The African trypanosome Trypanosoma brucei evades the immune system of the mammalian host by periodically switching its surface coat which is made up of Variant Surface Glycoprotein (VSG). T. brucei shows monoallelic expression of one VSG out of a repertoire of ~1200 genes with the active VSG gene expressed from one of ~15 telomeric expression sites (ESs). The mechanism behind the monoallelic exclusion of ESs is unclear. NLP was identified as a novel and essential AT-hook protein binding transcriptionally silent simple sequence repeats in T. brucei. I depleted NLP using RNAi in various T. brucei reporter lines containing an eGFP in different transcriptionally silent areas of the genome and monitored derepression of eGFP using flow cytometry. After NLP knock-down, I observed 45-65 fold derepression of silent ESs, and up to 5 fold derepression of other transcriptionally silent areas. Using chromatin immunoprecipitation (ChIP) I found an enrichment of NLP in certain non-transcribed loci including the rDNA spacers. I also found that blocking NLP synthesis results in a rapid fall in levels of the active VSG transcript. Lastly, I discovered using tandem affinity purification (TAP) followed by mass spectrometry that NLP is a part of a novel TbISWI complex in T. brucei, which also includes two previously unidentified protein partners. The high mobility group B (HMGB) protein family constitutes a major abundant class of non-histone chromatin associated DNA-binding proteins which play a role in chromatin architecture in a wide range of eukaryotes. In T. brucei, the HMGB protein TDP1, which contains two HMG boxes and one DEK C terminal DNA-binding domain, was first identified as binding to VSG ES promoter oligomer sequences. I report that TDP1 is an essential nuclear protein enriched in the nucleolus and expression site body, and is involved in facilitating transcription. Blocking TDP1 synthesis using RNAi mediated knock-down results in approximately 40-90% reduction in transcription of RNA polymerase I transcribed genes. Using ChIP, I find that TDP1 is enriched in the rDNA and on the active VSG ES in bloodstream form T. brucei. Additionally, the relative proportion of TDP1 binding the procyclin promoter compared with the upstream spacer and downstream EP1 genes is greater in procyclic form compared with bloodstream form T. brucei. Lastly, I performed TAP experiments with TDP1 and found that TDP1 interacts with the core histones. These results indicate that TDP1 is an architectural chromatin protein important for transcription control in T. brucei.

<p>Despite a largely static DNA sequence, our genomes are incredibly malleable. Comparative studies of chromatin features between different cell types, tissues, and species have revealed tremendous differences in how the genome is accessed, transcribed, and replicated. However, how the dynamics of chromatin accessibility contribute to development, environmental response, and disease status has only begun to be appreciated. In this work we identified chromatin accessibility changes by DNase-seq in three diverse processes: in granule neurons of the developing cerebellum, with intestinal epithelial cells in the absence of a normal microbiota, and with myelogenous leukemia cells in response to histone deacetylase inhibitor treatments. In all cases, we coupled these analyses with RNA-seq assays to identify concurrent transcriptional changes. By mapping the changes to these genome-wide signals we defined the contribution of local chromatin structure to the transcriptional programs underlying these processes, and improved our understanding of their relation to other chromatin changes like histone modifications. Furthermore we demonstrated use of the strongest accessibility changes to identify transcription factors critical for these processes by finding enrichment of their binding motifs. For a few of these key factors, depletion or overexpression of the protein was sufficient to regulate the expression of predicted target genes or exert limited chromatin accessibility changes, demonstrating the functional significance of these proteins in these processes. Together these studies have informed our understanding of the role chromatin accessibility changes play in development and environmental responses while also proving their utility for key regulator identification.</p> / Dissertation

DNA in eukaryotes is packaged into nucleosomes, which present steric impediments to many of the factors and enzymes that act on DNA, including DNA repair enzymes. Within the nucleosome, DNA remains vulnerable to oxidative damage that can result from normal cellular metabolism, ionizing radiation, and various chemical agents. Oxidatively damaged DNA is repaired in a stepwise fashion via the base excision repair (BER) pathway. Other DNA repair pathways, including Nucleotide Excision Repair (NER), Mismatch Repair (MMR), Homologous Recombination (HR), and Non-homologous End-Joining (NHEJ) are all thought to require nucleosome remodeling or disruption. In contrast, it was reported that the first step of BER does not require or induce nucleosome disruption. For example, the human DNA glycosylase hNTH1 (human Endonuclease III) was discovered to excise thymine glycol