The nucleus is a highly compartmentalized organelle where specific cellular activities are confined to discrete domains. One such domain is the promyelocytic leukemia nuclear body (PML NB). PML NBs are protein-based structures that make numerous contacts with neighboring chromatin domains. To elucidate the function of PML NBs, research has been focused on identifying the protein complement of PML NBs. More than 60 proteins have been shown to localize to PML NBs, implicating the bodies in numerous cellular activities such as transcription regulation, apoptosis, tumor suppression, and the antiviral response. This approach has not yielded a general model for PML NB function. Instead I have chosen to focus on the chromatin contacts made with PML NBs. Using live-cell microscopy, my observations support the hypothesis that changes in chromatin topology affect the structural integrity of PML NBs. Moreover, I have developed a technique, called immunoTRAP, which allows for the extraction of chromatin specifically associated with PML NBs. Analysis of these chromatin associations reveal that specific genes associate with PML NBs and these associations are cell type specific. Therefore, PML NBs make specific contacts with neighboring chromatin domains and these contacts are integral to PML NB morphology. Thus making PML NBs a meeting place for a specific set of genomic loci.

The nucleus is a highly compartmentalized organelle where specific cellular activities are confined to discrete domains. One such domain is the promyelocytic leukemia nuclear body (PML NB). PML NBs are protein-based structures that make numerous contacts with neighboring chromatin domains. To elucidate the function of PML NBs, research has been focused on identifying the protein complement of PML NBs. More than 60 proteins have been shown to localize to PML NBs, implicating the bodies in numerous cellular activities such as transcription regulation, apoptosis, tumor suppression, and the antiviral response. This approach has not yielded a general model for PML NB function. Instead I have chosen to focus on the chromatin contacts made with PML NBs. Using live-cell microscopy, my observations support the hypothesis that changes in chromatin topology affect the structural integrity of PML NBs. Moreover, I have developed a technique, called immunoTRAP, which allows for the extraction of chromatin specifically associated with PML NBs. Analysis of these chromatin associations reveal that specific genes associate with PML NBs and these associations are cell type specific. Therefore, PML NBs make specific contacts with neighboring chromatin domains and these contacts are integral to PML NB morphology. Thus making PML NBs a meeting place for a specific set of genomic loci.

During development, multipotent stem cells establish tissue-specific programmes of gene expression that underlie a process of differentiation into specialized cell types. It was shown in the study that changes in the nuclear architecture during terminal keratinocyte differentiation show correlation with the dynamics of the transcriptional and metabolic activity. In particular, terminal differentiation is accompanied by the decrease of nuclear volume, elongation of its shape, reduction of the number and fusion of nucleoli, increase in the number of centromeric clusters and a dramatic decrease of the transcriptional activity. Global changes in the nuclear architecture of epidermal keratinocytes are associated with marked remodelling of the higher-order chromatin structure of the epidermal differentiating complex (EDC). EDC is positioned peripherally in the epidermal nuclei at E11.5 when its genes show low expression levels and relocates towards the nuclear interior at E16.5 when EDC genes are markedly upregulated. P63 transcription factor serving as a master regulator of epidermal development is involved in the control of EDC relocation in epidermal progenitor cells. The epidermis of E16.5 p63KO exhibits significantly more peripheral positioning of the EDC loci, compared to wild-type. The genome organizer Satb1 serving as a direct p63 target controls higher order chromatin folding of the central part of EDC and Satb1 knockout mice show alterations of epidermal development and expression of the EDC encoded genes. Thus, this study shows that the programme of epidermal development and terminal differentiation is regulated by p63 and other factors and include marked remodelling of three-dimensional nuclear organization and positioning of tissue specific gene loci. In addition to the direct involvement of p63 in controlling the expression of tissue-specific genes, p63 via regulation of the chromatin remodelling factors such as Satb1 promotes establishing specific conformation of the EDC locus required for efficient expression of terminal differentiation-associated genes.

