Les télomères sont des structures critiques situées aux deux extrémités des chromosomes linéaire et empêchent que ces derniers soient dégradés, sujet à des réparations aberrantes ou subissent des recombinaisons homologues. Ces régions particulières sont compactées sous une forme de chromatine très dense que l’on nomme l’hétérochromatine. Une étape clef dans l’établissement et la maintenance de l’hétérochromatine est la tri-méthylation de l’histone H3 en lysine 9 (H3K9me3). Cette marque sert de point d’ancrage pour un certain nombre de protéines qui vont ensuite permettre de propager un environnement répressif. Les télomères étant hétérochromatiques, sont enrichis en H3K9me3 qui est déposée par l’histone methyltransférase SUV39H. Pourtant, la relation entre cette modification H3K9me3 et les télomères a été très peu étudiée. Il a été suggéré que cette marque est impliquée dans l’homéostasie de la taille des télomères, mais la fonction de H3k9me3 reste largement inconnue. Pendant ma thèse, j’ai empêché la catalyse de H3K9me3 aux télomères en supprimant l’histone methyltransférase responsable. Comme modèle d’étude j’ai travaillée sur des cellules embryonnaires de souris (mESC), étant donné que ces cellules de mammifère ont de très longs télomères hétérochromatiques. De façon surprenante, j’ai découvert que c’est l’enzyme SETDB1 qui installe H3K9me3 aux télomères de mESC. J’ai purifiée et comparée les changements de la composition moléculaire de télomères n’ayant plus d’histones trimethylés en lysine 9 (dans des cellules mESC ou SETDB1 est « knocked-out » (KO)) à des télomères sauvages en utilisant la technique de PICh (Proteomics of Isolated Chromatin segments) sur des cellules cultivées en SILAC (Stable Isotope Labelling Amino Aacids). J’ai montré que H3K9me3 contrôle le recrutement de chaperonnes d’histones; et de façon plus surprenante, cette marque semblerait contrôler l’élongation et/ou inhiber la terminaison de la transcription des télomères. En effet les télomères sont transcrits en un long ARN non-codant appelé TERRA. Nos données préliminaires suggèrent que cette voie n’est pas restreinte aux télomères mais aussi à d’autres gènes qui sont sous le contrôle de SETDB1. Il semblerait que la trimethylation de H3K9 dans le corps du gène est nécessaire pour maintenir la processivité de l’ARN polymérase II. Mes données suggèrent que SETDB1 contrôle la trimethylation de H3K9 aux télomères et dans certains corps de gènes ce qui est crucial pour la transcription générale dans les cellules embryonnaires de souris. / Telomeres are critical regions that protect chromosome ends from degradation or aberrant repair. These regions are assembled into heterochromatin. Trimethylation of histone H3 on lysine 3 (H3K9me3) is a biochemical modification found at telomeres and essential in the establishment and maintenance of constitutive heterochromatin. During my thesis, I investigated the function of H3K9 trimethylation. According to my data, this hallmark is deposited by SETDB1 at the telomeres in mouse embryonic stem cells. Using the quantitative PICh method, I showed that this mark controls the recruitment of histone chaperones. Heterochromatin is typically believed to repress gene expression but my data suggests that at telomeres, the H3K9me3 mark instructs transcriptional elongation and/or inhibit transcriptional termination of telomeres into the non-coding RNA TERRA. Preliminary data even suggest this pathway is not only restricted to telomeres but also to other genes under the control of SETDB1. It seems that H3K9 trimethylation in the gene body is necessary to maintain RNA polymerase II processivity. My data suggests SETDB1 controls H3K9 trimethylation at telomeres and gene bodies which is crucial for general transcriptional in mouse embryonic stem cells.