lesions from nucleosomes without nucleosome disruption, and could excise optimally oriented lesions with an efficiency approaching that seen for naked DNA (Prasad, Wallace, and Pederson 2007). To determine if the properties of hNTH1 are shared by other human DNA glycosylases, we compared hNTH1 with NEIL1, a human DNA glycoylase that also excises thymine glycol from DNA, with respect to their activities on nucleosome substrates. We found that the cellular concentrations and apparent kcat/KM ratios for hNTH1 and NEIL1 are similar. However, NEIL1 and hNTH1 differ in that NEIL1 binds undamaged DNA far more avidly than hNTH1. After adjustment for non-specific DNA binding, hNTH1 and NEIL1 proved to have similar intrinsic activities towards nucleosome substrates. We next wanted to examine the effects of nucleosomes on enzymes that catalyze the remaining steps in BER. We therefore assembled the entire four-step BER reaction with model, lesion-containing nucleosomes. The rates of substrate processing during the first three steps in BER, catalyzed by a DNA glycosylase, AP endonuclease, and DNA Polymerase Pol), varied with the helical orientation of the substrate relative to the underlying histone octamer. In contrast, the rate of action by DNA Ligase III- (in association with XRCC1) was independent of lesion orientation. These results are consistent with structural studies of BER enzymes and the previously proposed DNA unwrapping model for how BER enzymes gain access to lesions in nucleosomes (Prasad, Wallace, and Pederson 2007). During these investigations, we also discovered a synergistic interaction between Pol and Ligase III- complexed with XRCC1 that enhances the repair of lesions in nucleosomes. Together, our results support the hypothesis that DNA glycosylases have evolved to function in specific cellular environments (e.g. NEIL1 may function exclusively during DNA replication), but also possess DNA binding motifs and mechanisms of substrate recognition that impart a similar intrinsic activity on nucleosomes. In addition to hNTH1 and NEIL1, we have discovered that lesion orientation is also an important factor to the activities of APE and Pol and that the complete BER reaction can occur without requiring or inducing nucleosome disruption. Finally, protein-protein interactions between XRCC1 and Pol may be important for the efficient in vivo repair of lesions in nucleosomes.

La kinase Cdk8 est impliquée dans la régulation de la transcription. Pourtant, cette protéine est retrouvée sur la chromatine lors de la réplication dans le modèle d'extrait d'œufs de xénope, où la transcription n'est pas active. Mon projet de thèse avait pour but de caractériser les fonctions de Cdk8 sur la chromatine en cours de réplication.Les résultats de ma thèse montrent que Cdk8 est impliquée dans la réplication de l'ADN. Le recrutement de Cdk8 sur la chromatine est concomitant avec le recrutement de certaines protéines du complexe de pré-réplication, bien qu'elle ne soit pas accumulée au niveau des foyers de réplication.Cependant, la déplétion de Cdk8 induit des défauts de réplication de l'ADN.Ces défauts ne sont pas induits par une collision entre le réplisome et la machinerie transcriptionnelle. En effet, l'ARN polymérase II, engagée sur la chromatine mais inactive en condition normale, est moins abondante sur la chromatine en absence de Cdk8.La déplétion de Cdk8 conduit à la diminution du recrutement des complexes de pré-réplication et des complexes de pré-initiation de la réplication. Cette diminution conduit à une baisse du taux de réplication sans activation du checkpoint intra-S. L'ensemble de mes résultats montrent que Cdk8 est nécessaire à une réplication normale de l'ADN. Plusieurs mécanismes semblent être mis en jeu, à savoir, un défaut de recrutement de la machinerie de réplication, l'accumulation de la protéine Adenomatous polyposis coli (APC) sur l'ADN ainsi que des modifications post-traductionnelles des histones. / The Cdk8 kinase is involved intranscriptional regulation.This protein is found on chromatin during DNA replication in xenopus egg extract model when transcription is not active. My PhD project was to characterize Cdk8 functions on chromatin during replication.My results show that Cdk8 is involved in DNA replication.Cdk8 is not found at replication foci , but its recruitment on chromatin occurs at the same time as several components of the pre-replication complex.Moreover, Cdk8 depletion leads to DNA replication defects.These defects are not induced by collision between the replisome and transcriptional regulators (RNA polymerase II and transcription factors). Indeed, RNA polymerase II, which is on chromatin in an inactive form under normal conditions, is less abundant on chromatin in absence of Cdk8.Cdk8 depletion leads to a decrease in pre-replication complexes and pre-initiation complexes recruitment. This decrease induces a reduction in DNA replication rate without activating the intra-S checkpoint.My data show that Cdk8 is necessary for proper DNA replication. It seems that Cdk8 depletion involves several mechanisms : altered replication machinery recruitment, presence of Adenomatous Polyposis Coli (APC) protein on DNA, and post-traductional modifications of histones.

