Orientador: Doralice Maria Cella / Banca: Carlos Ribeiro Vilela / Banca: Claudio Juan Bidau / Banca: Francisco de Assis Ganeo de Mello / Banca: Luciana Bolsoni Lourenço / Resumo: Dentre todas as ordens de aracnideos conhecidas taxonomicamente, Araneae e a segunda mais diversa, com numero de especies menor somente em relacao a Acari. Atualmente, 39.725 especies ja foram descritas, sendo que centenas de novas descricoes sao feitas a cada ano em diversas familias de aranhas. O conhecimento citogenetico sobre a ordem restringe-se a analise de 638 especies (ca 2%) do total descrito do ponto de vista taxonomico. Este trabalho tem como objetivos fornecer uma compilacao dos dados citogeneticos existentes para a ordem na literatura ate a presente data, bem como caracterizar e estabelecer as estrategias de diferenciacao cromossomica em 13 especies de aranhas pertencentes ao grupo das haploginas, clado que corresponde a somente 3.257 especies (ca 8%) do total da ordem e a apenas 41 especies (ca 6%) do total cariotipado ate os dias atuais. Aliado a baixa representatividade dos dados cariologicos, outros pontos que fazem das haploginas um grupo interessante para estudos sao a predominancia de cromossomos meta/submetacentricos e de sistemas cromossomicos de determinacao sexual simples e multiplos, muitas vezes incluindo um cromossomo Y, ambas caracteristicas raras entre os outros clados de Araneae. As especies analisadas pertencem a tres familias de haploginas, Pholcidae (Mesabolivar luteus e Micropholcus fauroti), Sicariidae (Loxosceles amazonica, Loxosceles gaucho, Loxosceles hirsuta, Loxosceles intermedia, Loxosceles laeta, Loxosceles puortoi, Loxosceles similis e Sicarius tropicus) e Scytodidae (Scytodes fusca, Scytodes globula e Scytodes itapevi). Em Pholcidae, os resultados ineditos para os dois generos mostraram ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Mesabolivar luteus (Keyserling 1891) and Micropholcus fauroti (Simon 1887) specimens were collected in Ubatuba and Rio Claro, both in the state of São Paulo, Brazil. Mesabolivar luteus showed 2n(.) = 15 = 14 + X and 2n(.) = 16 = 14 + XX in mitotic metaphases and 7II + X in diplotenic cells. During late prophase I, all bivalents presented a ring shape, evidencing two chiasmata per bivalent. In this species, some diplotenic cells appear in pairs, maybe due to specific characteristics of the intercellular bridges. The metaphases II showed n = 7 or n = 8 = 7 + X chromosomes. Micropholcus fauroti evidenced 2n(.) = 17 = 16 + X in spermatogonial metaphases and 8II+X in diplotenic cells, with only one chiasma per bivalent, contrasting with M. luteus. In both species, all chromosomes were metacentrics. The X sexual chromosome was the largest element and appeared as a univalent during meiosis I. These are the first cytogenetical data for the genera Mesabolivar and Micropholcus. Additionally, M. luteus is the first chromosomally analyzed species of the New World clade and the observed diploid number for M. fauroti had not yet been recorded in Pholcidae. / Doutor

La chromatine embryonnaire subit des changements nécessaires pour l’établissement d’un nouveau programme développemental. Ce travail a étudié l’organisation de l’hétérochromatine au cours du développement sous trois facettes. La première étant celle de d’hétérochromatine constitutive, à travers, l’établissement forcé de la marque H4K20me3 qui provoque un arrêt du développement préimplantatoire. Ce phénotype dépend spécifiquement de l’activité de la methyltransferase SUV4-20h2 et induit l’activation de la voie de signalisation ATR qui bloque la phase de réplication. En deuxième partie, l’hétérochromatine facultative a été le sujet d’une analyse de l’expression des protéines du complexe non-canonique PRC1 et de la modification H2AK119ub qui en résulte. Finalement, une analyse de la chromatine embryonnaire a été mise en place et a permis la détection des changements de niveau de compaction au cours du développement préimplantatoire. / Embryonic chromatin undergoes necessary changes to establish a new developmental program. This work has addressed the organization of heterochromatin in preimplantation embryos from three angles. The first part probed the absence of constitutive heterochromatin by forcing the establishment of the H4K20me3 mark which results in an embryonic arrest prior to the 2-cell stage. This phenotype is due to the specific histone methyl-transferase activity of SUV4-20h2 and is induced by ATR activation which blocks replication. In the second part, facultative heterochromatin was studied by analyzing the levels of several members of the non-canonical PRC1 complex as well as the resultant modification H2AK119ub. Finally, an analysis of the embryonic chromatin was set up and allowed for the measurement of changes in the chromatin openness during preimplantation development.