In order to contain many millions, or even billions of base pairs within every nucleus of a eukaryotic cell, DNA must be extensively packaged. This is achieved by association of DNA with packaging proteins, resulting in the formation of chromatin, which can lead to various degrees of compaction. The most extreme form of compaction is the highly condensed mitotic chromosome, formation of which is necessary for proper resolution and segregation of the genetic material during cell division. However, the exact nature of the structure of chromatin within the mitotic chromosome and the factors which regulate it remain subjects of debate and continued investigation. The hybrid cell line F1.1 presents a unique tool for the study of mitotic chromosome structure. This mouse cell line has been observed to present a distinct chromatin structure in mitosis assembled over a large region of DNA inserted into one of its chromosomes and originating from the fission yeast Schizosaccharomyces pombe. Direct comparison of the structure of this distinct region of chromatin with that of the adjacent endogenous chromatin could provide insight into the nature of mitotic chromosome structure as well as the properties of the chromatin which are influencing this structure. Microscopy and Hi-C analyses showed that the mitotic chromatin organising or "scaffold" proteins are not altered over the region of S. pombe chromatin, but that the amount of chromatin organised around these proteins is diminished. In accordance with the "radial-loop" model of mitotic chromosome structure, we put forward a model whereby the S. pombe chromatin is organised into smaller chromatin loops around a constant organising scaffold. Examination of the histone post-translational modifications over the region of S. pombe chromatin revealed it to be highly heterochromatic, with high levels of H3K9me3 and associated factors such as HP1α and 5meC, and low levels of activating marks. Generation of further mammalian - S. pombe fusion cell lines recapitulated both the distinct mitotic structure and the heterochromatic profile of the inserted S. pombe chromatin. However, insertion of S. pombe DNA into a mouse cell by transfection rather than fusion resulted in a large region of S. pombe DNA that lacked both a distinct structure and heterochromatin. These results suggest that H3K9me3- mediated heterochromatin may influence the structure of chromatin in mitosis, leading to an organisation into smaller chromatin loops than non-heterochromatic regions.

No description available.

Les lymphocytes T CD4 naïfs sont des cellules plastiques, capables de moduler finement leur programmation selon les signaux environnementaux qu'ils intègrent. Ils adaptent ainsi leur phénotype et leur fonction au type de danger Lors d'une infection par un agent pathogène intracellulaire par exemple, ils acquièrent un phénotype Th1 sous l'influence de médiateurs solubles tels que l'IL-12 et l' IFN-γ. Ces signaux mobilisent un set restreint de facteurs de transcription, coordonné par Tbet, qui programment la cellule afin qu'elle induise l'élimination du danger par des mécanismes impliquant une production massive d'IFN-γ. En réponse à des allergènes ou à des parasites extracellulaires, les lymphocytes T peuvent aussi acquérir un phénotype Th2, caractérisé par l'expression du facteur de transcription Gata-3 et par la production d'IL-4, d'IL-5 et d'IL-13. Afin de garantir la stabilité des lignages, ces processus de différenciation peuvent s'accompagner d'une perte de potentialité. Contrairement aux cellules T naïves, les cellules Th1 sont par exemple incapables d'allumer le programme d'expression génique Th2 en présence d'IL-4, et les lymphocytes Th2 verrouillent le programme Th1. Si nous savons aujourd'hui que l'acquisition des fonctions effectrices, comme l'équilibre entre détermination cellulaire et plasticité, sont régulés par des mécanismes épigénétiques, la plupart des acteurs moléculaires qui contrôlent la programmation des lymphocytes T au niveau de la chromatine reste encore à identifier. Durant ma thèse, j'ai étudié le rôle de la lysine méthyltransférase SETDB1, qui catalyse la di- ou tri-méthylation de la lysine 9 de l'histone 3 (H3K9me3), dans la différenciation des lymphocytes T CD4. Il avait déjà été proposé qu'H3K9me3 ait un impact sur la programmation de ces cellules en réponse aux signaux de l'environnement, mais personne n'avait encore étudié le rôle de SETDB1 dans ces processus lorsque j'ai commencé ma thèse. A l'aide d'une lignée murine déficiente pour SETDB1 spécifiquement dans les lymphocytes T, nous avons montré in vitro et in vivo que la balance Th1/Th2 est fortement augmentée en l'absence de l'enzyme, et que cette dérégulation résulte d'une perte de répression du réseau génique Th1. [...] / Upon activation, naïve CD4 T cells differentiate into distinct helper or regulatory T cell subsets depending on environmental signals received. This process relies on complex and lineage-specific gene expression programs whose dynamics and stability are regulated at the level of the chromatin. The epigenetic pathways involved, however, remain largely unknown. Here, we report that the histone methyltransferase SETDB1 critically controls the Th1 gene expression program. SETDB1-deficient naïve CD4 T cells show exacerbated Th1 priming, and when exposed to a Th1-instructive signal, SETDB1-deficient Th2 cells cross lineage boundaries and transdifferentiate into Th1 cells. Surprisingly, SETDB1 does not appear to control Th1 gene promoter activity. Instead, it deposits the repressive H3K9me3 mark at a restricted and cell-type specific set of endogenous retroviruses (ERVs) strongly associated with genes involved in immune processes. Refined bioinformatic analyses indicated that these retrotransposons either flank and repress Th1 gene cis-regulatory elements or behave themselves as Th1 gene enhancers. In conclusion, H3K9me3 deposition by SETDB1 ensures T cell lineage integrity by repressing a repertoire of ERVs that have been exapted into cis-regulatory modules to shape and control the Th1 gene network.

