Transcription of the ribosomal genes accounts for the majority of transcription in the cell due to the constant high demand for ribosomes. The number of proteins synthesized correlates with an effective ribosomal biogenesis, which is regulated by cell growth and proliferation. In the work presented in this thesis, we have investigated the ribosomal RNA genes 45S and 5S rRNA, which are transcribed by RNA Pol I and RNA Pol III, respectively. The focus of this work is the chromatin remodelling complex B-WICH, which is composed of WSTF, the ATPase SNF2h and NM1. We have studied in particular its role in ribosomal gene transcription. We showed in Study I that B-WICH is required to set the stage at rRNA gene promoters by remodelling the chromatin into an open, transcriptionally active configuration. This results in the binding of histone acetyl transferases to the genes and subsequent histone acetylation, which is needed for ribosomal gene activation. Study II investigated the role of B-WICH in transcription mediated by RNA polymerase III. We showed that B-WICH is essential to create an accessible chromatin atmosphere at 5S rRNA genes, which is compatible with the results obtained in Study 1. In this case, however, B-WICH operates as a licensing factor for c-Myc and the Myc/Max/Mxd network. Study III confirmed the importance and the function of the B-WICH complex as an activator of ribosomal genes. We demonstrated that B-WICH is important for the remodelling of the rDNA chromatin into an active, competent state in response to extracellular stimuli, and that the association of the B-WICH complex to the rRNA gene promoter is regulated by proliferative and metabolic changes in cells. The work presented in this thesis has confirmed that the B-WICH complex is an important regulator and activator of Pol I and Pol III transcription. We conclude that B-WICH is essential for remodelling the rDNA chromatin into a transcriptionally active state, as required for efficient ribosomal gene transcription. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.</p><p> </p>

Le remodelage de la chromatine et la modification des histones jouent des rôles très importants dans l’établissement et la reprogrammation de l’état de l’expression génique. Il reste largement inconnu concernant les mécanismes de la régulation de ces processus chromatiniens dans le contrôle de l’expression génique impliquée dans le développement de la plante et son adaptation à l’environnement. Mon sujet de thèse se focalise sur l’analyse fonctionnelle d’un facteur de remodelage de la chromatine de type Chromodomain/Hélicase/DNA-binding 1 (CHD1) d’Arabidopsis, appelé CHR5 et une histone démethylase qui est spécifiquement impliquée dans la démethylation de l’histone H3 lysine 4 (H3K4), appelée JMJ15. Dans la première partie de cette étude, nous avons montré que le gène CHR5 est activé au cours de l’embryogénèse et que son expression se maintient élevé dans les tissues/organes en développement. L’analyse de mutants révèle que la perte de fonction de ce gène fait réprimer l’expression de gènes régulateurs de la maturation de l’embryon tels que LEC1, ABI3 et FUS3 pendant le développement des graines, et fait baisser l’accumulation des protéines de réserve. L’analyse de double mutants a permis de démontrer une fonction antagoniste entre CHR5 et PKL, une protéine du groupe « CHD3 », dans l’activité du promoteur de gènes régulateurs du développement de l’embryon et l’accumulation de réserve de graine. Nous avons montré que la protéine CHR5 s’associe directement avec les promoteurs d’ABI3 et FUS3 et que la mutation du gène CHR5 conduit à l’augmentation de présence de nucléosome dans la région du départ de transcription. Ces résultats suggèrent que CHR5 est impliquée dans le positionnement de nucléosome pour stimuler l’expression de gènes de la maturation de l’embryon, ce qui est contrebalancé par l’action de PKL au cours du développement de l’embryon. La deuxième partie de cette étude a permis de montrer que l’expression du gène de l’histone démethylase JMJ15 manifeste une forte spécificité tissulaire. L’analyse de mutants du gène a permis de l’identification de 2 allèles de gain de fonction (avec surexpression du gène), et un allèle de perte de fonction. La surexpression du gène réduit la croissance d’hypocotyle et de tige de la plante avec accumulation de lignine dans la tige, mais le perte de fonction du gène ne produise pas de phénotype apparent. Par ailleurs, la surexpression du gène renforce la tolérance de la plante au stress salin, alors la perte de fonction du gène rend la plante plus sensible. L’analyse du transcriptome a révélé beaucoup plus de gènes réprimés qu’activés par la surexpression du gène JMJ15. Ces gènes réprimés sont préférentiellement marqué la H3K4me2 ou H3K4me3, parmi lesquels beaucoup codent de facteurs de transcription. Ces données suggèrent que l’induction de JMJ15 pourrait réguler le programme de l’expression génique qui coordonne la restriction de la croissance de la plante et la tolérance au stress. Ces travaux de thèse a permis ‘identifier quelques nouveaux éléments dans la compréhension de la fonction de régulateurs chromatiniens dans l’expression génique de la plante. / Chromatin