others as part of an oligogenic or multifactorial model. / Els mecanismes causants de les malformacions congènites són poc coneguts malgrat l’elevada incidència d’aquestes patologies, que afecten el 2-3% de recent nascuts. Un coneixement més ampli de les causes de les anomalies congènites proporcionaria informació rellevant pel que fa al pronòstic de l’anomalia, el desenvolupament i establiment de protocols diagnòstics, el disseny d’estratègies terapèutiques, així com l’assessorament genètic a la família. En la tesi que es presenta s’han utilitzat diferents estratègies, pel que fa a tecnologies i models de malalties, amb l’objectiu d’esbrinar la contribució d’alteracions genètiques i epigenètiques en l’etiopatogènia de les malformacions congènites. S’han analitzat variacions en número de còpia, patrons de metilació, així com mutacions puntuals. D’altra banda, també s’ha realitzat un estudi per aprofundir en l’assessorament genètic en relació a una de les noves tècniques moleculars utilitzades. Els resultats obtinguts indiquen que les altercacions genètiques i epigenètiques tenen una contribució molt rellevant en l’etiologia de les malformacions congènites, en alguns casos com a causa única de la malaltia i en altres com a component d’un model oligogènic o multifactorial.