L’insuffisance rénale aiguë (IRA) est une dysfonction d’organe fréquente. Alors que la fonction rénale récupère le plus souvent, on sait depuis 2009 que le pronostic rénal est malgré tout engagé à long terme. L’objectif de ce travail est d’étudier les mécanismes de réparation pathologique de l’épithélium tubulaire afin de mieux comprendre les conséquences à long terme d’un épisode d’IRA.Le parcours des patients après IRA a été transposé dans un modèle à deux agressions (souris C57Bl6/J) : ischémie-reperfusion rénale, suivie à distance par l’administration continue d’angiotensine 2. L’agression aiguë a été calibrée pour obtenir une récupération fonctionnelle et une histologique (microarchitecture normale à la fin du processus de réparation). La fibrose rénale sous angiotensine 2 était plus importante après un antécédent de nécrose tubulaire ischémique résolutive. En isolant les cellules du tube proximal différenciées, une reprogrammation durable du métabolisme et une probable compartimentalisation de la fibrogénèse ont été mises en évidence.L’hypothèse d’un mécanisme épigénétique, faisant le lien entre ischémie-reperfusion et fibrose à distance, a été explorée. Des modifications d’acétylation des histones dans les cellules tubulaires ont été constatées sur des biopsies des greffons humains en post-IRA. Ces modifications ont été reproduites chez la souris et modélisées in vitro après hypoxie-réoxygénation sur une culture primaire de cellules tubulaires. L’acétylation du locus du gène du micro-ARN miR21, dont les cibles sont impliquées dans la progression de la fibrose, est augmentée après ischémie-reperfusion et associée à son induction. / Acute kidney injury (AKI) is a frequent organ dysfunction. While renal function generally recovers, it has been shown since 2009 that AKI carries a poor long-term renal prognosis. The objective of this study was to investigate the maladaptive repair of the tubular epithelium in order to better understand the long-term consequences of AKI. The course of patients after AKI was transposed into a two-hit animal model (C57Bl6/J mice): renal ischemia-reperfusion, followed by continuous administration of angiotensin 2. AKI was calibrated so as to obtain full functional recovery and normal microarchitecture after ischemic tubular necrosis. There was greater renal fibrosis under angiotensin 2 after a history of resolving ischemic tubular necrosis. By isolating differentiated proximal tubular cells, sustained metabolism reprogramming and compartmentalization of fibrogenesis were highlighted. The hypothesis of an underlying epigenetic mechanism, linking ischemia-reperfusion to fibrosis, was explored. Histone post-translational modifications (H3K18 acetylation) in tubular cells were found in human graft biopsies. These changes were reproduced in mice and modeled in vitro after hypoxia-reoxygenation on a primary culture of tubular cells. Histone acetylation peaked at the locus of the miR21 microRNA gene, whose targets are involved in the progression of fibrosis, and was implicated in miR21 expression following our model of AKI.

