The aim of this thesis was to gain further insight into the biology of normal human skin and basal cell carcinoma (BCC). Morphology in combination with microdissection was used as primary tool for sampling. Using the X-chromosome inactivation assay, we found normal human skin to consist of a mosaic of cells, with either the maternal or the paternal X-chromosome inactivated. We believe that each tile is made up of several epidermal proliferative units with identical X-chromosome inactivation patterns. Using the same method, we found BCC to be a monoclonal neoplasm imbedded in polyclonal stroma. However, one tumor displayed clear evidence of being composed of two intermingled monoclonal tumors. To better enable molecular analysis of defined cells from tissue sections, we investigated a zinc-based fixative as alternative to neutral-buffered formalin. Zinc-based fixative preserves good quality of genomic DNA, with only slight impairment of morphology. In addition, it partly abrogates the need for antigen retrieval. The patched gene is involved in BCC development. We analyzed the distribution of a coding polymorphism (Pro/Leu) at codon 1315 in populations with different skin types. We found a reduced Pro/Pro genotype frequency in populations with lighter pigmentation. This in combination with genotype analyses of patients with multiple BCCs, showed that failure to lose the Pro allele during a shift towards lighter pigmented skin may be associated with an increased risk of developing BCC. We compared the expression profile of BCC cells with putative progenitor cells in the basal layer of epidermis. In addition to discovering several unknown genes, we found the Wnt signaling pathway to upregulated. Furthermore, differentiation markers were downregulated together with proteins important for scavenging of oxygen radicals. In conclusion, the combination of morphology, microdissection and subsequent molecular applications provided valid information deepening our understanding of normal skin and BCC.

<p>PIWI proteins belong to an evolutionary conserved protein family as the sister sub-family of ARGONAUTE (AGO) proteins. While AGO proteins are functionally well-characterized and shown to mediate small-RNA guided gene regulation, the function of PIWI proteins remain elusive. Here we pursued functional characterization of PIWI proteins by studying MILI and MIWI, two PIWI proteins in the mouse.</p><p>We first show that both MIWI and MILI co-immunoprecipitate with a novel class of non-coding small RNAs from the post-natal mouse testis extract, which are named Piwi-interacting RNAs (piRNAs). Our cloning efforts identified thousands of different piRNA sequences, mostly derived from intergenic regions. Interestingly, both MILI and MIWI piRNAs correspond to the same regions on the genome and differ primarily in length. We propose piRNAs in the adult testis are produced by the processing of long, single stranded RNA precursors, based on the observation that piRNAs originate in clusters from a number of sites on the genome in a head-to-tail homology. In support, we bioinformatically predicted putative promoters, and yeast one hybrid analysis on two such regions found out that they interact with Krueppel C2H2 type zinc finger transcription factors. We did not observe the features of the "ping-pong" mechanism in their biogenesis: Both MILI and MIWI piRNAs are biased for 5` Uracil without an Adenine bias on the 10th nucleotide position, and do not significantly consist of sequences complementary to each other along their first 10nt. Moreover, MILI piRNAs are not down-regulated in Miwi-/- testis. These results indicate that the post-natal testicular piRNAs are produced independent of the ping-pong mechanism. </p><p>Although piRNAs are highly complex, PAGE and in situ analyses showed that piRNAs are germ cell-specific with predominant expression in spermatocytes and round spermatids, suggestive of a meiotic function. Correspondingly, we found that Miwi-/-; Mili-/- mice undergo only male infertility with terminal spermatogenic arrest during meiosis. piRNAs show a nucleo-cytoplasmic distribution, with enrichment in the chromatoid and dense bodies, two male germ cell-specific structures. The dense body has been implicated in synapsis and in the heterochromatinization of the sex chromosomes during male meiosis, a process known as meiotic sex chromosome inactivation (MSCI). Our histological analysis on Miwi-/-; Mili-/- testes showed that, while the overall synapsis is not affected, the sex chromosomes retain the euchromatin marker acetyl-H4K16 and lacks the heterochromatin marker H3K9-dimethyl. These observations indicate that murine PIWI proteins are necessary for MSCI. Moreover, we identified piRNA production from the X chromosome before MSCI, and propose PIWI proteins utilize piRNAs to target and silence unpaired chromosomal regions during meiosis.</p> / Dissertation