Chez Saccharomyces cerevisiae, la methylation de la lysine 4 de l'histone H3 (H3K4) est catalysée par le complexe à activité methyltransférase Set1, conservé au cours de l'évolution. Durant la méiose, l'absence de Set1 conduit à un retard de démarrage de la phase S, et à un défaut dans la formation des coupures double-brin de l'ADN (CDBs). Nous avons cherché à mieux caractériser ces deux conséquences phénotypiques liées à l'absence de Set1. Nous montrons que le retard de réplication est lié à la perte de méthylation de H3K4 mais qu'il ne résulte pas d'un défaut d'activité des kinases responsables de l'activation des origines de réplication ou de l'activation des voies canoniques de surveillance moléculaire liées aux dommages de l'ADN. L'importante diminution de fréquence de CDB sur la majorité des points chauds chez le mutant set1&#8710; a été corrélée à l'absence de la marque de H3K4 triméthylée. Nous avons confirmé le role de la méthylation de H3K4 sur la base de la diminution générale de la fréquence des CDBs observée en absence des différentes sous-unités du complexe associé à Set1 (COMPASS) ou chez un mutant exprimant une histone H3 non-méthylable (H3K4R). Pour tester la relation de causalité entre méthylation et CDBs, différentes sous-unités du COMPASS, telles que Set1 et Spp1, ont été fusionnées avec le domaine de fixation à l'ADN de Gal4 pour les cibler vers des régions non méthylées et dépourvues de CDB. Gal4BD-Spp1 stimule fortement la fréquence des CDBs à certains loci, y compris en contexte mutant H3K4R. Ainsi, le ciblage de Spp1 peut etre suffisant pour recruter et/ou activer la machinerie de CDB. / In Saccharomyces cerevisiae, the methylation of the lysine 4 of histone H3 (H3K4) is catalysed by the evolutionary conserved Set1 methyltransferase complex. During meiosis, the absence of Set1 leads to a delay of S-phase onset and to a defect in the formation of double-strand breaks (DSBs). Our work was intended to give some clues about these two phenotypic consequences of Set1 loss. We show that the replication delay is linked to the absence of H3K4 trimethylation but does not result from a defect of the kinases responsible for the activation of replication origins or the activation of the canonical DNA-damage checkpoints. The severe decrease of DSB levels at the majority of recombination hotspots in set1&#8710; has been correlated with the specific marking of DSB sites by H3K4 trimethylation at some loci. We have confirmed the role of H3K4 methylation by observing a general decrease in DSB frequency similar to that of set1&#8710; in mutants lacking various subunits of the Set1- associated complex (COMPASS) or expressing a nonmethylatable histone H3 (H3K4R). To test for a causal relationship between H3K4 methylation and DSB formation, we have fused different proteins of the COMPASS, such as Spp1 or Set1, with the DNA binding domain of Gal4, in order to target them to H3K4-unmethylated and DSB-cold regions. Remarkably, Gal4BD-Spp1 strongly stimulates DSB formation in naturally cold DSB regions, even in the H3K4R mutant context. Thus, the specific tethering of Spp1 to a chromosome site is sufficient to recruit and/or activate the DSB machinery.