remodeling and histone modification play important roles in the establishment and dynamic regulation of gene expression states. However, little is known regarding to the regulatory mechanism of chromatin modification and remodeling that control gene expression involved in plant development and responses to environmental cues. My thesis work concerns functional analysis of an Arabidopsis Chromodomain/Helicase/DNA-binding 1 (CHD1) type chromatin remodeling gene known as CHR5 and a histone demethylase gene that specifically removes methyl groups from methylated histone H3 lysine 4 (H3K4me), called JMJ15 in regulating chromatin structure or in resetting chromatin modifications that control the expression of plant developmental and stress responsive genes. In the first part of the study we found that CHR5 expression is activated during embryogenesis and remained to be expressed in developing organs/tissues. Analysis of mutants revealed that loss-of-function of the genes led to decreased expression of key embryo maturation genes LEC1, ABI3 and FUS3 in developing seeds and reduced seed storage protein accumulation. Analysis of double mutants revealed an antagonistic function between CHR5 and PKL, a CHD3 gene, in embryo gene promoter activity and seed storage protein accumulation. CHR5 was directly associated with the promoters of ABI3 and FUS3 and chr5 mutations led to increased nucleosome occupancy near the transcriptional start site. The results suggest that CHR5 is involved in nucleosome occupancy to regulate embryo identity genes expression, which is counterbalanced by PKL during embryo development. The second part of this study showed that expression of JMJ15 was restricted to a few tissues during vegetative growth. The jmj15 gain-of-function mutations reduced the length of seedling hypocotyls and inflorescence stems with higher accumulation of lignin in the stem, while the loss-of-function mutants did not show any visible phenotype. The gain-of-function mutants enhanced salt tolerance, whereas the loss-of-function mutants were more sensitive to salt. Transcriptomic analysis revealed a much higher number of genes down-regulated in JMJ15 over-expression plants, which are highly enriched for H3K4me3 and H3K4me2. Among the down-regulated genes, many encode transcription regulators of stress responsive genes. The data suggest that increased JMJ15 levels may regulate the gene expression program that may coordinate plant growth restrains and enhances stress tolerance. Taken together, my thesis work brought a few new elements to the current understanding of chromatin regulators function in plant gene expression.

Although skeletal myogenesis is largely controlled by myogenic regulatory factors, epigenetic modifications have recently emerged as an essential regulatory mechanism of gene expression. Molecular regulation of stem cell differentiation is exerted through both genetic and epigenetic factors over distal enhancer regions. Understanding the mechanistic action of active or poised enhancers is therefore, imperative for the control of stem cell differentiation. Based on the genome-wide co-occurrence of different epigenetic marks in proliferating myoblasts, we have generated a chromatin state model to profile differentiation- and rexinoid-responsive histone acetylation in early myoblast differentiation. Here, we delineate the functional mode of transcription regulators during early myogenic differentiation using genome-wide chromatin state association. We define a role of transcriptional coactivator p300, when recruited by muscle master regulator MyoD, in the establishment and regulation of myogenic loci at the onset of myoblast differentiation. In addition, we reveal an enrichment of loci-specific histone acetylation at p300 associated active or poised enhancers, mainly when enlisted by MyoD. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor (RXR), promotes the specification and differentiation of skeletal muscle lineage. Hence, we investigated the genome-wide impact of rexinoids on myogenic differentiation and uncovered a new mechanism of rexinoid action, which is mediated by the nuclear receptor and largely reconciled through direct regulation of MyoD gene expression. In addition, we determined rexinoid-responsive residue-specific histone acetylation at a distinct chromatin state associated with MyoD and myogenin. Finally, through ChIP-seq and RNA-seq analyses, we have identified dystroglycan (Dag1) as a differentiation-dependent and a rexinoid-responsive model target, and we revealed a possible co-regulation of Dag1 by p300 and MyoD accompanied by enrichment of loci-specific histone acetylation. Taken together, we provide novel molecular insights into the regulation of myogenic enhancers by p300 in concert with MyoD. Furthermore, we provide novel mechanistic perceptions into the interplay between RXR signaling and chromatin states pertinent to myogenic programs in early myoblast differentiation. Our studies present a valuable insight for driving condition-specific chromatin state or enhancers pharmacologically to treat muscle-related diseases and for the identification of additional myogenic targets and molecular interactions for therapeutic development.