Made available in DSpace on 2014-06-11T19:30:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-04-27Bitstream added on 2014-06-13T21:01:36Z : No. of bitstreams: 1 araujo_d_dr_rcla.pdf: 1858376 bytes, checksum: dbeb43d42be45d0e0d9524437faa5d74 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Dentre todas as ordens de aracnideos conhecidas taxonomicamente, Araneae e a segunda mais diversa, com numero de especies menor somente em relacao a Acari. Atualmente, 39.725 especies ja foram descritas, sendo que centenas de novas descricoes sao feitas a cada ano em diversas familias de aranhas. O conhecimento citogenetico sobre a ordem restringe-se a analise de 638 especies (ca 2%) do total descrito do ponto de vista taxonomico. Este trabalho tem como objetivos fornecer uma compilacao dos dados citogeneticos existentes para a ordem na literatura ate a presente data, bem como caracterizar e estabelecer as estrategias de diferenciacao cromossomica em 13 especies de aranhas pertencentes ao grupo das haploginas, clado que corresponde a somente 3.257 especies (ca 8%) do total da ordem e a apenas 41 especies (ca 6%) do total cariotipado ate os dias atuais. Aliado a baixa representatividade dos dados cariologicos, outros pontos que fazem das haploginas um grupo interessante para estudos sao a predominancia de cromossomos meta/submetacentricos e de sistemas cromossomicos de determinacao sexual simples e multiplos, muitas vezes incluindo um cromossomo Y, ambas caracteristicas raras entre os outros clados de Araneae. As especies analisadas pertencem a tres familias de haploginas, Pholcidae (Mesabolivar luteus e Micropholcus fauroti), Sicariidae (Loxosceles amazonica, Loxosceles gaucho, Loxosceles hirsuta, Loxosceles intermedia, Loxosceles laeta, Loxosceles puortoi, Loxosceles similis e Sicarius tropicus) e Scytodidae (Scytodes fusca, Scytodes globula e Scytodes itapevi). Em Pholcidae, os resultados ineditos para os dois generos mostraram... / Mesabolivar luteus (Keyserling 1891) and Micropholcus fauroti (Simon 1887) specimens were collected in Ubatuba and Rio Claro, both in the state of São Paulo, Brazil. Mesabolivar luteus showed 2n(.) = 15 = 14 + X and 2n(.) = 16 = 14 + XX in mitotic metaphases and 7II + X in diplotenic cells. During late prophase I, all bivalents presented a ring shape, evidencing two chiasmata per bivalent. In this species, some diplotenic cells appear in pairs, maybe due to specific characteristics of the intercellular bridges. The metaphases II showed n = 7 or n = 8 = 7 + X chromosomes. Micropholcus fauroti evidenced 2n(.) = 17 = 16 + X in spermatogonial metaphases and 8II+X in diplotenic cells, with only one chiasma per bivalent, contrasting with M. luteus. In both species, all chromosomes were metacentrics. The X sexual chromosome was the largest element and appeared as a univalent during meiosis I. These are the first cytogenetical data for the genera Mesabolivar and Micropholcus. Additionally, M. luteus is the first chromosomally analyzed species of the New World clade and the observed diploid number for M. fauroti had not yet been recorded in Pholcidae.