No description available.

Epigenetic modifications are alterations in the cell nucleus that affect gene expression and can occur in chromatin at the level of DNA methylation or histone modifications. Such ‘epigenetic marks’ can be heritable through cell division but leave the DNA sequence unchanged. Post-­translational modifications can be found on the histone proteins associated with DNA; the majority of histone modifications are found on the lysine-­rich N-‐terminal amino acid “tails”. Histone acetylation and methylation influence the chromatin structure by loosening or tightening the packaging of DNA, respectively, in association with other chromatin modifiers. Condensed chromatin is linked to transcriptional silencing and genetic imprinting and also occurs at chromosomal centromeres, where it is linked to kinetochore binding. Heart development is well studied, but the epigenetic processes involved are not yet completely understood. While active chromatin mechanisms such as histone acetylation and chromatin remodelling have been described in the heart, the role of gene repressive epigenetic mechanisms has been poorly investigated. Cardiomyocytes are post-­mitotic cells that do not divide to regenerate a damaged heart. The regeneration of cardiomyocytes after myocardial infarction is an important topic of interest in cardiovascular science. There are various approaches to heart repair after infarction, including activating cardiomyocytes so they become mitotic once again, or growing cardiomyocytes in vitro to attach to a lesion site. An important factor in these approaches is understanding the epigenetic mechanisms controlling cell division. In this thesis, we aim to advance the current knowledge of the epigenetic repressive mechanisms involved in cardiomyocyte formation and heart development to explain their lack of regenerative capacities. We studied the epigenetic changes that occur during cardiac development leading to a non-­‐regenerative state to pinpoint the moment at which these changes arise. We found that the epigenetic process is independent of whether cardiac lineage differentiation occurs during embryogenesis or during differentiation in vitro. We discovered that cardiac heterochromatin displays a singular epigenetic signature during development as compared to brain, another post-­mitotic tissue, or liver, an actively regenerative tissue. We observed an epigenetic change in the repressive histone modification histone H3 lysine 9 trimethylation that was specific to heart development. This change involved a nuclear reorganisation of heterochromatin and a reduction of the levels of this mark in E13.5 and E14.5 embryos, as compared to E10.5 embryos. This was consistent with our observations of the histone lysine methyltransferase SUV39H1, the levels of which were lower after stage E10.5 of development. However, contradictorily, in differentiated cardiomyocytes in vitro, SUV39H1 was increased but showed low levels of H3K9me3, compared to ES cells, which had low levels of SUV39H1 and high levels of H3K9me3. We detected extremely low levels of the H3K9me3 in adult heart tissue. We observed that in adult hearts, the myocardium had maintained these major changes in H3K9me3, while this effect was not observed in the epicardium. Genomic studies were carried out to determine changes at a genomic level between the two key epigenetic stages in heart development we identified at E10.5 and E13.5. Methylated DNA immunoprecipitation sequencing and chromatin immunoprecipitation sequencing for H3K9me3 analyses were carried out to find overall changes in methylation patterns. No global changes in DNA methylation were detected between these developmental stages. These results imply that the differences observed in H3K9me3 are due to remodelling of the heterochromatin during heart development and cardiomyocyte formation, rather than quantitative changes.