L’épissage, une étape majeure de l’expression des gènes, consiste en l’élimination des introns et la production de transcrits matures ou ARNm. La régulation ou des perturbations de l’épissage sont impliquées dans de nombreuses situations physiopathologiques. Dans ce travail, j’ai utilisé et analysé par des approches de bio-informatiques un grand nombre de données générées à large échelle afin de mieux définir les règles gouvernant la reconnaissance des exons au cours de l’épissage. Je montre que les mécanismes de reconnaissance des exons dépendent du biais de la composition nucléotidique des gènes qui les hébergent. Ainsi, la reconnaissance des exons hébergés par des gènes enrichis en guanine et cytosine dépend essentiellement de leur site 5’ d’épissage qui peut être masqué par des structures secondaires. La reconnaissance des exons hébergés par des gènes enrichis en thymine et adénine dépend essentiellement des signaux d’épissage situés en amont des exons. Je montre également que l’organisation chromatinienne est différente selon les biais de composition nucléotidique des gènes et que cela a un impact spécifique sur la reconnaissance des exons. De nombreuses études démontrent que les gènes ne sont pas organisés de façon aléatoire dans un génome et que l’architecture des gènes et des chromosomes dépend de leur composition nucléotidique. Par conséquent, mes travaux suggèrent qu’il existe un lien direct entre composition nucléotidique d’une région du génome, architecture de la chromatine et sélection des exons au cours de l’épissage. / Splicing, a major step in gene expression, consists in the removal of the introns and the production of mature transcripts or mRNA. The regulation of or the disturbances in splicing are involved in numerous physiopathological situations. In this work, I used and analysed with bio-informatic approaches a lot of genome-wide datasets in order to define better the rules governing exon recognition during the splicing step. I show in this work that the mechanisms of exon recognition depend on the nucleotidic composition bias of the genes which host these exons. Thus, the recognition of the exons located in genes enriched with guanine and cytosine essentially depends on their 5' splicing site, which can be hidden by secondary structures. The recognition of the exons located in genes enriched with thymine and adenine essentially depends on splicing signals placed upstream the exons. Moreover, I show that the chromatin organization varies according to the nucleotidic composition bias in the genes, and that it has a particular impact on exon recognition. A lot of studies have shown that the genes are not randomly organized in a genome and that the architecture of the genes and of the chromosomes depends on their nucleotidic composition. Put together, my work suggests that it exists an direct link between the nucleotidic composition of a genomic region, the chromatin architecture and the recognition of the exons during the splicing step.

no / The nucleus is a complex and highly compartmentalized organelle, which undergoes major organization changes during cell differentiation, allowing cells to become specialized and fulfill their functions. During terminal differentiation of the epidermal keratinocytes, the nucleus undergoes a programmed transformation from active status, associated with execution of the genetic programs of cornification and epidermal barrier formation, to a fully inactive condition and becomes a part of the keratinized cells of the cornified layer. Tremendous progress achieved within the past two decades in understanding the biology of the nucleus and epigenetic mechanisms controlling gene expression allowed defining several levels in the regulation of cell differentiation–associated gene expression programs, including an accessibility of the gene regulatory regions to DNA–protein interactions, covalent DNA and histone modifications, and ATP-dependent chromatin remodeling, as well as higher-order chromatin remodeling and nuclear compartmentalization of the genes and transcription machinery. Here, we integrate our current knowledge of the mechanisms controlling gene expression during terminal keratinocyte differentiation with distinct levels of chromatin organization and remodeling. We also propose directions to further explore the role of epigenetic mechanisms and their interactions with other regulatory systems in the control of keratinocyte differentiation in normal and diseased skin.

During development, multipotent stem cells establish tissue-specific programmes of gene expression that underlie a process of differentiation into specialized cell types. It was shown in the study that changes in the nuclear architecture during terminal keratinocyte differentiation show correlation with the dynamics of the transcriptional and metabolic activity. In particular, terminal differentiation is accompanied by the decrease of nuclear volume, elongation of its shape, reduction of the number and fusion of nucleoli, increase in the number of centromeric clusters and a dramatic decrease of the transcriptional activity. Global changes in the nuclear architecture of epidermal keratinocytes are associated with marked remodelling of the higher-order chromatin structure of the epidermal differentiating complex (EDC). EDC is positioned peripherally in the epidermal nuclei at E11.5 when its genes show low expression levels and relocates towards the nuclear interior at E16.5 when EDC genes are markedly upregulated. P63 transcription factor serving as a master regulator of epidermal development is involved in the control of EDC relocation in epidermal progenitor cells. The epidermis of E16.5 p63KO exhibits significantly more peripheral positioning of the EDC loci, compared to wild-type. The genome organizer Satb1 serving as a direct p63 target controls higher order chromatin folding of the central part of EDC and Satb1 knockout mice show alterations of epidermal development and expression of the EDC encoded genes. Thus, this study shows that the programme of epidermal development and terminal differentiation is regulated by p63 and other factors and include marked remodelling of three-dimensional nuclear organization and positioning of tissue specific gene loci. In addition to the direct involvement of p63 in controlling the expression of tissue-specific genes, p63 via regulation of the chromatin remodelling factors such as Satb1 promotes establishing specific conformation of the EDC locus required for efficient expression of terminal differentiation-associated genes.

No description available.