Orientador: Marion Burkhardt de Koivisto / Banca: Gisele Mingoti / Banca: Cássia Orlandi / Resumo: O objetivo deste estudo foi avaliar o empacotamento da cromatina e morfometria da cabeça de espermatozoides criopreservados de touros Bos taurus indicus da raça Nelore de diferentes idades e a influência do grau de compactação da cromatina na produção in vitro de embriões (PIV). Foram utilizados 40 animais mantidos em centro de coleta e processamento de sêmen (CCPS) e distribuídos em três grupos: Grupo Jovens (entre 1,8 e 2 anos), Grupo Adultos (entre 3,5 e 7 anos) e Grupo Senis (entre 8 e 14,3 anos). Os ejaculados foram congelados de acordo com os padrões pré-estabelecidos do CCPS. Utilizou-se a coloração de azul de toluidina, que permite a avaliação simultânea da cromatina e morfometria da cabeça espermática, a cromomicina A3 (CMA3) para analisar a protaminação espermática e a PIV para o desenvolvimento embrionário. O azul de toluidina foi avaliado pela microscopia óptica e a CMA3 pelo citômetro de fluxo. Na PIV foram realizadas quatro repetições por grupo, com 25 a 30 oócitos em cada repetição. A análise seminal revelou que espermatozoides de touros jovens obtiveram maiores valores de área (A), perímetro (P) e largura (L) quando comparados a adultos e senis (Jovens: A=1848,5±119,79, P=10,23±0,29, L=1,95±0,1; Adultos: A=1672,9±104,46, P=9,86±0,33, L=1,81±0,06; Senis: A=1723,1±124,41, P=9,97±0,33, L=1,83±0,09; P<0,0001) e apresentaram maior deficiência de protaminação quando analisado pela CMA3 (Jovens: 1,57±0,76; Adultos: 1,09±0,63, Senis: 0,90±0,59; P<0,05). Da mesma forma, variáveis de tamanho (A, P, L) e protaminação espermática, avaliado pela CMA3, obtiveram correlação negativa com a idade e positiva com a elipsidade (P<0,05). Espermatozoides com anormalidades na cromatina obtiveram maior área quando comparado àqueles sem alteração de cromatina (P<0,0001). Não houve diferença significativa na PIV quando sêmen com maior e menor parcela de alteração de cromatina foi ... / Abstract: The aim of this study was to evaluate chromatin condensation and sperm head morphometry of cryopreserved semen samples from Bos taurus indicus bulls of different ages and the influence of the degree of chromatin condensation on in vitro embryo production (IVP). A total of 40 animals kept in an Artificial Insemination Centre were divided into three groups: Young Group (1.8 to 2 years), Adult Group (3.5 to 7 years) and Senile Group (8 to 14.3 years). The ejaculates were frozen in accordance with established standards of the Artificial Insemination Centre. The thawed semen samples were evaluated with toluidine blue, which analyzes the chromatin condensation and sperm head morphometry simultaneosly, chromomicin A3 (CMA3) to analyze the protamination and in vitro embryo production to analyze the embryonic development. The toluidine blue was evaluated by optical microscopy and the CMA3 by flow cytometry. Semen analyses revealed that spermatozoa of young bulls had higher values of area (A), perimeter (P) and width (W) when compared to adults and senile (Young: A = 1848.5 ± 119.79, P = 10. 23 ± 0.29, W = 1.95 ± 0.1; Adults: A = 1672.9 ± 104.46, P = 9.86 ± 0.33, W = 1.81 ± 0.06; Senile: A = 1723.1 ± 124.41, P = 9.97 ± 0.33, W = 1.83 ± 0.09; P<0.0001) and had higher protamination deficiency when analyzed with CMA3 (Young: 1.57 ± 0.76, Adults: 1.09 ± 0.63, Senile: 0.90 ± 0.59, P<0.05). Variable size (A, P, W) and sperm protamination evaluated by CMA3 showed negative correlation with age and a positive with ellipticity (P<0.05). Spermatozoa with abnormal chromatin obtained larger area when compared to those with normal chromatin (P<0.0001). There was no significant difference in IVP using semen with higher and lower altered chromatin condensation, evidencing that the proportion of spermatozoa with abnormal chromatin (4 to 16.15%) did not affect the embryonic development. Our results indicate that sperm head of young bulls are ... / Mestre

Eukaryotic genes contain non-coding sequences - introns that are removed during pre-mRNA splicing by the spliceosome. The spliceosome is composed of five snRNPs (U1, U2, U4/U6 and U5) which assemble on pre-mRNA in a step-wise manner and together with additional non-snRNP proteins catalyse splicing. Mutations in splicing factors can cause severe diseases, for example a point missense mutation (called AD29) in hPrp31 (U4/U6 snRNP specific protein) induces retinitis pigmentosa, disease often leading to complete blindness. In this PhD thesis we show that the hPrp31 AD29 mutant is unstable and is not properly incorporated into spliceosomal snRNPs. In addition, the expression of the mutant protein reduces cell proliferation, which indicates that it interferes with cellular metabolism (likely splicing) and could explain the induction of retinitis pigmentosa. Next, we focus on a role of nuclear environment in pre-mRNA splicing. It was shown that new U4/U6·U5 snRNPs are preferentially assembled in non-membrane nuclear structure - Cajal body. Here we expand this finding and provide evidence that Cajal bodies are also important for U4/U6·U5 snRNP recycling after splicing. In addition, we analyzed a role of chromatin and particularly histone acetylation modulates in splicing regulation. Using inhibitor of...