L’épissage, une étape majeure de l’expression des gènes, consiste en l’élimination des introns et la production de transcrits matures ou ARNm. La régulation ou des perturbations de l’épissage sont impliquées dans de nombreuses situations physiopathologiques. Dans ce travail, j’ai utilisé et analysé par des approches de bio-informatiques un grand nombre de données générées à large échelle afin de mieux définir les règles gouvernant la reconnaissance des exons au cours de l’épissage. Je montre que les mécanismes de reconnaissance des exons dépendent du biais de la composition nucléotidique des gènes qui les hébergent. Ainsi, la reconnaissance des exons hébergés par des gènes enrichis en guanine et cytosine dépend essentiellement de leur site 5’ d’épissage qui peut être masqué par des structures secondaires. La reconnaissance des exons hébergés par des gènes enrichis en thymine et adénine dépend essentiellement des signaux d’épissage situés en amont des exons. Je montre également que l’organisation chromatinienne est différente selon les biais de composition nucléotidique des gènes et que cela a un impact spécifique sur la reconnaissance des exons. De nombreuses études démontrent que les gènes ne sont pas organisés de façon aléatoire dans un génome et que l’architecture des gènes et des chromosomes dépend de leur composition nucléotidique. Par conséquent, mes travaux suggèrent qu’il existe un lien direct entre composition nucléotidique d’une région du génome, architecture de la chromatine et sélection des exons au cours de l’épissage. / Splicing, a major step in gene expression, consists in the removal of the introns and the production of mature transcripts or mRNA. The regulation of or the disturbances in splicing are involved in numerous physiopathological situations. In this work, I used and analysed with bio-informatic approaches a lot of genome-wide datasets in order to define better the rules governing exon recognition during the splicing step. I show in this work that the mechanisms of exon recognition depend on the nucleotidic composition bias of the genes which host these exons. Thus, the recognition of the exons located in genes enriched with guanine and cytosine essentially depends on their 5' splicing site, which can be hidden by secondary structures. The recognition of the exons located in genes enriched with thymine and adenine essentially depends on splicing signals placed upstream the exons. Moreover, I show that the chromatin organization varies according to the nucleotidic composition bias in the genes, and that it has a particular impact on exon recognition. A lot of studies have shown that the genes are not randomly organized in a genome and that the architecture of the genes and of the chromosomes depends on their nucleotidic composition. Put together, my work suggests that it exists an direct link between the nucleotidic composition of a genomic region, the chromatin architecture and the recognition of the exons during the splicing step.