Les noyaux des cellules eucaryotes contiennent différents compartiments définis fonctionnellement ou structurellement et à multiples échelles qui présentent une distribution spatiale très ordonnée. Un défi majeur est alors d'identifier les règles selon lesquelles les compartiments nucléaires sont organisés dans l'espace et de décrire comment ces règles peuvent varier en fonction des conditions physiologiques ou expérimentales. Les statistiques spatiales ont rarement été utilisées à cette fin et se sont généralement limitées à l'évaluation de l'aléatoire complet. Ici, nous développons une approche de statistiques spatiales qui combine la cytologie, l'analyse d'image et la modélisation spatiale pour mieux comprendre les configurations spatiales à l'intérieur du noyau. Notre première contribution est un cadre méthodologique qui permet de tester des modèles d'organisation spatiale au niveau de la population. Plusieurs modèles spatiaux ont été proposés et mis en œuvre, en particulier l'aléatoire, l'aléatoire orbitale, la régularité maximale, l'aléatoire territoriale et l'aléatoire territoriale orbitale, pour analyser la distribution d'objets biologiques dans des domaines 3D finis et de formes arbitraires. De nouveaux descripteurs spatiaux, combinés aux descripteurs classiques, sont utilisés pour comparer les motifs observés à des configurations attendues sous les modèles testés. Une version non biaisée d'un test statistique publié précédemment est proposé pour évaluer la qualité de l'ajustement des modèles spatiaux sur les distributions observées. Après, nous étudions les propriétés de l'approche proposée à partir de données réelles et simulées. La robustesse de l'approche proposée aux erreurs de segmentation et la fiabilité des évaluations spatiales sont examinées. En outre, la base d'une méthode pour comparer les distributions spatiales entre différents groupes expérimentaux est proposée. Dans la dernière partie de ce travail, notre approche est appliquée à des images de noyaux cellulaires de la feuille chez A. thaliana, pour analyser la distribution spatiale de compartiments dynamiques et plastiques d'hétérochromatine, les chromocentres, qui ont un rôle important dans la structure du génome. Des noyaux isolés et des cryo-sections provenant de plantes de type sauvage ont été analysés. Nous montrons que les chromocentres présentent une distribution très régulière, ce qui confirme les résultats publiés précédemment. En utilisant nos nouveaux descripteurs, nous démontrons pour la première fois, objectivement et quantitativement, que les chromocentres présentent une localisation préférentielle périphérique. En employant un nouveau modèle spatial, nous rejetons l'hypothèse selon laquelle l'organisation régulière observée est uniquement expliquée par un positionnement périphérique. Nous démontrons en outre que les chromocentres affichent une régularité spatiale proche de la régularité maximale à l'échelle globale, mais pas à l'échelle locale. Enfin, nous utilisons des simulations pour tester un modèle selon lequel le positionnement des chromocentres est déterminé par les territoires chromosomiques et par des interactions avec l'enveloppe nucléaire. Nous avons ensuite vérifié s'il la distribution des chromocentres pouvait être modifiée par différentes mutations. Nous avons analysé les données de noyaux des mutants crwn et kaku, qui sont connus pour influencer la morphologie nucléaire. Les résultats suggèrent que ces mutations impactent en effet la morphologie nucléaire et les caractéristiques de l'hétérochromatine, mais ne modifient pas la régularité de la distribution des chromocentres même si la distance à la frontière du noyau est affectée. La généricité du cadre proposé pour analyser les distributions d'objets dans des domaines 3D finis et la possibilité d'ajouter de nouveaux modèles et descripteurs spatiaux devrait permettre d'analyser des organisations spatiales au sein de différents systèmes biologiques et à différentes échelles. / Eukaryotic cell nuclei contain distinct functionally or structurally defined compartments at multiple scale that present a highly ordered spatial arrangement. Several studies in plants and animals have pointed out to links between nuclear organization and genome functions. A key challenge is to identify rules according to which nuclear compartments are organized in space and to describe how these rules may vary according to physiological or experimental conditions. Spatial statistics have been rarely used for this purpose, and were generally limited to the evaluation of complete spatial randomness. In this Thesis, we develop a spatial statistical approach, which combines cytology, image analysis and spatial modeling to better understand spatial configurations inside the nucleus. Our first contribution is a methodological framework that allows to test models of spatial organization at the population level. Several spatial models have been developed and implemented, including randomness, orbital randomness, maximum regularity, territorial randomness or orbital territorial randomness of biological objects within finite 3D domains of arbitrary shape. New spatial descriptors, in combination with classical ones, are used to compare observed patterns to expected configurations under the tested models. An unbiased version of a previously published statistical test is proposed to evaluate the goodness-of-fit of spatial models over populations of observed patterns. In the second part of this Thesis, we investigate the properties of the proposed approach using simulated and real data. The robustness of the proposed approach to segmentation errors and the reliability of the spatial evaluations are examined. Besides, the basis for a method to compare spatial distributions between different experimental groups is proposed. In the last part of this work, the proposed approach is applied on A. thaliana leaf cell nuclei images to analyze the spatial distribution of chromocenters, which are dynamic and plastic heterochromatic compartments that have an important structural role in the genome. A first application was to analyze isolated and cryo-section nuclei from wild type plants. We show that chromocenters present a highly regular distribution, confirming previously published results. Using new spatial statistical descriptors, we then demonstrate objectively and quantitatively, for the first time, that chromocenters exhibit a preferentially peripheral localization. Employing a new spatial model, we then reject the hypothesis that the regular organization is explained solely by the peripheral positioning. We further demonstrate that chromocenters organization displays a close-to-maximum spatial regularity at the global scale, but not at the local one. Lastly, we use simulations to examine a model according to which chromocenters positioning is constrained by chromosome territories and by interactions with the nuclear boundary. The second application was to elucidate whether chromocenters distribution could be altered under different mutations. We analyze nuclei data from crwn and kaku mutants, which are known to affect nuclear morphology. The results suggest that these mutations impact on nuclear morphology and on heterochromatin features but do not alter the regularity of chromocenters distribution even when the relative distance to the border is affected. The genericity of the proposed framework to analyze object distributions in finite 3D domains and its expandability to add more spatial models and spatial descriptors should be of interest to decipher spatial organizations within biological systems at various scales.

Cytogenetics of mesothelid spiders is largely unkown. The presented diploma thesis is focused on the karyotype evolution of these spiders. As it is the most basal group of spiders, the analysis of its cytogenetics can bring important data about ancestral spider karyotype. In the framework of my thesis, I analysed diploid chromosome numbers, chromosome morphology, meiotic division, sex chromosomes and the pattern of selected molecular markers that were detected by fluorescence in situ hybridization. According to my results, mesothelid spiders have a high number of chromosomes and the prevalence of monoarmed chromosomes. Unlike other spiders, mesothelids have little differentiated sex chromosomes. Key words: evolution, spider, chromosome, karyotype, fluorescence in situ hybridization, nucleolar organiser region, sex chromosomes

1 Abstract: The diploma thesis focuses on study of sex chromosomes evolution and repetitive organized genes of chosen mygalomorph and araneomorph spiders. Spiders are characterized by complexicity of sex chromosome systems, their karyotypes contain multiple sex chromosomes X. Besides multiple X chromosomes they also contain a pair or two pairs of nondiferentiated sex chromosomes X and Y. The used methods include methods of classical cytogenetics (preparation of chromosome slides, C-banding) and methods of molecular cytogenetics (fluorescent in situ hybridization and comparative genome hybridization). Complex sex systems were discovered in the studied Theraphosidae spiders. In Theraphosidae spiders Atropothele socotrana and Poecilotheria vittata neo-sex chromosomes were found. Analysis of molecular differentiation of sex chromosomes suggests low differentiation of Y chromosome in neo-sex chromosomes and pair of nondifferentiated sex chromosomes XY. In haplogyne spider Kukulcania aff. hibernalis (X1X2Y), the Y chromosome was significantly differentiated, male specific signal covered the whole chromosome. Detection of 18S rDNA showed that karyotypes of majority of analysed Theraphosidae spiders and haplogyne spiders contain low number (1 or 2) of nucleolar organizing regions localized terminally, which...

Karyotypes of mygalomorph spiders are not satisfactorily known. This thesis is focused on the basic cytogenetic analysis of selected species of African clades of theraphosid mygalomorphs. It includes four subfamilies: Eumenophorinae, Harpactirinae, Ischnocolinae and Stromatopelminae. Diploid numbers, chromosome morphology, sex chromosome systems and chromosome behaviour in male germline in the selected species of African theraphosid subfamilies were studied. The findings support published results, that refer of high karyotype diversity in Theraphosidae. Diploid chromosome number reduction is probably a basic trend of theraphosid karyotype evolution. The majority of analysed species exhibited one, two or three sex chromosomes. In some species neo-sex chromosome systems were found. In some species one or two sex chromosome pairs (SCP), composed of chromosomes which lack morphological differentiation were detected. Nucleolus organizer regions were detected by fluorescent in situ hybridization in several species. Constitutive heterochromatin detection was performed by C-banding in two species. Keywords: constitutive heterochromatin, diploid number, karyotype, fluorescence in situ hybridization, Mygalomorphae, nucleolus organizer region, SCP, sex chromosome, spider, Theraphosidae

Pour se défendre des effets délétères des éléments transposables, les pezizomycotina ont développé un système de défense génétique et épigénétique appelé « Repeat Induced Point Mutation » (RIP). Chez N. crassa, le RIP survient dans la cellule dicaryotique avant la caryogamie et conduit à la méthylation de novo des cytosines (5mC) inclues dans les séquences répétées de chacun des noyaux parentaux haploïdes. De plus, certaines de ces cytosines sont la cible d’un processus de mutation qui les transforme en thymines. Cette étape est suivie par la mise en place locale de l’hétérochromatine constitutive permettant une répression transcriptionnelle durable des séquences cibles du RIP au cours des divisions nucléaires. L’acteur majeur du RIP correspond à une cytosine méthyltransférase putative appelée RID (RIP Defective). Bien que son génome ne montre pas une quantité significative de 5mC, l’inactivation de PaRid chez Podospora anserina aboutit à un blocage du développement sexué survenant après la fécondation. Dans ce contexte, nous avons voulu déterminer si la fonction de PaRid dans le développement sexué consiste à éteindre l’expression de gènes cibles via l’installation de foyers d’hétérochromatine constitutive aux loci concernés. Pour ce faire, nous avons identifié les gènes PaKmt1 et PaHP1, codant respectivement l’histone méthyltransférase PaKmt1 (l’homologue de SU(VAR)39 qui catalyse la tri-méthylation du résidu H3K9 (H3K9me3) et PaHP1 (l’homologue de Heterochromatin Protein 1 qui se lie à H3K9me3). Les deux protéines interviennent dans une même voie de régulation qui aboutit à la mise en place de l’hétérochromatine constitutive. Par opposition, PaKmt6, homologue de l’histone méthyltransférase E(Z), correspond à la sous-unité catalytique du complexe PRC2 qui catalyse la marque H3K27me3 pour permettre l’établissement de l’hétérochromatine facultative. Nos résultats ont montré que l’absence de PaKmt1 et PaHP1 ne provoquent que des défauts mineurs. A l’inverse, l’inactivation du gène PaKmt6 conduit à un ensemble de défauts sévères : croissance végétative altérée, surproduction des gamètes mâles, malformations critiques des fructifications, production très réduite d’ascospores dont la germination est pour partie déficiente. Une étude d’épistasie a montré que les protéines PaRid et PaKmt6 interviennent chacune dans deux voies développementales distinctes. Par ailleurs, nous avons établi par immuno-précipitation de la chromatine les profils de distribution à l’échelle du génome entier des modifications H3K9me3, H3K27me3 et H3K4me3. Caractéristique rare, la marque H3K9me3 colocalise avec H3K27me3 sur des gènes transcriptionnellement réprimés et les séquences répétées ripées. Conformément à sa fonction canonique, H3K4me3 est présente en 5’ des gènes transcrits et est exclue des domaines H3K9me3 et H3K27me3. Comme attendue, PaKmt6 est essentielle à la mise en place de la marque H3K27me3, mais, de manière surprenante, elle serait aussi impliquée dans le dépôt et/ou le maintien d’une partie des marques H3K9me3, dévoilant ainsi une voie de méthylation non canonique de ces résidus. / In pezizomycotina, transposable elements are targeted by a genome defense system named Repeat Induced Point Mutation (RIP). First described in Neurospora crassa, RIP occurs before karyogamy in each parental haploid nucleus of the dikaryotic cells and results, within the repeats, in de novo methylation of cytosine (5mC) and mutations, mainly C to T transitions. This initial step triggers local assembly of constitutive heterochromatin, which allows transcriptional gene silencing. RID (RIP Defective) is a putative cytosine methyltransferase essential for RIP. Despite the absence of 5mC in its genome, PaRid inactivation in Podospora anserina results in sexual reproduction arrest right after fertilization. In this context, we asked whether PaRid is required to silence expression of some of sexual development-specific genes by nucleation of constitutive heterochromatin. To this end, we identified PaKmt1 and PaHp1 genes encoding respectively the histone methyltransferase PaKmt1 (SU(VAR)39 homologue protein) and the heterochromatin protein 1 (PaHP1). To assemble constitutive heterochromatin, PaKmt1 catalyses tri-methylation of H3K9 (H3K9me3), latter on bound by PaHP1. By contrast, the E(Z) histone methyltransferase homologue PaKmt6, as part of the PRC2 complex, catalyses tri-methylation of H3K27 (H3K27me3) to form facultative heterochromatin. Our results showed that loss of either PaKmt1 or PaHP1 does not cause major defects. Conversely, PaKmt6 gene inactivation results in severe defects: altered mycelium and vegetative growth rate, overproduction of male gamete, development of crippled fructifications, reduced production ascospores, part of which does not germinate. Furthermore, epistatic study showed that PaRid and PaKmt6 likely act in two different developmental pathways, with respect to sexual reproduction. In addition, using chromatin immuno-precipitation we characterized H3K9me3, H3K27me3 and H3K4me3 genome-wide distribution patterns. We observed an uncommon overlapping distribution between H3K9me3 and H3K27me3 on transcriptionally repressed genes and RIP target repeats. As expected, H3K4me3 localizes in 5’ of the transcribed genes and is excluded from the H3K9me3 and H3K27me3 domains. As expected, PaKmt6 is essential for H3K27me3 modification, but surprisingly, could also be responsible for some of the H3K9me3 setting up or maintenance.

Cytogenetics of mesothelid spiders is largely unkown. The presented diploma thesis is focused on the karyotype evolution of these spiders. As it is the most basal group of spiders, the analysis of its cytogenetics can bring important data about ancestral spider karyotype. In the framework of my thesis, I analysed diploid chromosome numbers, chromosome morphology, meiotic division, sex chromosomes and the pattern of selected molecular markers that were detected by fluorescence in situ hybridization. According to my results, mesothelid spiders have a high number of chromosomes and the prevalence of monoarmed chromosomes. Unlike other spiders, mesothelids have little differentiated sex chromosomes. Key words: evolution, spider, chromosome, karyotype, fluorescence in situ hybridization, nucleolar organiser region, sex chromosomes