A epigenética aborda o controle da expressão gênica através de diversos fatores que agem sob a cromatina, os melhor estudados são a metilação do DNA e a acetilação em histonas, relacionadas à repressão e ativação gênica, respectivamente. Em mamíferos, existem dois fenômenos epigenéticos interessantes: a inativação do cromossomo X (ICX) em fêmeas, que garante o equilíbrio transcricional gênico entre os sexos, e o imprinting genômico, caracterizado pela expressão monoalélica dependente da origem parental. No presente estudo, propusemos verificar a manutenção do controle epigenético em células humanas normais e transformadas em condições semelhantes de hipometilação do DNA e hiperacetilação em histonas (após uso das drogas 5-aza-2-\'deoxicitidina (5-aza-dC) e ácido valproico, respectivamente), através do monitoramento da expressão alelo-específica pelo uso de polimorfismos de única base presentes em regiões codificadoras. Em células normais houve manutenção da ICX e do imprinting genômico, enquanto que em células transformadas hipometiladas foram observadas indução de XIST, e perda de imprinting dos genes IGF2, H19 e PEG10. Observamos que ambas as drogas podem diminuir a expressão de DNMT1, e 5-aza-dC altera o equilíbrio entre acetilação e desacetilação da histona H4. Ainda, a ordem de adição dos reagentes ocasionou diferenças no nível de acetilação da histona H4 e na expressão gênica de XIST e PEG10. Nossos dados sugerem que: células humanas normais apresentam maior estabilidade do controle epigenético comparadas às células humanas transformadas, genes submetidos à ICX e \"imprintados\" não apresentam diferenças na rigidez do controle de expressão, e a cascata de reação seguida após perturbação de marcas epigenéticas pode ser alterada dependendo da modificação inicial. / Epigenetics refers to mechanisms related to gene activity through conformational modifications in DNA without changes in the nucleotide sequence. Key players in the epigenetic control are DNA methylation and histone acetylation, which are related to gene activation and repression, respectively. Two striking epigenetic phenomena in mammalians are X chromosome inactivation (XCI) and genomic imprinting. XCI triggers the transcriptional silencing of all but one X chromosome in each female cell, while genomic imprinting is a process that leads to mono-allelic gene expression based on parental origin. In the present study, we intended to verify the maintenance of epigenetic control in normal and transformed human cells under the same conditions of epigenetic disturbance. For this purpose, 5-aza-2\'-deoxycytidine (5-aza-dC) and valproic acid (VPA) were used to cause DNA hypomethylation and histone hyperacetylation, respectively. By monitoring allelic-specific expression using single nucleotide polymorphisms present in coding regions, we were able to check the effects of the modifications in the expression pattern of imprinted or subjected to XCI genes. While in female normal cells XCI and genomic imprinting were not affected by VPA or 5-aza-dC treatments, transformed male cells showed XIST activation and loss of imprinting of PEG10, IGF2 and H19 genes in the hypomethylation scenario. In addition, both drugs can decrease the expression of DNMT1, and 5-aza-dC alters the balance between acetylation and deacethylation of histone H4. Furthermore, we could see different degrees of histone H4 acetylation levels and of XIST and PEG10 expression, depending on which of the drugs was added first. Our data suggest that the epigenetic control in normal human cells is more stable when compared to transformed human cells. In addition, both XCI and genomic imprinting are epigenetic features equally hard to disturb. Finally, depending on the initial epigenetic modification (global demethylation or acethylation), it will induce different epigenetic control networks, with consequence to the final status of gene expression.