L'antigène de prolifération cellulaire Ki-67 est exprimé de manière constitutive dans les cellules de mammifères. Ki-67 est régulièrement utilisé en tant que marqueur de prolifération cellulaire pour classer les tumeurs. Cependant, malgré son utilisation fréquente en histopathologie, ses fonctions sont encore mal caractérisées. Mes travaux de thèse ont eu pour objectif d'améliorer la compréhension des fonctions biologiques de Ki-67 ainsi que d’étudier l’importance de son expression dans l’initiation et la progression des cancers. Nous avons montré que Ki-67 était dispensable à la prolifération cellulaire. Quant aux souris mutantes Ki-67, elles ne présentaient aucune anomalie de développement, étaient fertiles et vieillissaient normalement. Néanmoins, l’expression de Ki-67 s’est révélée être requise pour l’organisation de l'hétérochromatine dans les cellules prolifératives. En étudiant le contrôle de l'expression de Ki-67, nous avons pu mettre en évidence que les différents niveaux d’expression de Ki-67, souvent observés dans les lignées cellulaires transformées ou non, les tissus et les échantillons de tumeurs des patients, seraient expliqués par une régulation via la machinerie du cycle cellulaire.En utilisant nos souris mutantes Ki-67, nous avons également montré que l’absence de Ki-67 permettait de protéger les souris contre la carcinogenèse intestinale dans les deux différents modèles expérimentaux utilisés. De plus, l'analyse de la conséquence de l'ablation de Ki-67 dans la lignée tumorale murine, 4T1, a révélé que Ki-67 est requis pour le maintien des propriétés souches de ces cellules cancéreuses. En outre, la déplétion de Ki-67 a fortement affecté la croissance des tumeurs et la formation de métastases pulmonaires chez les souris. De façon similaire, l'absence de Ki-67 a fortement altéré le développement des xénogreffes de la lignée MDA-MB-231 dans des souris immuno-déficientes. De plus, le séquençage de l'ARN dans les cellules 4T1 a révélé l’existence d’altérations importantes au niveau transcriptomique, suite à la déplétion de Ki-67.L’ensemble de ces résultats suggère une implication spécifique de Ki-67 dans l'initiation et la progression tumorale et que Ki-67 serait une cible thérapeutique potentielle et intéressante dans le traitement du cancer. / The cell proliferation antigen Ki-67 is constitutively expressed in cycling mammalian cells and is widely used as a cell proliferation marker to grade tumours. Despite its use in cancer histo-pathology its functions are poorly understood. The aim of this project is to improve understanding of Ki-67 functions and its requirements in cancer initiation and progression. We found that Ki-67 is dispensable for cell proliferation and Ki-67 mutant mice did not exhibit any developmental abnormalities, and were fertile and aged well. Although Ki-67 was uncoupled from cell proliferation, Ki-67 was found to promote heterochromatin organization in proliferating cells. Studying Ki-67 expression control, we have found that cell cycle regulation accounts for Ki-67 variability levels in normal human cells, proliferating tissues in mice, human cancer cell lines and caner patients.Using our Ki-67 mutant mice, we found that Ki-67 depletion can protect mice from intestinal carcinogenesis in two different experimental models used. Moreover, analysis of the consequence of Ki-67 ablation in the mouse breast cancer cell line, 4T1 has revealed its requirements for the maintenance of the stem-like proprieties of these cancer cells. More importantly, Ki-67 depletion strongly affects 4T1 tumour growth and formation of lung metastases in vivo. Similarly, Ki-67 absence strongly impaired the development of the TNBC-derived MDA-MB-231 xenografts in vivo. Moreover, comparison of Ki-67 dependent alterations in gene expression in 4T1 cells by RNA sequencing revealed widespread transcriptome changes following Ki-67 depletion. Together, these results suggest a specific involvement of Ki-67 in cancer initiation and progression and may constitute a potential therapeutic target in cancer therapy.

The eukaryotic nuclear processes such as replication, DNA damage repair (DDR) and transcription are highly dependent on the regulation of chromatin structure. The dynamic changes in chromatin accessibility are controlled by a class of chromatin-remodeling factors which form multimeric complexes and use ATP as the source of their helicase activity. In this study we have established a mouse embryonic fibroblast in vitro model with conditional inactivation of chromatin remodeling ATPase Smarca5 and used this powerful tool to test the regulation of cell cycle, proliferation and DDR signaling in conditions with low Smarca5 activity. Our results show that decreased dosages lead to decreased proliferation apparent already within few days post induction of Smarca5 deletion that is accompanied with decrease of cells in S and M phases of cell cycle, increasing cell ploidy and accelerated cell senescence. Additionally, the Smarca5 depleted cells upregulated many protein markers associated with DNA damage and cellular stress. Our results thus indicate that Smarca5 has indispensable roles during cell proliferation including in the maintenance of genome integrity during S phase of cell cycle.

La différenciation cellulaire implique une régulation transcriptionnelle coordonnée et finement contrôlée qui passe par le recrutement de facteurs de transcription (FT) cellules-spécifiques sur des régions génomiques régulatrices appelées enhancers. Parmi ces FT, des protéines nommées « facteurs pionniers » (FP) lient la chromatine condensée et favorisent la transition des enhancers d’un état inactif vers un état « préparé » (étape de « priming »), facilitant ainsi la fixation d’autres FT et permettant l’activation de ces régions. L’engagement vers un lignage cellulaire particulier est donc associé à l’engagement des FP au niveau d’enhancers dont la structure chromatinienne subit des changements architecturaux associés à la mise en place de marques spécifiques. Celles-ci incluent, la monométhylation de la lysine 4 de l’histone H3 (H3K4me1), l’acétylation de la lysine 27 de l’histone H3 (H3K27ac) ou encore des modifications des résidus cytosine (5-méthylcytosine, 5mC ; 5-hydroxyméthylcytosine, 5hmC). La 5hmC est un intermédiaire de la voie de déméthylation active : elle résulte de l’oxydation de la 5mC par les enzymes « Ten Elven Translocation » (TET) et peut être à son tour oxydée en 5-formylcytosine (5fC) et 5-carboxylcytosine (5caC) qui sont ensuite remplacées par des cytosines via l’intervention du système « Base Excision Repair ». Cependant, du fait de sa stabilité et de sa capacité à lier des protéines particulières, la 5hmC pourrait également jouer un rôle spécifique. De précédents travaux ont d’ores et déjà mis en évidence un lien entre le recrutement des FP et les modifications des cytosines. Néanmoins, l’implication des processus de méthylation/déméthylation dans la régulation spatio-temporelle des étapes de « priming » et d’activation des enhancers n’a pas encore été caractérisée. Dans ce contexte, l’objectif de cette étude à été de définir le rôle des modifications de cytosines (5mC et 5hmC) lors de l’activation des enhancers liés par des FP. Pour ceci, nous avons analysé d’une part, l’implication des processus de méthylation et déméthylation des cytosines sur le « priming » et l’activation des enhancers, en utilisant des inhibiteurs des ADN méthyltransférases ou des enzymes TET. D’autre part, nous avons entrepris d’identifier les dynamiques de « priming » et d’activation des enhancers à l’échelle du génome au cours de la différenciation neurale, en lien avec la présence de la 5hmC. Les résultats obtenus nous ont notamment permis de proposer un schéma d’activation des enhancers dans lequel les dynamiques de méthylation/déméthylation de l'ADN jouent un rôle essentiel dans la structuration de la chromatine. / Cell differentiation relies on a coordinated and finely regulated transcriptional regulation involving the recruitment of cell-type transcription factors (TFs) on genomic regions called enhancers. Some of these TFs, named pioneer factors (PFs), are able to bind to condensed chromatin and favour enhancer transition from an inactive to a primed state, thus facilitating the binding of other TFs and enhancer activation. Therefore, lineage commitment is associated to the engagement of PFs at enhancers where the chromatin structure undergoes architectural modifications related to the set up of specific marks. These include, the monomethylation of the lysine 4 of the histone H3 (H3K4me1), the acetylation of the lysine 27 of the histone H3 (H3K27ac) or cytosine modifications (5-methylcytosine, 5mC; 5-hydroxymethylcytosine, 5hmC). The 5hmC base is an intermediate in the process of active demethylation coming from the oxidation of the 5mC by the Ten Elven Translocation (TET) enzymes and can itself be further oxidized in 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), two bases which are then replaced by cytosines through the Base Excision Repair mechanism. Nevertheless, due to its stability and its ability to bind some specific proteins, 5hmC might also play specific roles. Previous works already highlighted a link between the recruitment of PFs and cytosine modifications. However, the involvement of the methylation/demethylation processes in the spatio-temporal regulation of the priming and activation of enhancers has not yet been characterized. In this context, the aim of this study was to define the role of cytosine modifications (5mC and 5hmC) during the activation of enhancers bound by PFs. For this, we analyzed the implication of cytosine methylation and demethylation processes on enhancer priming and activation by using DNA methyltransferases or TET inhibitors. In addition, we identified the dynamics of enhancer priming and activation genome-wide during neural differentiation, in relation to the presence of 5hmC. The results allow us to propose a scheme of enhancer activation in which DNA methylation/demethylation dynamics play an essential role in the chromatin structure of these regulatory elements.