Des centaines de mutations du gène LMNA codant les lamines A/C, protéines nucléaires de la famille des filaments intermédiaires, causent des pathologies. Pour ma thèse, j’ai étudié la mutation LMNA p.R388P, nouvellement identifiée comme responsable de dystrophie musculaire congénitale (L-CMD) associée à une lipodystrophie. Mes objectifs étaient de caractériser les propriétés des lamines mutées et leur impact dans des cellules et dans un muscle squelettique.Résultats : 1) La culture ex vivo de fibroblastes de peau de la patiente a révélé leur entrée prématurée en sénescence. 2) Dans des modèles de cellules immortalisées, la lamine A mutante surexprimée, qui s’accumule exclusivement dans le nucléoplasme et est anormalement soluble a modifié les propriétés de ses partenaires LAP2α et émerine, augmenté le nombre de gènes liés par les lamines A, diminué la compaction de la chromatine et induit des dysmorphies nucléaires. Le traitement des cellules avec des inhibiteurs d’histones acétyltransférases ou désacétylases n’a pas restauré la forme des noyaux. 3) Dans le muscle tibial antérieur de souris injecté avec des virus adéno-associés codant les lamines A mutantes, le nombre de fibres oxydatives de type IIA est diminué et l’expression de quelques gènes est modifiée.Conclusion : Nous avons montré que les lamines A R388P altèrent la structure du noyau, l’intégrité de l’enveloppe nucléaire et l’organisation/expression du génome, avec des conséquences sur le typage des fibres de muscle squelettique. De par ses effets pléiotropes, la lamine A mutante apparaît particulièrement toxique, en accord avec la sévérité de la pathologie observée chez la patiente. / Hundreds of mutations in the LMNA gene coding lamins A/C, nuclear intermediate filament proteins, cause several diseases. For my thesis, I studied the p.R388P LMNA mutation, newly identified as responsible for congenital muscular dystrophy (L-CMD) associated with lipodystrophy. My goals were to determine the properties of the mutant lamin A and its impact in cells and a skeletal muscle.Results: 1) Ex vivo culture of patient skin fibroblasts revealed their premature entry into senescence. 2) In immortalised cell lines, the overexpression of the mutant lamin A, which accumulates exclusively in the nucleoplasm and is abnormally soluble, modified the properties of two partners, LAP2α and emerin, increased the amount of genes bound by lamin A, decreased the compaction of chromatin and induced nuclear dysmorphies. Treatment of cells with histone acetyltransferase or deacetylase inhibitors did not rescue nuclear shape. 3) In mouse tibialis anterior muscle injected with adeno-associated virus coding for mutant lamin A, the number of oxidative type IIA myofibres was decreased and expression of few genes modified. Conclusion: We showed that R388P lamins A alter the structure of nuclei, nuclear envelope integrity and the organisation/expression of the genome, with consequences on skeletal muscle fibre typing. Because of its pleiotropic effects, the mutant lamin A appears particularly toxic, in agreement with the severity of the patient’s disease.

Notre génome est constamment attaqué par des facteurs endogènes et exogènes qui menacent son intégrité et conduisent à différents types de dommages. Les cassures double brins (CDBs) font partie des dommages les plus nuisibles car elles peuvent entraîner la perte d'information génétique, des translocations chromosomiques et la mort cellulaire. Tous les processus de réparation se déroulent dans le cadre d'une chromatine hautement organisée et compartimentée. Cette chromatine peut être divisée en un compartiment ouvert transcriptionnellement actif (euchromatine) et un compartiment compacté transcriptionnellement inactif (hétérochromatine). Ces différents degrés de compaction jouent un rôle dans la régulation de la réponse aux dommages à l’ADN. L'objectif de mon premier projet était de comprendre l'influence de l'organisation 3D du génome sur la réparation de l'ADN. Pour cela, j’ai utilisé deux approches complémentaires dans le but d’induire et de cartographier les CDBs dans le génome de souris. Mes résultats ont mis en évidence un enrichissement de γH2AX, facteur de réparation des dommages à l’ADN, sur différentes régions du génome de cellules souches embryonnaires de souris, et ont également montré que les dommages persistent dans l’hétérochromatine, contrairement à l’euchromatine qui est protégée des dommages. Pour mon deuxième projet, j'ai cartographié l'empreinte génomique de 53BP1, facteur impliqué dans la réparation des CDBs, dans des cellules U2OS asynchrones et des cellules bloquées en G1 afin d’identifier de nouveaux sites de liaison de 53BP1. Mes résultats ont permis d’identifier de nouveaux domaines de liaison de 53BP1 couvrant de larges régions du génome, et ont montré que ces domaines de liaison apparaissent dans des régions de réplication moyenne et tardive. / Our genome is constantly under attack by endogenous and exogenous factors which challenge its integrity and lead to different types of damages. Double strand breaks (DSBs) constitute the most deleterious type of damage since they maylead to loss of genetic information, translocations and cell death. All the repair processes happen in the context of a highly organized and compartmentalized chromatin. Chromatin can be divided into an open transcriptionally active compartment (euchromatin) and a compacted transcriptionally inactive compartment (heterochromatin). These different degrees of compaction play important roles in regulating the DNA damage response. The goal of my first project was to understand the influence of 3D genome organization on DNA repair. I used two complementary approaches to induce and map DSBs in the mouse genome. My results have shown that enrichment of the DNA damage repair factor γH2AX occurs at distinct loci in the mouse embryonic stem cell genome and that the damage persists in the heterochromatin compartment while the euchromatin compartment is protected from DNA damage. For my second project, I mapped the genomic footprint of 53BP1, a factor involved in DSBs repair, in asynchronous and G1 arrested U2OS cells to identify novel 53BP1 binding sites. My results have identified novel 53BP1 binding domains which cover broad regions of the genome and occur in mid to late replicating regions of the genome.

No description available.