Since the discovery of DNA packaging into chromatin, and McClintock's (1951) work on position-effect variegation providing evidence of non-mendelian inheritance, the principal of a genome maintaining 'on' and 'off' states has been widely adopted. However, the underlying mechanisms that regulate these dynamic chromatin states and their effect on disease are still poorly understood. DNA methylation and histone trimethylation at H3K9 and H4K20 are the core hallmarks of the heterochromatic constitutively 'off' state. Constitutive heterochromatin is predominantly comprised of repetitive satellite containing pericentromeric regions and telomeres and in mouse heterochromatin clusters into large chromocenters. These regions are cytologically more compact and generally transcriptionally silent across embryonic and differentiated mouse cell types. However, in addition to increased genomic instability, mouse tumour cells sustain increased satellite expression suggesting constitutive heterochromatin is disrupted. Therefore how constitutive heterochromatin is maintained has important implications for genome regulation and disease, and remains poorly understood. While satellite DNA sequences are not evolutionarily conserved, pericentromeric and telomeric heterochromatin occurs across species. Heterochromatin formation is therefore independent of the underlying DNA sequence, supporting the hypothesis that epigenetic components can regulate chromatin structure. DNA methylation is generally thought to be associated with transcriptional silencing and chromatin compaction. However, Gilbert et al (2007) showed that the complete loss of DNA methylation did not affect the compaction at heterochromatin or global genome compaction. The role of H3K9me3 in regulating heterochromatin has also been an area of keen interest. H3K9me3 patterns are established by suppressor of variegation 3-9 homologues and provide the binding site for heterochromatic protein 1 [HP1] which can in turn recruit Suv39h1. This Suv3-9h-HP1-H3K9 axis enables its propagation throughout heterochromatin. Peters et al (2001) demonstrated that in mice loss of suv39 homologues 1 and 2 caused a loss of H3K9me3 at constitutive heterochromatic domains. These Suv39h null mice demonstrated decreased genome stability, and an increased prevalence of oncogenesis. However cytological chromocenters are still present in the absence of H3K9me3. Therefore the function of H3K9me3 as a causative agent in heterochromatin formation is still debated. Broadly the aim was to investigate the phenotypic role of heterochromatic epigenetic components in cancer progression, and address whether H3K9me3 effects large scale chromatin structure. To identify heterochromatic gene silencing components, an inhibitor screen was performed in an artificial silenced reporter system. The reporter fluorophore was silenced by the presence of centromeric arrays from yeast/bacterial artificial chromosomes and human alpha satellite repeats enriched for H3K9me3. To address the function of the de-silencing components identified in cancer, the fitness of colon cancer cells [HCT116] was investigated before and after the development of resistance to the MEK inhibitor trametinib. The most intriguing result was that BET protein inhibition resulted in derepression of the reporter construct and trametinib resistant HCT116 cells were more sensitive to BET inhibitors, while subsequent investigation showed HP1 protein levels were altered. Analysis of publically available datasets of tumour drug resistance, showed elevated BET protein binding at HP1 promoters in resistant cell lines suggesting an indirect role in gene silencing. To investigate the consequence of H3K9me3 loss on chromatin structure, mouse embryonic stem cells that lacked both Suv39 homologues were used. Microccocal nuclease digestion and sucrose sedimentation demonstrated a global decompaction of large-scale chromatin fibres whilst re-expression of suv39h1 rescued H3K9me3 at chromocenters and global chromatin decompaction. Loss of Suv39h also increased chromatin associated RNA levels that were also rescued by Suv39h1 re-expression. This suggests that H3K9me3 has a role chromatin fibre compaction globally as well as at constitutive heterochromatin, potentially mediated by chromatin associated RNA. To conclude, multiple components were identified that are involved in transcriptional silencing. Evaluating their function in tumour progression demonstrated a possible role of BET proteins in the development of MEKi resistance that may be mediated through HP1 proteins. H3K9me3 and its binding partner HP1 affect global chromatin compaction. The global decompaction after Suv39h loss correlates with an increase in chromatin associated RNA, suggesting a possible mechanism for changes in chromatin compaction beyond H3K9me3.

No description available.

No description available.

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.