Foi estudado a influência das estações não reprodutiva e reprodutiva, dos crioprotetores glicerol e etilenoglicol e do processo de congelação e descongelação sobre a motilidade, o vigor, a morfologia e o complexo DNA-proteína de espermatozóides em garanhões, comparando o sêmen fresco, o exposto a congelação e descongelação sem crioprotetores, o exposto aos crioprotetores sem congelação e o exposto aos crioprotetores com congelação e descongelação. Foram utilizados seis garanhões da raça Mangalarga Paulista, colhendo 12 ejaculados de cada animal na estação não reprodutiva (1) e 12 ejaculados na estação reprodutiva (2), analisando a motilidade, o vigor, a concentração, a morfologia e a patologia do complexo DNA-Proteína. A patologia do complexo DNA-Proteína foi avaliada em sêmen fixado com etanol-ácido-acético glacial 3:1 (v/v), tratado com HCL 4N a 25oC e corado com azul de toluidina a 0,025% em tampão Mcllvaine, empregando microscopia óptica com aumento de 1000x. Os resultados mostraram que a motilidade, o vigor, a morfologia e a anomalia do complexo DNA-Proteína dos espermatozóides diferem entre os grupos congelado e não congelado (P<0,05). Para o grupo fresco, a taxa de patologia do complexo DNA-Proteína apresentou diferença significativa (P<0,05) entre as estações 1 e 2. O processo de congelação e descongelação exerce influência negativa sobre o complexo DNA-Proteína de espermatozóides em garanhões. / To study the effects of freezing and thawing on DNA-protein complexes in spermatozoa, 12 ejaculate were collected from each of 6 stallions (Mangalarga Paulista breed) in each of two consecutive breeding seasons. Motility, vigor, concentration, morphology and incidence of the DNA-protein complex pathologies of spermatozoa were evaluated and compared among fresh semen, semen expose to freezing and thawing without cryoprotectants and semen exposed to the cryoprotectors glycerol and ethylene glycol left at room temperature or frozen. Incidence of the DNA-protein complex pathologies was evaluated in semen smear fixed in na ethanol-acetic-acid mixture (3:1, v/v) for 1 minute, washed in 70% ethanol for 3 minutes and air dried. To induce nuclear metachromasy, smears were treated with 4N HCL at 25ot for 20 minutes followed by rinsing in distilled water. Preparation were stained with a 0.025% toluidine blue solution in Mailvaine buffer for 15 minutes. Frequency of spermatozoa exhibiting nuclear metachromasy was determined in 1000 cells/animal by light microscopy at 1000X magnification. Motility, vigor, morphology and DNA-protein complex pathologies of spermatozoa were different for semen frozen compared to not frozen (P<0.05). For fresh semen, there were effects of seasons on the incidence of DNA-protein complex pathologies (P<0.05) For semen frozen without cryoprotectants there were significant effects seasons (P<0.05) The process of cryopreservation and thawing influences negatively the DNA-protein complexes in stallion spermatozoa.

Galectina-3 é uma lectina animal que apresenta afinidade por b- galactosídeos e que tem sido associada à progressão tumoral e metástase. A expressão de galectina-3 encontra-se alterada durante a progressão tumoral de diferentes neoplasias. Em tumores como carcinoma de tiróide e bexiga a expressão de galectina-3 encontra-se aumentada, enquanto que em tumores como carcinoma de mama e ovário a expressão desta lectina encontra-se diminuída. Neste trabalho nós utilizamos um modelo de progressão tumoral de melanoma murino para investigar os mecanismos envolvidos na perda de expressão de galectina-3. Este modelo é composto por uma linhagem de melanócitos imortalizados (melan-a) e duas linhagens de melanoma de crescimento vertical (Tm1 e Tm5) estabelecidas após submeter a linhagem melan-a a inúmeros ciclos de de-adesão. Enquanto melan-a acumula grandes quantidades de galectina-3, as linhagens Tm1 e Tm5 deixaram de expressar o gene de galectina-3. Análise da região 5\' do gene de galectina-3 demonstrou que esta região apresentava grande conteúdo de dinucleotídeos CpG e vários sítios SP1. O seqüenciamento desta região após tratamento do DNA com bissulfito de sódio mostrou que esta região estava totalmente metilada nas linhagens Tm1 e Tm5 e desmetilada na linhagem melan-a. O tratamento da linhagem Tm1 com 5-Aza-2\'-deoxicitidina (5-Aza-CdR), um inibidor da DNA metiltransferase, provocou um decréscimo significativo nos níveis de metilação da região 5\' do gene de galectina-3 que por sua vez levou a re-expressão do RNAm e da proteína. O tratamento de Tm1 com os inibidores de histono deacetilases tricostatina A e 4-ácido-fenilbutírico em combinação com 5-Aza-CdR não aumentou os níveis de expressão do gene de galectina-3 e curiosamente, reverteu o efeito induzido por 5-Aza-CdR. Em adição, a expressão da enzima DNMT1 apresentou um discreto aumento nas linhagens Tm1 e Tm5 em relação a melan-a. Em conjunto esses resultados sugerem que mecanismos epigenéticos como a metilação estão envolvidos no controle de expressão do gene de galectina- 3 ao longo da progressão tumoral de melanoma murino. / Galectin-3 is a b-galactoside-binding animal lectin, shown to be involved in tumor progression and metastasis. Galectin-3 expression has been found altered along tumor progression of different tumors. In some types of cancers such as thyroid carcinoma and bladder carcinoma, galectin-3 expression has been found increased, whereas in tumors such as breast carcinoma and ovary carcinoma the expression of this lectin has been found decreased along tumor progression. In this study, we have used a murine melanoma model to investigate the mechanisms responsible for the loss of galectin-3 gene expression. This model consists of a cell line of immortalized melanocytes (melan-a) and two cell lines of vertical growth phase melanoma (Tm1 and Tm5) established after submitting melan-a cells to several deadhesion cycles. While melan-a expressed high amounts of galectin-3, both Tm1 and Tm5 cells lost galectin-3 gene expression. Analysis of the 5\' upstream region of the galectin-3 gene demonstrated the presence of a high CpG content and several SP1 binding sites. Bisulfite sequencing of this region showed that it was fully methylated in Tm1 and Tm5 cells and unmethylated in melan-a cells. Treatment of Tm1 cells with 5-aza-2\'-deoxycytidine (5-Aza-CdR), a DNA methyltransferase inhibitor, led to a marked decrease in the methylation levels of the 5\' upstream region of the galectin-3 gene, which led to transcription of the galectin-3 gene. Treatment of Tm1 cells with the histone-deacetylase inhibitors trichostatin A and 4- acid-phenilbutyrate in combination with 5-Aza-CdR did not increase the levels of galectin-3 gene expression and intriguingly, reverted the effect of 5-Aza-CdR alone. In addition, the expression of DNMT1 showed a modest, but significant increase in Tm1 and Tm5 cells as compared with melan-a cells. Altogether these results indicate that epigenetic mechanisms such as methylation play a role in the regulation of the galectin-3 gene expression along murine melanoma progression.

Regulation of gene expression is an essential process for all living organisms. Transcriptional regulation, associated with chromatin, is governed by: (1) DNA sequence, which creates regulatory sites (promoters, enhancers and silencers), where sequence motifs and features (e. g. CpG) can attract transcription factors (TFs) and influence chromatin structure or RNA polymerase II (Pol II) binding, initiation and elongation; (2) non-sequence, epigenetic factors - histone modifications, TF binding, chromatin remodelling (histone placement, eviction and reconstitution), and non-coding RNA regulation. These factors interact with each other, creating a complex network of interactions. In this thesis I describe computational studies of heterochromatin factors in regulation of gene and repeat expression, an analysis of active regulatory elements, and global analyses of big datasets in C. elegans. I first show that a team of heterochromatin factors - HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 - collaborates with piRNA and nuclear RNAi pathways to silence repetitive elements and protect the germline. I also found that the TACBGTA motif is particularly enriched on repeats and heterochromatin factors binding sites, and that repeat elements are derepressed in the soma during normal C. elegans ageing. I then describe the work on active regulatory regions. I show that CFP-1/CXXC1 binds CpG dense, nucleosome depleted promoters and, along SET-2, is required for H3K4me3 deposition at these loci. Using expression profiling I determined that the majority of CFP-1 binding targets are not significantly mis-regulated in cfp-1 mutants, but are weakly upregulated in bulk analyses. I also show that CFP-1 functionally interacts with the Sin3S/HDAC complex. In cfp-1 mutant I observed both loss and gain of SIN-3 binding, depending on chromatin context. Finally, I performed a data driven study on a large collection of ChIP-seq profiles using non-parametric sparse factor analyses (NSFA) and compared it to other, unsupervised machine learning algorithms. This study uncovered interactions and structure in genomic datasets. In addition, I present a collection of computational tools and methods I developed to facilitate processing, storage, retrieval, annotation, and analyses of large datasets in genomics.