La complexe protéique Sir (Silent Information Regulator) de la levure bourgeonnante est l’acteur principal dans la formation de l’hétérochromatine, qui provoque l’atténuation de l’expression génique par un mécanisme épigénétique. Le complexe Sir lié à la chromatine maternelle est démonté lors de la réplication génomique et puis réformé sur les deux brins nouvellement répliqué. La dynamique de maintien de Sir sur la chromatine pendant le cycle cellulaire et dans de variables conditions de croissance n’est pas bien comprise. Pour comprendre comment la structure chromatinienne telle que l’hétérochromatine peut être héritée et par conséquent comment les structures épigénétiques sont transmises d’une génération cellulaire à l’autre, nous avons besoin de mesurer la vitesse d’échange des sous-unités du complexe Sir au cours du cycle cellulaire dans différentes conditions de croissance. Nous avons donc utilisé le système RITE qui permet d’échanger deux épitopes attachés à Sir3 (une des sous-unités de Sir) et par la suite mesurer la cinétique de remplacement de Sir3. Nous avons constaté que la Sir3 maternelle est complètement remplacée par la Sir3 nouvellement synthétisées dans les régions télomériques durant le premier cycle cellulaire après la sortie de la phase stationnaire. Nous proposons que cette reprogrammation du complexe hétérochromatique est un mécanisme d’adaptation qui assure l’activation des gènes de réponse au stress par la déstabilisation transitoire de la structure hétérochromatinienne. / The budding yeast SIR complex (Silent Information Regulator) is the principal actor in heterochromatin formation, which causes epigenetically regulated gene silencing phenotypes. The maternal chromatin bound SIR complex is disassembled during replication and then, if heterochromatin is to be restored on both daughter strands, the SIR complex has to be reformed on both strands to pre-replication levels. The dynamics of SIR complex maintenance and re-formation during the cell-cycle and in different growth conditions are however not clear. Understanding exchange rates of SIR subunits during the cell cycle and their distribution pattern to daughter chromatids after replication has important implications for how heterochromatic states may be inherited and therefore how epigenetic states are maintained from one cellular generation to the next. We therefore used the tag switch RITE system to measure genome wide turnover rates of the SIR subunit Sir3 before and after exit from stationary phase and show that maternal Sir3 subunits are completely replaced with newly synthesized Sir3 at subtelomeric regions during the first cell cycle after release from stationary phase. We propose that the observed “reset” of the heterochromatic complex is an adaptive mechanism that ensures the activation of subtelomeric stress response genes by transiently destabilizing heterochromatin structure.