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La transition fleur-fruit, appelée nouaison, est déclenchée par la pollinisation des fleurs et ce processus est essentiel pour cycle reproducteur des plantes, la formation des semences et le rendement de production. Les mécanismes moléculaires contrôlant cette importante transition développementale ont été peu explorés. Les marques histones et la méthylation de l'ADN sont les deux principaux modes de régulation épigénétique, mais à ce jour, leurs contributions respectives à la reprogrammation transcriptionnelle qui est associée au programme d’initiation des fruits charnus n’ont pas fait l’objet d’aucune étude sur aucune espèce de plante. Afin d’explorer l’importance dans la transition fleur-fruit de ces deux types de régulation épigénétique, des approches de transcriptomique "genome-wide", de ChIP-seq se et de séquençage bisulfite d'ADN ont été mises en place chez la tomate, une espèce économique majeure et un modèle d’étude pour les fruits charnus. Les résultats révèlent une corrélation étroite entre le repositionnement des marques histones et les changements observés de l'expression génique globale. L’étude montre aussi que les marques H3K9ac et H3K4me3 agissent en synergie pour activer la transcription génique, alors que la marque H3K27me3 a un effet répressif. A l’inverse, il n’y a pas de corrélation entre les variations de la méthylation de la cytosine et l’évolution des profils transcriptomiques. Il ressort donc que ce sont les changements au niveau des marques histones plutôt que de la méthylation de l'ADN qui constituent le moteur principal de la reprogrammation génétique associée au processus de transition fleur-fruit chez la tomate. En concordance avec cette idée, le niveau d'expression des gènes associés à l’initiation du fruit, tels que ceux liés au métabolisme hormonal, à la division cellulaire ou au développement embryonnaire, est corrélé avec les modifications des marques H3K9ac ou H3K4me3, mais pas avec la méthylation de l'ADN. En outre, l'étude comparative des profils transcriptomiques associés à la formation du fruit dépendant et indépendant de la pollinisation révèle l'intervention complexe de multiples voies de signalisation hormonales. Au total, notre étude présente un nouvel aperçu du contrôle de la reprogrammation génétique nécessaire à l’initiation du développement du fruit et révèle le rôle important du contrôle épigénétique dans ce processus de transition développementale. Dans le même temps, l’étude identifie un groupe de gènes impliqués dans la régulation épigénétique qui offrent des cibles potentielles pour les programmes d’amélioration de la nouaison des fruits, un processus majeur affectant le rendement de production / The flower-to-fruit transition, so-called fruit setting, is triggered by flower pollination and this process is essential for plant reproductive success, seed formation and crop yield. The underlying molecular mechanisms controlling this developmental transition remain unclear. Histone marking and DNA methylation are the main epigenetic modes for genetic reprogramming, however, their respective contribution to the fruit set-associated transcriptomic reprogramming is also unknown. To address the contribution of the two types of epigenetic regulation to fruit set, genome-wide transcriptomic profiling, ChIP-sequencing and DNA bisulfite sequencing were applied to tomato, a major economic crop and a model system for fleshy fruit. The study emphasizes the tight correlation between histone repositioning and gene expression changes revealing that H3K9ac and H3K4me3 histone marks synergistically promote gene transcription, whereas H3K27me3 marking has a repressive effect. We concluded that changes in histone marks rather than in DNA methylation are the main drivers of genetic reprogramming associated with the fruit set transition in tomato, and H3K9ac and H3K4me3 marking is the primary players in this control mechanism. Consistently, the expression level of fruit set-associated genes such as those related to hormone metabolism, cell division, and embryo development correlated with changes in H3K9ac or H3K4me3 marking, but not with DNA methylation. In addition, comparative study of transcriptomic profiling between pollination-dependent and -independent fruit set, uncovered the complex intervention of multiple hormone signaling pathways involved in the flower-to-fruit transition. Auxin appears as the central hormone triggering the extensive transcriptomic reprogramming associated with the initiation of early fruit growth. Altogether, the study provides new insight into the control of gene reprogramming underlying fruit the shift from flower to fruit and uncovers a set of genes encoding modifiers of epigenetic marks which may provide new targets for breeding programs aiming to improve fruit setting, a major process impacting crop yield.

La régulation transcriptionelle fine assurée par les Eléments Cis Régulateurs (ECR, eg. promoteurs et «enhancers») et les facteurs protéiques associés, est à la base de la mise en place et le maintien de l'identité tissulaire. Les modifications de la chromatine corrèlent avec l’activité d’ECRs et constituent l’épigénome de la cellule. Au cours de ma thèse, je me suis intéressée aux transitions des modifications des histones (H3K4me1/me2/me3, H3K36me3, H3K27me3 and H3K9me2) accompagnant le développement précoce de la cellule T. Pour cela, j’ai utilisé un modèle murin reproduisant une étape cruciale de la thymopoïèse - la sélection β - et la technique d’Immunoprecipitation de la chromatine couplée à des puces à ADN (ChIP-chip). Au sein des enhancer connus, nos analyses ont mis en évidence une nouvelle signature épigénétique liée à leur activité. De plus, nous montrons que l'étendue d'enrichissement d’H3K4me2 au sein des régions géniques des gènes exprimés, constitue une signature épigénétique des gènes tissus spécifiques. Tout ceci a permis de mieux comprendre le rôle de l’épigénétique dans l'établissement et le maintien de l'identité cellulaire.Le traitement anti-cancer moderne est basé sur les analyses de différents marqueurs d'agressivité (MA) et par la suite, de l’établissement de la thérapie personnalisée. Durant la dernière partie de ma thèse, j’ai participé à un projet collaboratif avec le laboratoire de Thérapie Cellulaire de l’Institut Paoli Calmettes à Marseille, qui visait l’isolation des MA des Leucémies Aiguës Myéloïdes à caryotype normal (LMAcn) grâce aux études de profilage épigénétique (H3K27me3) des blastes des patients atteints de LMAcn. / Precise transcriptional regulation underlies the establishment and maintenance of cell type specific identity and is governed by dedicated DNA sequences (i.e., cis regulatory elements (CREs): eg.: promoters, enhancers) and transcription factors. Chromatin modifications (eg.: histone modifications, DNA methylation) impinge on CREs activity and constitute the epigenome of the cell.During my PhD, I was interested in the transitions of a set of histone modifications (H3K4me1/me2/me3, H3K36me3, H3K27me3 and H3K9me2), during one of the major checkpoints of thymopoiesis - the β-selection. I used a dedicated mouse model and Chromatin Immunoprecipitation coupled with microarrays (ChIP-chip) technique. Our data evidenced a previously unappreciated epigenetic signature linked to enhancer activity. In parallel, computational analyses of the patterns of gene body enrichment of H3K4me2 highlighted an epigenetic signature linked to the regulation of the tissue specific gene expression. Altogether, this enabled to deepen the relationship between chromatin states and regulation of cell type specific identity.Modern anticancer treatment is based on the analyses of a number of cancer aggressiveness markers (CAM) and results in a highly personalized therapy. Epigenetic profiling can constitute a powerful tool for CAM’s isolation. In the second part of the presented work, I participate in a collaborative project (with Cellular Therapy Centre at the Paoli Calmettes Institut, Marseille) aiming to isolate new CAM for Acute Myeloid Leukemia with normal karyotype (AMLnc) patients. For this purpose I performed epigenetic (H3K27me3) profiling of blasts of AMLnc.

Transcriptional regulation of cell cycle controlled genes is fundamental to cell division in eukaryotes and a broad spectrum of physiological processes directly related to cell proliferation. Expression of the cell cycle dependent human H4, H3 and H1 histone genes is coordinately regulated at both the transcriptional and posttranscriptional levels. We have systematically analyzed the protein/DNA interactions of the immediate 5'regions of three prototypical cell cycle controlled histone genes, designated H4-F0108, H3-ST519 and H1-FNC16, to define components of the cellular mechanisms mediating transcriptional regulation. Multiple biochemically distinct protein/DNA interactions were characterized for each of these genes, and the binding sites of several promoter-specific nuclear DNA binding activities were delineated at single nucleotide resolution using a variety of techniques. These findings were integrated with results obtained by others and revealed that the in vitro factor binding sites in H4, H3 and H1 histone promoters coincide with genomic protein/DNA interaction sites defined in vivofor the H4-F0108 and H3-STS19 genes, and with evolutionarily conserved cis-acting sequences shown to affect the efficiency of histone gene transcription. Specifically, we have defined binding sites for Sp1, ATF, CP1/NF-Y, HiNF-D, HiNF-M, HiNF-P and HMG-I related factors. Based on sequence-similarities and cross-competition experiments, we postulate that most of these protein/DNA interaction elements are associated with more than one class of histone genes. Thus, the protein/DNA interactions characterized in this study may represent components of a cellular mechanism that couples transcription rates of the various histone gene classes. Regulation of the protein/DNA interactions involved in transcriptional control of these H4, H3 and H1 histone genes was investigated in a spectrum of cell types using several distinct in vitro cell culture models for the onset of differentiation and quiescence, as well as cell cycle progression. Moreover, we studied control of histone gene associated DNA binding activities during hepatic development from fetus to adult in transgenic mice reflecting the onset of differentiation and quiescence in vivo. We show that the H4 histone promoter protein/DNA interaction mediated by factor HiNF-D is selectivelymodulated, and directly at the level of DNA binding activity, during the entry into, progress through and exit from the cell cycle in normal diploid cells, as well as during hepatic development. The regulation of this protein/DNA interaction occurs in parallel with analogous interactions occurring in H3 and H1 histone genes. Moreover, these proliferation-specific protein/DNA interactions are collectively deregulated during the cell cycle in four distinct cell types displaying properties of the transformed phenotype. Hence, the cellular competency to coordinately transcribe distinct classes of histone genes during the cell cycle may be mediated by the intricate interplay of constitutively expressed general transcription factors and temporally regulated, cell growth controlled nuclear factors interacting specifically with cell cycle dependent histone genes. Finally, we show that HiNF-D is represented by two electrophoretically distinct species. The ratio of these forms of HiNF-D fluctuates dramatically during the cell cycle of normal diploid cells, but remains relatively constant in tumor cells. Total HiNF-D binding activity embodied by both HiNF-D species is negatively influenced in vitro by incubation with exogenous phosphatase activity. These observations provide a first indication for the hypothesis that HiNF-D may exist in distinct post-translationally modified forms that are subject to a stringent cell growth control mechanism involving protein kinases and phosphatases. Such a cellular post-translational modification mechanism, which directly impinges on (or activates) the DNA binding activity of a key factor controlling histone genes, would provide a highly efficient means by which to influence the rate of transcription in rapid response to intra-cellular requirements for histone mRNA and extra-cellular cues signalling the onset and cessation of cell proliferation.

Cancer cells are able to adapt to different stress factors such as hypoxia, which is caused by insufficient tumor vascularization. An increased acetylation status of histones H3 and H4 in UKF-NB-3 and UKF-NB-4 neuroblastoma cell lines was found to be a mechanism of adaptation of these cells to hypoxia. An increase in acetylation of histones H3 and H4 is suggested to cause changes in the structure of chromatin that lead to activation of gene transcription. In addition, cultivation of tested neuroblastoma cells under hypoxic conditions changes expression of proteins of a transcription factor N-myc, which is essential for development of neuroblastomas. This transcription factor is also responsible for a metabolic adaptation of neuroblastoma cells, increases their aggressiveness and its expression leads to a worse prognosis of the disease. Inhibitors of histone deacetylases (HDAC) are suggested to be the promising agents exhibiting various anticancer effects. They can induce cell cycle arrest, differentiation or programmed cell death in sensitive tumors. In this study, the effect of one of inhibitors of HDACs, valproate, on expression of proteins of transcription factors N-myc and hypoxia inducible factor 1α (HIF-1α) was investigated. Valproate decreases protein levels of both transcription factors in...

The oviduct plays an important role in the complex process of fertilization and in the early phase of embryo development. Isolation and characterization of some components of bovine oviduct participating in the formation of oviductal sperm reservoir was a subject of the present study. Two affinity sorbents containing immobilized components of bull seminal plasma (non-separated proteins of bull seminal plasma and their phosphorylcholine binding fraction) were prepared and used for the study of interaction of immobilized ligands with components of oviductal epithelium. Two types of preparation of oviductal membrane proteins of the isthmus region were isolated: complete membrane proteins and the apical fraction of membrane proteins. These preparations were separated using prepared affinity matrices. in both cases only an insignificant amount of proteins was found in the adsorbed fractions. Further attention has been paid to the identification of four protein zones detected after electrophoretic separation in the presence of SDS (rel. mol. wt. 15 500 - 18 500) in the fraction of apical membrane proteins. These proteins were identified after the electrophoretic separation and tryptic digestion using MS analysis as bovine histones H4, H2A typ 2-C, H2B typ 1-K a H3.3. Proteins identified as bovine...

Histone Nuclear Factor P (HiNF-P) is a known transcriptional regulator that is critical for the activation of replication dependent histone H4 genes during S phase. HiNF-P is a 65 kDa zinc finger protein that binds to its consensus binding sequence in the Cell Cycle Control Element (Site II) of the proximal promoter region of 11 of the 14 histone H4 genes. HiNF-P is a known co-factor of the global histone gene regulator and cyclinE/CDK2 substrate p220NPAT, however it was not known if this regulatory function reflected a physical interaction. In addition, other HiNF-P interacting proteins have yet to be identified. The work presented in this thesis identifies and characterizes HiNF-P interactions with various proteins within the cell, including p220NPAT. A yeast two-hybrid interaction screen identified candidate interacting proteins of HiNF-P and provided insight into novel cellular functions and transcriptional targets. A candidate yeast two-hybrid approach identified an interaction between HiNF-P and p220NPAT. This direct physical interaction links the cyclin E/CDK2 signaling pathway governing the G1/S phase transition with replication dependent histone gene transcription in S phase. An unbiased yeast two-hybrid screen for HiNF-P interacting proteins revealed an interactome library which suggests roles of HiNF-P in multiple cellular processes. This screen identified 67 candidate HiNF-P interacting proteins that are RNA processing factors, known and putative gene regulators, uncharacterized proteins, proliferation related proteins, as well as metabolic and signaling proteins. Identification of multiple RNA binding and processing factors, including the splicing cofactor, SRm300, links HiNF-P to mRNA processing. HiNF-P is potentially functioning in mRNA processing by interacting with these proteins directly and functioning in complex with them, or more likely, by recruiting these and other splicing factors to sites of transcription. We identified a number of known and putative gene regulators which are candidate HiNF-P interacting proteins. We isolated the atypical C2CH zinc finger protein, THAP7, a known transcriptional repressor. THAP7 interacts with HiNF-P by co-immunoprecipitation and co-immunofluorescence experiments. We show forced expression of THAP7 abrogates HiNF-P/p220 mediated activation of histone H4 gene transcription. THAP7 may represent a novel co-factor of HiNF-P and p220 mediated regulation of histone H4 genes. Identification of interacting proteins of HiNF-P that are involved in transcriptional regulation provides insight into other transcriptional targets of HiNF-P. HiNF-P is localized throughout the nucleus, presumably at multiple gene foci. These interacting proteins may represent novel co-factors of HiNF-P regulation of these other multiple target genes. HiNF-P has been identified as a regulator of cell cycle dependent histone genes, therefore we were interested in identifying other proliferation related proteins with which HiNF-P is interacting. We identified a number of proteins thought to be involved in cellular proliferation, including Ki-67 and an unknown protein XTP2. The functions of these proteins have not been identified. An interaction with HiNF-P might suggest a role for these proteins in histone gene regulation. In addition, Ki-67 has been implicated transcriptional control of ribosomal genes, although no role of HiNF-P in this function has been identified. HiNF-P is a known regulator of histone gene expression via a functional interaction with the global histone gene regulator and cyclin E/CDK2 substrate, p220. This thesis demonstrates HiNF-P directly interacts with the N-terminus of p220. This interaction requires multiple regions within the N-terminus including a LisH-like domain known to function in protein-protein interactions, a region (aa 121-145) known to be required for histone gene transactivation, and another uncharacterized region (209-318). In addition a phylogenically conserved region within the C-terminus of HiNF-P, the HiNF-P Specific Conserved Region (PSCR) is necessary for this interaction. Mutational analysis of these regions abrogates this interaction. HiNF-P and p220 co-localize at specific foci within the cell corresponding to Cajal bodies, which are known sites of histone gene clusters. This work shows that this interaction is necessary for histone gene transcriptional activation and HiNF-P dependent recruitment of p220 to histone H4 gene promoters. In addition HiNF-P as well as p220 interact with the Stem Loop Binding Protein (SLBP) and co-localize in situ. SLBP is a necessary factor for histone pre-mRNA processing events which also occur at Cajal bodies. These interactions provide evidence of the coupling of transcription and processing of histone genes and the involvement of common factors in both processes. This would allow for rapid production of abundant histone proteins which is needed during S phase. This thesis has identified multiple candidate interacting proteins of HiNF-P. These proteins establish HiNF-P as a protein involved in many cellular processes and mechanisms beyond transcriptional control of cell cycle dependent histone genes.

There are two copies of each core histone in a nucleosome, however, it is unclear whether post-translational modifications on each molecule function redundantly or if symmetrical modifications are required to properly regulate gene expression. We tried to address this question by breaking nucleosomal symmetry and measuring its impact on gene expression. Our strategy includes re-engineering specific residues at the H3-H3 interface, generating pairs of mutant proteins, which were predicted by computational methods to form obligate heterodimers. Using S. cerevisiae as a model system, we tested the viability of strains with mutant histones, and analyzed the interaction between by co-immunoprecipitation from mononucleosome preparations. We also measured the changes of gene expression in the strains bearing single-tailed or tailless H3 heterodimers. The data suggested that the best computationally-derived H3 pair was frequently, but not exclusively heterodimeric in vivo. In order to obtain a more stringent H3 heterodimer, random mutagenesis was performed on four codons in the original computational design, and then genetic screening of the mutant libraries was performed.

Dans les cancers, la transcription des gènes peut être altérée par des mécanismes génétiques ou épigénétiques. En 2011, mon laboratoire a montré que la progression des cancers de la vessie pouvait être liée à un mécanisme épigénétique appelé MRES (« Mutiple Regional Epigenetic Silencing »). Les tumeurs possédant ce phénotype présentent une inactivation simultanée de gènes voisins dans 7 régions du génome. A l’aide d’une nouvelle approche bio-informatique : « SegCorr », nous avons identifié plus de 400 régions du génome dont l’expression des gènes est corrélée indépendamment du nombre de copie du gène. Ces régions se répartissent en 7 groupes et sont associées à 6 phénotypes de cancer de la vessie. De plus, l’extinction de l’expression des gènes d’une faible proportion de régions est associée à la méthylation de l’ADN et/ou une perte sur les histones de de marques d’activation de la transcription : H3K9ac et H3K4me3 ou des gains de marques de répression de la transcription : H3K27me3 et H3K9me3. Grâce au nouvel algorithme « Musette », J’ai montré que le phénotype MRES n’était probablement pas dû à des altérations génétiques. Enfin, pour comprendre à quel stade de la progression tumorale du cancer de la vessie le phénotype MRES pourrait apparaître, j’ai montré que les tumeurs de cancer de vessie induites chez les souris par ingestion d’un carcinogène (N-butyl-N-(4-hydroxybutyl)nitrosamine) pouvait être un bon modèle d’étude. / In cancers, gene transcription can be altered by genetic or epigenetic mechanisms. In 2011, my laboratory showed that the progression of bladder cancer could be linked to an epigenetic mechanism called MRES ("Mutiple Regional Epigenetic Silencing"). Tumors with this phenotype exhibit simultaneous inactivation of neighboring genes in 7 regions of the genome. Using a new bioinformatics approach: "SegCorr", we have identified more than 400 genomic regions in which gene expression is correlated. These regions fall into 7 groups and are associated with 6 phenotypes of bladder cancer. In addition, the extinction of gene expression from a small proportion of regions is associated with DNA methylation and / or loss of histone marks associated with active transcription: H3K9ac and H3K4me3 or gains of histone marks associated with transcription repression: H3K27me3 and H3K9me3. Using a new algorithm “Musette”, I have shown that the MRES phenotype is probably not due to genetic alterations. Finally, to understand at which stage of tumor progression of bladder cancer the MRES phenotype might appear, I have shown that bladder cancer tumors induced in mice by ingestion of a carcinogen (N-butyl-N-(4-hydroxybutyl) nitrosamine) could be a good model.