Em fêmeas de mamíferos, um dos cromossomos X é inativado proporcionando compensação de dose entre os produtos gênicos de machos e fêmeas. A inativação do cromossomo X (ICX) ocorre no embrião em desenvolvimento, e se caracteriza pela aquisição de marcas heterocromáticas no cromossomo X inativado (Xi), que são mantidas nas células somáticas ao longo das divisões celulares. O melhor modelo para estudo do início da ICX são as células-tronco embrionárias femininas. Provenientes da massa celular interna de blastocistos, elas representam um embrião em desenvolvimento e possuem os dois X ativos; a diferenciação das células promove a ICX in vitro, o que permite a identificação dos fatores e mecanismos moleculares envolvidos. A derivação de linhagens de célulastronco embrionárias humanas (human embryonic stem cells - hESCs) em 1998 permitiu novas possibilidades de estudo da ICX, pois a maioria dos trabalhos procurou esclarecer o mecanismo da ICX no modelo murino. Tradicionalmente, a manutenção da ICX em humanos tem sido investigada em células somáticas híbridas ou transformadas; porém, sabe-se que estas não representam um contexto celular natural. Assim, o presente trabalho teve como objetivos principais explorar a potencialidade de hESCs no estudo do início da ICX, e ainda investigar a função de três fatores na manutenção da ICX em células humanas imortalizadas: DNMT1 (enzima responsável pela manutenção da metilação do DNA), SMCHD1 (proteína da família de coesinas/condensinas), e XIST (um RNA não-codificador que inicia o processo de heterocromatinização do futuro Xi) foram selecionados para este estudo, uma vez que todos participam da manutenção da ICX em camundongos. Até o momento foram derivadas em nosso laboratório quatro linhagens de hESCs, as primeiras da América Latina. A caracterização das linhagens mostrou que, apesar de se manterem indiferenciadas, as hESCs femininas encontram-se em estágio pós-ICX, pois mesmo indiferenciadas já apresentam um dos X inativado. Nossos dados indicam que, submetidas às atuais condições de cultivo, as hESCs não são bons modelos para o estudo do início da ICX, e é possível que a inativação de um cromossomo X durante o cultivo confira alguma vantagem seletiva às células. A estratégia utilizada no estudo da manutenção da ICX foi o silenciamento dos três genes por interferência de RNA (RNAi). Não foi possível diminuir significativamente a expressão dos genes XIST e SMCHD1. Porém, o silenciamento de DNMT1 foi expressivo, e em resposta foi observada reativação do gene MAOA, localizado no cromossomo X e submetido à inativação. Apesar de nossas análises mostrarem que os efeitos da diminuição de DNMT1 foram restritos ao gene MAOA, estes resultados sugerem a existência de diferentes hierarquias de controle epigenético dos genes submetidos à ICX em células humanas / In female mammals, one of the X chromosomes is inactivated to achieve dosage compensation between males and females. The X chromosome inactivation (XCI) occurs early during embryogenesis and is characterized by the acquisition of heterochromatic features on the inactive X (Xi), which are maintained during all the subsequent cell divisions. Embryonic stem cells are the most suitable cells to study the establishment of XCI. They are obtained from the inner cell mass (ICM) of blastocysts, and can represent a developing female embryo, possessing two active X-chromosomes; when differentiated, these cells recapitulate XCI in vitro, and thus one can identify XCI regulators and factors involved. The derivation of human embryonic stem cells (hESCs) in 1998 offered new possibilities to study XCI, since most of the mechanistic studies of XCI have so far been investigated in the mouse model system. Traditionally, maintenance of XCI in humans has been addressed in somatic cell hybrids or transformed cells; however, they do not represent a natural cellular context. The main goals of the present work were to verify the potential of hESCs as models of XCI, and also to study the function of three important factors in XCI maintenance in immortalized human cells. DNMT1 (DNA-methyltransferase 1), SMCHD1 (a cohesin/condensin protein family member) and the XIST gene (a non-coding RNA which triggers XCI and promotes X heterochromatin formation on the future Xi) were selected, as they are key factors in XCI maintenance in the mouse. Until now four hESCs lines were derived in our lab. Their characterization showed that, in spite of been undifferentiated, the female hESCs have already undergone XCI. Our data suggest that, under the actual culture conditions, hESCs are not good models to study XCI, and it is also possible that X inactivation confers selective advantage to hESCs. Knockdown by RNA interference was used to study the roles of three genes in XCI maintenance. We could not efficiently knockdown XIST or SMCHD1. However, the DNMT1 silencing was substantial, and led to the reactivation of MAOA, an X-linked gene subjected to XCI. Although the effect of DNMT1 silencing was restricted to MAOA, our data suggest that there are different epigenetic hierarchies to control the expression of the genes subjected to XCI in human cells.

Klinefelter Syndrome (KS) is a multisystemic disorder associated with a plethora of phenotypic features including mental retardation, cardiac abnormalities, osteoporosis, infertility, gynecomastia, type two diabetes and increased cancer risk. KS is the most common aneuploidy in humans (with a prevalence of 1:500 to 1:1000 born males) and is characterized by one or more supernumerary X-chromosomes (47-XXY, 48-XXXY, and 49-XXXXY karyotypes). While X-chromosome inactivation (XCI) represses extra Xs, few genes called “escape genes” elude the XCI mechanism and are actively transcribed from X inactive. The overdosage of escape genes has been considered the molecular landscape that underlies KS clinical features. In this project, we exploit an integration-free reprogramming method to generate the largest described cohort of iPSCs from seven patients with KS and healthy donor fibroblasts from two relatives. The unicity of this cohort relies on the derivation of 47-XXY iPSCs and their isogenic 46-XY healthy counterparts, along with multiple rare 48-XXXY and 49-XXXXY iPSC lines. Through X chromosome inactivation (XCI) assessment, we show consistent retention of n-1 XCI in all derived KS-iPSCs. We identify the genes within the PAR1 region as the most susceptible to dosage-dependent transcriptional dysregulation and therefore putatively responsible for the progressively worsening phenotype in higher grade X aneuploidies. Moreover, we explore the transcriptional impact of X overdosage on autosomes and identify that the X-dosage-sensitive autosomal transcription factor NRF1 is a master regulator of the X-linked escape gene ZFX. Finally, we dissect the potential pathological impact of the escape gene KDM6A on low- and high-grade supernumerary X iPSCs and differentiated derivatives. We highlight a considerable proportion of KDM6A targets that could be responsible for paradigmatic clinical manifestations of KS.

O imprinting genômico, processo regulado epigeneticamente segundo o qual os genes se expressam de acordo com sua origem parental (paterna ou materna), está envolvido no desenvolvimento placentário. Na região cromossômica 11p15.5 encontram-se vários genes importantes para o desenvolvimento fetal e da placenta, os quais são regulados por duas principais regiões controladoras de imprinting (ICR1 e 2) onde se encontram as regiões diferencialmente metiladas H19DMR e KvDMR1, respectivamente. O imprinting genômico e a inativação aleatória do cromossomo X são processos epigenéticos presentes em mamíferos placentários. O presente trabalho teve como objetivo principal verificar a presença de mosaicismo do perfil epigenético entre tecidos extraembrionários de estágios precoces da gravidez (primeiro trimestre), e em vilosidade coriônica de placentas a termo (terceiro trimestre). Foram coletadas amostras de 10 gestações de primeiro trimestre (vilosidade coriônica, âmion, membrana de cordão umbilical e tecido embrionário) e 14 de terceiro trimestre (vilosidade coriônica), das quais 10 foram consideradas como controles e quatro utilizadas para estudo de mosaicismo restrito à vilosidade coriônica (coleta de amostras de todos os cotilédones). Após extração do DNA, foi utilizado o Método de Digestão Enzimática Sensível à Metilação Associada à PCR em Tempo Real para o estudo do padrão de metilação da KvDMR1 e da H19DMR em diferentes tecidos do primeiro trimestre gestacional e em tecido placentário do terceiro trimestre. O padrão de inativação do cromossomo X foi avaliado em todos os cotilédones de duas placentas a termo, de fetos do sexo feminino, por meio do ensaio do receptor de andrógeno humano (HUMARA assay), utilizando eletroforese capilar, e com acréscimo de um novo marcador de inativação do cromossomo X (ICX1). Na análise estatística foram utilizados o teste t não pareado, teste de Turkey e teste t pareado. A média de metilação da KvDMR1 das amostras de vilosidade coriônica do primeiro trimestre gestacional foi estatisticamente diferente da média de metilação do terceiro trimestre. Enquanto que a metilação da H19DMR não apresentou diferença estatística entre amostras de vilosidade coriônica do primeiro e do terceiro trimestre gestacionais. Com relação ao mosaicismo, a KvDMR1 não apresentou variação com relação ao tamanho ou a posição dos cotilédones, enquanto que a H19DMR apresentou diferença estatisticamente significativa na média de metilação com relação ao tamanho dos cotilédones e ao posicionamento nos quadrantes; em consequência da hipometilação em cotilédones pertencentes a uma das placentas estudadas. Não foram observadas diferenças estatisticamente significativas na média de metilação da KvDMR1 e da H19DMR entre diferentes tecidos das amostras do primeiro trimestre gestacional. No entanto, a comparação entre tecidos pareados de um mesmo indivíduo mostrou que a metilação não é correspondente entre os tecidos. Os dados obtidos mostram que o imprinting genômico provavelmente é um processo dinâmico, que evolui ao longo da gestação, estando relacionado a formação e ao amadurecimento da placenta. No presente estudo foi possível verificar que cotilédones de uma mesma placenta apresentam diferentes padrões de inativação do cromossomo X. Diferenças que podem ser explicadas pela expansão clonal das células trofoblásticas progenitoras com o cromossomo X paterno ou o cromossomo X materno inativo. Devido à variabilidade epigenética, exames em tecidos placentários devem considerar as diferenças intra-placentárias e as diferenças entre tecidos embrionários e extraembrionários. / Genomic imprinting, a mechanism of allele-specific expression depending on parental origin, is an epigenetic process that regulates the expression of many genes involved in placental development. Several important genes for fetal and placental growth are located on the human chromosome region 11p15.5, which are regulated by two imprinting control regions (ICR1 e 2), which have the differentially methylated regions H19DMR and KvDMR1, respectively. Genomic imprinting and random inactivation of X chromosome are two epigenetic processes present in placental mammals. The present study aimed to verify the presence of epigenetic mosaicism between extra-embryonic and embryonic tissues from early stages of pregnancy (first trimester), and in chorionic villi of term placentas (third trimester). Samples were collected from 10 pregnancies in the first trimester (chorionic villous, amnion, umbilical cord membrane, and embryonic tissue) and 14 from third trimester (chorionic villus sampling), of which 10 were considered as controls and four used to study mosaicism restricted to chorionic villi (sampling of all cotyledons). After DNA extraction, we used real time PCR associated to enzymatic restriction with a methylation sensitive enzyme to study the methylation pattern of KvDMR1 and H19DMR in different tissues from first trimester and placental third trimester tissue. The pattern of X chromosome inactivation was evaluated in all cotyledons from two term placentas of female fetuses, using the human androgen receptor (HUMARA) assay, capillary electrophoresis, and adding a new X chromosome inactivation (ICX1) marker. Unpaired and paired t and Turkey tests were used in statistical analysis. The average methylation of KvDMR1 of chorionic villi samples in first trimester was statistically different from average methylation of the third trimester. While the methylation of H19DMR showed no statistically significant difference between chorionic villi samples in the first and third trimester of pregnancy. In relation to the mosaicism, the KvDMR1 methylation did not vary in respect to the size or position of the cotyledons, while H19DMR showed statistically significant difference in average methylation relative to the size of the cotyledons, to the position in quadrants, due to the hypomethylation in cotyledons from one studied placenta. There were no statistically significant differences in the mean methylation KvDMR1 and H19DMR among different tissues from the first trimester of pregnancy, however, the comparison between paired tissues from the same individual showed that the methylation is different between tissues. The data from this study showed that genomic imprinting is probably a dynamic process and evolved across human pregnancy. This process is probable connected to placenta formation and maturation. We observed different patterns of X chromosome inactivation in cotyledons from the same placenta. This difference could be explained by clonal expansion of a limited number of trophoblastic progenitor cells with either an inactive maternal or paternal X chromosome. Due to the epigenetic variability, placental tissue examinations must consider the differences intra-placental and differences between embryonic and extra-embryonic tissues.

Em mamíferos a inativação do cromossomo X (ICX) consiste no silenciamento gênico de um dos dois X presentes nas células somáticas normais das fêmeas, garantindo a compensação de dose transcricional em relação aos machos. Existem duas formas de ICX: aleatória, na qual a escolha do cromossomo X inativado se dá ao acaso (X paterno ou materno); e de maneira completamente desviada, na qual a atividade do cromossomo X dependerá de sua origem parental. Nas fêmeas marsupiais a inativação ocorre de forma completamente desviada, sendo o X paterno preferencialmente inativado em todas as células, já nas células embrionárias de eutérios, o que se observa é a ICX aleatória. Entretanto, naquelas células que darão origem aos tecidos extra-embrionários, de camundongos e bovinos, a ICX se dá de forma equivalente à dos marsupiais, ou seja, o X paterno é preferencialmente inativado. Há mais de 30 anos o padrão de ICX em tecidos extra-embrionários humanos tem sido alvo de intenso debate. A crítica que se faz aqui é que tais estudos foram realizados com base na expressão de apenas um ou dois genes ligados ao X com amostras de tecidos extra-embrionários em diferentes idades gestacionais e, por vezes, em poucas amostras, o que deve ter levado às contradições entre as conclusões. O diferencial deste trabalho foi a utilização de técnicas de genotipagem de SNPs presentes em regiões codificadoras, para analisar o padrão de atividade alelo-específica de um grande número de genes presentes ao longo de todo o cromossomo X, gerando um panorama mais representativo da ICX em placenta humana. Neste estudo é comprovado o padrão aleatório de ICX em placenta humana a termo e demonstrado que este órgão se apresenta como um 65 mosaico em relação à escolha do X inativo. A análise global da atividade gênica no cromossomo X indicou ainda que a manutenção do estado epigenético do X inativo parece ser heterogêneo. Em conjunto, os dados gerados são capazes de explicar as incongruências entre as conclusões previamente publicadas. Este trabalho também ilustra as diferenças nos mecanismos de ICX entre humanos e camundongos e reforça a importância de se avaliar esse tema em outras espécies de mamíferos eutérios na tentativa de se elucidar os processos evolutivos envolvidos na compensação de dose em mamíferos / Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 23 X-linked genes, including XIST, using 28 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this chromosome-wide analysis indicated heterogeneous maintenance of the epigenetic state along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals

Le développement embryonnaire précoce des mammifères femelles s’accompagne de l’inactivation transcriptionnelle d’un de leurs deux chromosomes X. Cet évènement est initié suite à l’expression mono-allélique de l’ARN non codant Xist, qui est contrôlée par de nombreux éléments cis-régulateurs présents dans le centre d’inactivation du chromosome X (Xic) – tel son anti-sens répresseur Tsix. Mon travail de thèse a consisté à développer des approches permettant d’appréhender le paysage structural dans lequel s’exerce cette régulation. La caractérisation de l’architecture tridimensionnelle du Xic, par des techniques basées sur la capture de conformation chromosomique (3C) et l’hybridation in situ en fluorescence (FISH), m’a permis de mettre en évidence que les promoteurs respectifs de Xist et Tsix sont engagés dans des interactions physiques intimes avec des loci distaux, localisés au sein du Xic, et de montrer qu’au moins certaines de ces régions exercent un effets régulateurs à longue-distance. Les éléments du Xic contactés par les régions promotrices de Xist et de Tsix sont en outre fondamentalement différents, chacune engageant des associations chromosomiques sur plusieurs centaines de kilobases dans leur direction 5’ respective.Ce travail a également permis de révéler des propriétés insoupçonnées de l’architecture chromosomiques. En effet, le Xic apparaît scindé en plusieurs sous-régions, couvrant chacune entre 200kb et 1Mb, à l’intérieur desquelles les interactions chromosomiques sont préférentiellement établies. L’existence de ces domaines d’interaction s’intègre avec d’autres propriétés structurales du génome, tels la composition de la chromatine sous-jacente et l’association à la lamine nucléaire, mais n’apparaît pas en dépendre directement. En étudiant la dynamique de la conformation chromosomique du Xic au cours de la différenciation cellulaire, j’ai pu constater la robustesse de cette organisation, sauf sur le chromosome X inactif, qui se distingue par la perte des contacts chromosomiques préférentiels détectables sur son homologue actif.Enfin, j’ai pu mettre en évidence que la variabilité du repliement général du chromosome X amène à un instant donné chaque allèle de Tsix à contacter physiquement des jeux de séquences distales différents, suggérant que l’environnement structural instantané de chacun de ces allèles à l’orée de l’activation mono-allélique de Xist est différent. Ce travail, combinant des approches à l’échelle de la population cellulaire d’une part et de la fibre de chromatine unique d’autre part, apporte une nouvelle vision du paysage structural et régulateur dans lequel s’inscrit le contrôle de l’activité transcriptionnelle de Xist, et fourni de nouvelles perspectives concernant les principes fondamentaux de l’organisation topologique des chromosomes chez les mammifères. / Early development of female mammals is accompanied by transcriptional inactivation of one of their two X chromosomes. This event is initiated following mono-allelic expression of the Xist non-coding RNA – what is achieved by the interplay of numerous cis-regulatory elements present within the X inactivation center (Xic), such as its repressive antisense Tsix. Our work aimed at throwing light on the structural landscape that underlies such long-range regulation. Characterization of the three-dimensional architecture of the Xic, by the means of Chromosome Conformation Capture (3C)-based techniques and in situ fluorescence hybridization (FISH), revealed that the respective promoters of Xist and Tsix contact many distal genomic elements within the Xic, and that at least one of such interacting region exerts long-range cis-transcriptional control. Noticeably, Xist and Tsix promoters associate with different sets of elements in their respective 5’ direction that are spread out over several hundreds of kilobases These experiments also revealed unforeseen properties of chromatin architecture. Indeed, the Xic appears to be partitioned in several sub-regions, each spanning between 200kb and 1Mb, inside which chromosomal interactions are preferentially established. The existence of these interaction domains integrates with other structural features of the genome, such as underlying chromatin composition and association with the nuclear lamina, but does not seem to directly depend on them. By analyzing chromosome conformation of the Xic during cell differentiation we document the robustness of this organizational principle, with the noticeable exception of the inactive X chromosome that assumes a folding pattern that is more random than its active homolog. Finally we also bring evidence that variability in the folding pattern of the two X chromosomes in the same cell brings each Tsix allele in association with different sets of chromosomal partners at a given moment, suggesting that the instantaneous structural environment of each allele at the onset of mono-allelic Xist up-regulation is different.By combining approaches at the scale of cell populations on the one hand, and at the single chromatin fiber level on the other, this study provides a first vision of the structural landscape in which Xist regulation takes place, and brings new insights concerning fundamental properties of chromosome organization in mammals.

<p>A previous model of morphological pathogenesis assumed that cervical carcinoma is of monoclonal origin and progresses through multiple steps from normal epithelium via CINS into invasive carcinomas. The aim of this study was to investigate the molecular mechanism of pathogenesis of cervical neoplasia. </p><p>In the clonality study, we found that 75% (6/8) of informative cases of cervical carcinoma had identical patterns of loss of heterozygosity (LOH) in the multiple synchronous lesions, while the remaining cases had different LOU patterns. In an extensively studied "golden case", the multiple carcinoma and cervical intraepithelial neoplasia (CIN) lesions could be divided into several different clonal groups by the X-chromosome inactivation patterns, HPV 16 mutations and LOH patterns. The biggest clonal family included one CIN II, one CIN III and four carcinoma samples, while four other monoclonal families of carcinoma did not include CIN lesions. These results suggested that cervical carcinoma can be either monoclonal or polygonal and contains clones developing either directly or via multiple steps. In the study of HPV types and HPV16 variations, the results confirmed that specific HPV types are the cause of cervical carcinoma but failed to support the previous opinion that HPV16 E6 variants are more malignant than the prototype. We established a novel classification called oncogene lineage of HPV16, and found that additional variations of HPV 16 oncogenes might be a weak further risk factor for cervical carcinoma. In the study of LOH, we found that interstitial deletion of two common regions of chromosome 3p, i.e., 3p2l.1-3p2l.3, and 3p22, was an early event in the development of cervical carcinoma. The results showed that the hMLH1 gene, located in 3p22 and showing LOH in 43% of the studied cases, was not involved in the development of cervical carcinoma because neither the expression level of protein nor the gene sequence was altered in these cases. </p><p>In summary, a suggested model of molecular pathogenesis of cervical carcinoma is as follows. Specific types of HPV infect one or more committed stem cells in the basal layer of the epithelium. Fully efficient LOH events turn one (monoclonal origin) or more (polyclonal origin) HPV-infected stem cells into carcinoma cells without CIN steps. Less efficient LOH events would lead to CIN steps where some other unknown factors require to be added to facilitate the formation of carcinoma. In the absence of LOH events no carcinoma develops from the HPV-infected stem cells.</p>

A previous model of morphological pathogenesis assumed that cervical carcinoma is of monoclonal origin and progresses through multiple steps from normal epithelium via CINS into invasive carcinomas. The aim of this study was to investigate the molecular mechanism of pathogenesis of cervical neoplasia. In the clonality study, we found that 75% (6/8) of informative cases of cervical carcinoma had identical patterns of loss of heterozygosity (LOH) in the multiple synchronous lesions, while the remaining cases had different LOU patterns. In an extensively studied "golden case", the multiple carcinoma and cervical intraepithelial neoplasia (CIN) lesions could be divided into several different clonal groups by the X-chromosome inactivation patterns, HPV 16 mutations and LOH patterns. The biggest clonal family included one CIN II, one CIN III and four carcinoma samples, while four other monoclonal families of carcinoma did not include CIN lesions. These results suggested that cervical carcinoma can be either monoclonal or polygonal and contains clones developing either directly or via multiple steps. In the study of HPV types and HPV16 variations, the results confirmed that specific HPV types are the cause of cervical carcinoma but failed to support the previous opinion that HPV16 E6 variants are more malignant than the prototype. We established a novel classification called oncogene lineage of HPV16, and found that additional variations of HPV 16 oncogenes might be a weak further risk factor for cervical carcinoma. In the study of LOH, we found that interstitial deletion of two common regions of chromosome 3p, i.e., 3p2l.1-3p2l.3, and 3p22, was an early event in the development of cervical carcinoma. The results showed that the hMLH1 gene, located in 3p22 and showing LOH in 43% of the studied cases, was not involved in the development of cervical carcinoma because neither the expression level of protein nor the gene sequence was altered in these cases. In summary, a suggested model of molecular pathogenesis of cervical carcinoma is as follows. Specific types of HPV infect one or more committed stem cells in the basal layer of the epithelium. Fully efficient LOH events turn one (monoclonal origin) or more (polyclonal origin) HPV-infected stem cells into carcinoma cells without CIN steps. Less efficient LOH events would lead to CIN steps where some other unknown factors require to be added to facilitate the formation of carcinoma. In the absence of LOH events no carcinoma develops from the HPV-infected stem cells.