Orientador: José Luiz Laus / Coorientador: Alvio Isao Shiguematsu / Banca: Andreia Vitor Couto do Amaral / Banca: Antonio Carlos Alessi / Banca: Jayter Silva de Paula / Banca: Noeme Sousa Rocha / Resumo: A córnea atua como principal elemento refrativo do olho, para tal tem que manter-se transparente. O endotélio corneal é um peça chave para essa manutenção, possuindo mecanismos como a bomba de Na+ e K+ que ajudam a garantir a desturgescência corneal. Descompensações endoteliais constituem uma importante indicação de transplante da córnea, uma vez que as células endoteliais corneais apresentam limitada capacidade proliferativa. Entretanto, transplantes são procedimentos cirúrgicos complicados e de elevado custo. Alternativas e coadjuvantes medicamentosos vêm sendo estudadas. O fucoidam é uma substância que, dentre outras propriedades, promove migração e proliferação celular, portanto objetivou-se, com a presente pesquisa, avaliar seus efeitos sobre a morfologia, a ploidia e o metabolismo de células endoteliais da córnea de coelhos, após criolesão experimental. Para tal, foram realizadas avaliações quanto à morfologia e viabilidade celular empregando-se dupla marcação com corantes vitais (alizarina vermelha e azul de tripan) e ultraestrutural pela microscopia eletrônica de transmissão e de varredura. Outrossim, avaliou-se a morfometria in vivo e in vitro de seguintes parâmetros: número de células, densidade, hexagonalidade e coeficiente de variação celulares. Estudou-se o metabolismo dessas células empregando-se a imunofluorescência com observação em confocal dos anticorpos Ki-67, Na+K+/ATPase, n-Caderina e Zo-1, conjugados com Alexafluor-488. Visando-se a conseguirem conhecime... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The cornea as the main refractive element of the eye, which has to remain transparent. The corneal endothelium is a key piece for this maintenance, having mechanisms such as the Na + and K + pump that help to ensure corneal dysurgescence. Endothelial decompensations are an important indication for corneal transplantation, since the corneal endothelial cells have limited proliferative capacity. However, transplants are complicated and expensive surgical procedures. Alternatives and drug coadjuvants have been studied. Fucoidam is a substance that, among other properties, promotes cell migration and proliferation, therefore, the objective of this research was to evaluate its effects on the morphology, ploidy and metabolism of rabbit cornea endothelial cells after experimental cryoinjury. For this, evaluations were made for morphology and cell viability using double labeling with vital dye (alizarin red and tripan blue) and ultrastructural analysis by transmission and scanning electron microscopy. Morphometry (in vivo and in vitro) of the following parameters were also evaluated: cell number, cell density, hexagonality and coefficient of variation. The metabolism of these cells was studied using immunofluorescence with confocal observation of the Ki-67, Na + K + / ATPase, n-Caderin and Zo-1 antibodies, conjugated to Alexafluor-488. In order to obtain additional knowledge regarding the nuclear activity during the healing process of the corneal endothelium in the presence of fucoidam were analyzed, from the feulgen reaction, nuclear perimeter and area, in addition to the chromatin supraorganization. Cryoinjury resulted in worsening of all morphometric parameters, with cell decrease, cell density, the percentage of standard cells with 6 sides and increase in coefficient of variation, the recovery to normal values with time was better in eyes tre... (Complete abstract click electronic access below) / Doutor

HIV-1 infections can be treated but not cured by the current antiretroviral therapy regimens. One of the major barriers to HIV-1 eradication is the persistence of the virus in treated HIV+ individuals under the form of reservoirs. A continuum of molecular mechanisms, at the epigenetic, transcriptional and post-transcriptional levels maintains HIV-1 gene expression silent in its reservoirs. A better understanding of HIV-1 molecular mechanisms of persistence thus allows to devise novel therapeutic approaches to eradicate the virus. In this context, our thesis aimed at characterizing the molecular mechanisms of HIV-1 persistence in its T-lymphoid and myeloid reservoirs. More specifically, we have studied the epigenetic and transcriptional mechanisms of HIV-1 persistence at three different levels. First, we have investigated the DNA methylation-mediated mechanisms underlying the heterogeneity of the DNA methylation inhibitor 5-aza-2’-deoxycytidine potency in the reactivation of HIV-1 gene expression from latently-infected CD4+ T cells. Second, we have studied the contribution of the intragenic binding sites for the cellular PU.1 transcription factor in the specific regulation of HIV-1 gene expression in myeloid lineages. Finally, in a third study, we have designed a new tool to study the transcriptional landscape of HIV-1 in LTRs-suppressed proviruses. Collectively, our work has offered individual insights into the molecular mechanisms underlying the heterogeneity of HIV-1 T-lymphoid and myeloid reservoirs, with the ultimate goal of developing new HIV-1 curative strategies and improving the quality of life of HIV+ individuals. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished