Genomic imprinting marks a subset of autosomal loci expressed in parent of origin-dependent monoallelic expression in a non-Mendelian fashion. To restore totipotency and to reset the imprint according to the sex of the individual, the mark must be erased during germline development. The imprinted Igf2-H19 loci located distally on chromosome 7 in mouse and 11p15.5 in human, share common regulatory elements that regulate differential expression. Where the H19 is silenced when paternally inherited, the Igf2 is silenced when maternally inherited. The differentially methylated 5'-flank of H19 gene, termed imprinting control region (ICR), shown to display a unique chromatin organisation harbours hypersensitive sites in linker regions flanked by positioned nucleosomes on the maternal allele. This unique chromatin conformation functions as a methylation-sensitive and unidirectional chromatin insulator, which later was found to depend on the chromatin insulator protein CTCF. The H19 ICR exhibits default-silencing functions in promoter-proximal positions. The maximal distance between the H19 ICR and the promoter of the reporter gene required for this effect was 1.2 ± 0.3kb which can be compared to the 1.9 kb distance between the endogenous H19 ICR and H19 promoter. Results suggest that the H19 ICR adopts a chromatin conformation that must be separated by a minimal distance from pivotal cis-regulatory elements to avoid adverse effects on neighbouring promoters. Poly(ADP-ribosy)lation represents a novel post-translational epigenetic mark that segregates with exclusively the maternal derived H19 ICR and associated with factors that interact with the CTCF target sites. CTCF is itself poly(ADP-ribosy)lated and the poly(ADP-ribose) polymerase inhibitor 3-aminobenzamide relieves the insulator function of the H19 ICR. Designed zinc finger proteins were applied to examine if epigenetic marks provided an obstacle for targeted activation and silencing. The zinc finger protein ZFP809 with activator/repressor domain able to efficiently activate/silence the IGF2 target. Murine hybrid cell lines of human chromosome 11, demonstrated that the ZFP809 overcame the epigenetic marks that repressed maternal IGF2 and paternal H19 allele, respectively. Results suggested that imprinted genes are not normally exposed to strong cis-regulatory elements and that the designed ZFPs can be exploited to develop a therapeutic method for rectifying epigenetic lesions.

An overall coordination between the expressions of genes is required for the proper development of an individual. Although most genes are expressed from both the constituent alleles of the genome, a small subset of autosomal genes are preferentially expressed from only one of the parental alleles, a phenomenon known as genomic imprinting. The imprinted H19 and Igf2 genes are considered paradigms of genomic imprinting as their monoallelic expression pattern is coordinated by a short stretch of sequence located upstream of H19, known as the imprinting control region (ICR). This region shows differential methylation, with hypermethylation specifically on the paternal allele. On the maternal allele this region acts as an insulator and harbours maternal specific hypersensitive sites. The hypersensitive sites were identified as the result of association of the vertebrate insulator protein CTCF with the region. This association was investigated in both an in vitro episomal system and in an in vivo mouse model system by mutating the CTCF target sites at the H19 ICR. The importance of CTCF for the insulator property of the region was confirmed in both instances. In the mouse model, the disruption of the binding was also observed to affect the methylation profile of the ICR, which ultimately resulted in the de-repression of the maternal Igf2 allele. The relevance of multiple CTCF target sites in higher vertebrates for the proper insulator function was investigated using another knock-in mouse model with mutation at a single CTCF target site in the H19 ICR. The investigation confirmed the cooperation between the target sites for the establishment of a functional insulator on the maternal allele. Target sites in the ICR were also analysed for their differential binding affinity for the CTCF protein. The utilisation of the CTCF target sites was examined in different human tumours and cell lines. Methylation analysis conveyed a lack of correlation between the loss of insulator function and methylation status of the ICR with the loss of imprinting (LOI) of IGF2. Investigations also identified a novel mechanism, which neutralised the chromatin insulator function of the H19 ICR without affecting its chromatin conformation. This principle might also help in explaining the loss of IGF2 imprinting observed in some instances. In conclusion, this thesis confirms the importance of CTCF in the formation of an epigenetically regulated chromatin insulator at the ICR, which in turn controls the expression pattern of H19 and Igf2. The studies also confirm the role of CTCF in the maintenance of the methylation profile of the region. Investigations into the loss of IGF2 imprinting in human cancer indicate the involvement of other novel mechanisms besides CTCF in the regulation of insulator function.

The development of a new individual from the fertilized oocyte can ultimately be seen as the consequence of the establishment and maintenance of specific patterns of gene expression. Although regulation of gene activity occurs at different levels, cellular specialization and differentiation are the results of developmental cues that essentially take place at the transcriptional level. The involvement of epigenetics in this process has become increasingly clear during the last decade. Imprinted genes constitute an excellent example as monoallelic expression seems to reflect differential epigenetic marks on the two alleles. This is the case of the imprinted H19 and Igf2 genes were the monoallelic expression is coordinated through a differentially methylated region (hypermethylated on the paternal allele), known as ICR (imprinted control region). In the mouse the ICR harbours four binding sites for the methylation sensitive insulator protein CTCF. Previous studies with episomal constructs had shown that this region behaved as an insulator and that CTCF is required for the insulator activity of the H19 ICR This thesis establish a clear link between the insulator function and the chromatin structure at the H19 ICR and indicates that the precise allocation of the CTCF target sites in the linker regions can play a critical role in this process. The importance of the CTCF interaction at the ICR was also confirmed in vivo using a mouse model that showed how intact CTCF target sites are needed to manifest insulator activity and methylation protection. We have investigated the role of CTCF and a related protein BORIS in establishing the maternal to paternal imprint transition in chromatin structure at the H19/Igf2 locus in the male germline. This thesis also describe the development of a new technique for the localization of chromatin associated factors and modifications with higher sensitivity and resolution compared to existing approaches.

The imprinted expression of the IGF2 and H19 genes is controlled by the imprinting control region 1 (ICR1) located at chromosome 11p15.5. This methylation-sensitive chromatin insulator works by binding the zinc-finger protein CTCF in a parent-specific manner. CTCF binds the unmethylated maternal allele and is required for preventing de novo methylation at ICR1. DNA methylation defects involving the ICR1 IGF2/H19 domain result in two growth disorders with opposite phenotypes: an overgrowth disorder, the Beckwith-Wiedemann syndrome (ICR1 gain of methylation in 10% of BWS cases) and a growth retardation disorder, the Silver-Russell syndrome (ICR1 loss of methylation in 60% of SRS cases). Little information is available regarding the mechanism of ICR1 DNA methylation defects. Several deletions removing part of ICR1 (1.4 to 2.2 kb) have been described in a few familial BWS cases with dominant maternal transmission. In order to evaluate precisely the incidence of ICR1 mutations, we investigated, by long range PCR and sequencing, 21 BWS patients (including two brothers) with ICR1 gain of methylation and 16 SRS patients with ICR1 loss of methylation. No mutation of the seven CTCF binding sites was detected in the familial BWS cases. Two additional cases of constitutional genetic lesions were identified in BWS patients with apparently-sporadic forms. One patient was identified with a 8 bp deletion within the B3 repeat, 116 bases 3' of the CTCF binding site 4. Another patient was identified with a 1.8 kb deletion which eliminates CTCF binding sites 2 and 3. A single-nucleotide variation was identified in a SRS patient. Our data showed that ICR1 deletions, including new small deletions, account for apparently sporadic forms of BWS with ICR1 gain of methylation. ICR1 deletions are associated with a high incidence of Wilms' tumour, making their molecular diagnosis particularly important for genetic counseling and tumor surveillance.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Chez les mammifères, l'ADN des cellules interphasiques s'organise en une fibre chromatinienne confinée à l'intérieur de « territoires chromosomiques ». Ce confinement autorise l'établissement d'interactions à longue distance permettant une régulation fine des fonctions génomiques. Toutefois, l'organisation et la dynamique de la chromatine à l'échelle dite supranucléosomale (10 à 500 kb) reste méconnue. Afin d'étudier la chromatine à cette échelle, nous avons utilisé la méthode dite de 3C-qPCR qui permet de mesurer les fréquences d'interactions entre deux portions génomiques. Dans un premier temps, nous avons analysé les collisions aléatoires afin de déterminer l'organisation intrinsèque de la chromatine à l'échelle supranucléosomale. Nos résultats indiquent que, en l'absence d'interactions spécifiques, les collisions aléatoires dans les régions riches en gènes présentent une modulation d'une périodicité d'environ 90kb. Cette modulation semble être sous-jacente à de nombreuses interactions spécifiques et avoir des répercutions sur leur positionnement génomique contribuant ainsi à l'évolution des génomes. Des modèles, dérivés de la physique des polymères, suggèrent que la chromatine s'organise dans ces régions en une hélice statistique. Dans un second temps, nous avons abordé l'organisation tridimensionnelle du locus murin Igf2/H19 soumis à l'empreinte génomique parentale. Les interactions spécifiques identifiées entre des « enhancers » endodermiques et certaines portions du locus ont confirmé l'existence d'une hiérarchie des interactions et ont permis la découverte d'un nouveau locus soumis à l'empreinte (PIHit). Ce locus produit un ARN non codant que nous avons caractérisé mais dont la fonction exacte reste à déterminer.Finalement, mes travaux de thèse ont aussi conduit à la mise au point d'une nouvelle technologie (HRS-SEQ) qui permettra d'aborder l'organisation génomique globale par le biais des séquences récupérées à haut-sel (HRS). / In mammal, the DNA of interphasic cells is organized into the chromatin fiber which is itself confined inside “chromosome territories”. This compact organization allows the establishment of long-range interactions involved in the fine regulation of genomic processes. However, the organization and the dynamic of the chromatin at the so-called supranucleosomal scale (10 to 500kb) remain unclear. In order to study the chromatin at this scale, we used the 3C-qPCR method that allows to measure interaction frequencies between two genomic regions. Firstly, we have analyzed random collisions in order to determine the intrinsic organization of the chromatin at the supranucleosomal scale. Our data indicates that, in the absence of specific interactions, random collisions in gene-rich regions show a periodic modulation of about 90kb. This modulation seems to be underlying numerous locus-specific interactions and have repercussions on their genomic location, thus contributing to genome evolution. Models, derived from polymers physics, suggest that, in these regions, the chromatin is shaped in a statistical helix. Secondly, we have investigated the tridimensional organization of the Igf2/H19 mouse locus which is subject to genomic imprinting. Specific interactions identified between endodermic enhancers and some regions of the locus have confirmed the existence of a hierarchy of interactions and allowed the discovery of a new imprinted locus (PIHit). This locus produces a non-coding RNA that we have characterized but for which the function remains to be determined.Finally, my work also led to the development of a new technology (HRS-SEQ) that allows to study global genome organization through mapping of high-salt recovered sequences (HRS).

L'utilisation de transgènes actifs dans le cortex surrénalien de souris a permis de dériver de nouvelles lignées cellulaires de la zone fasciculée de la corticosurrénale (lignées ATC) et de tester le pouvoir transformant de gènes candidats au développement de tumeurs corticosurrénaliennes. Les cellules ATC produisent de la corticostérone et expriment l'ensemble des gènes impliqués dans la stéroïdogenèse sous le contrôle de l'ACTH. Elles ont permis d'explorer les rôles antagonistes des facteurs de transcription SF1 et DAX1 dans le mécanisme d'action de l'ACTH. Les modèles cellulaires et murins surexprimant IGF2 ou ayant perdu en partie l'expression de p57kip2 ont conduit à rejeter leur implication individuelle dans le développement des corticosurrénalomes. Nous avons montré que l'expression dans la corticosurrénale de souris d'une sous unité régulatrice RIalpha tronquée de la PKA reproduit l'hyperactivité endocrine rencontrée dans les hyperplasies micronodulaires pigmentées des surrénales

Domestic animals have become very different from their wild ancestors during domestication and animal breeding. This provides a good model to unravel the molecular mechanisms underlying phenotypic variation. In my thesis I have studied genes affecting two important traits, leanness in pigs and hair greying-associated melanoma in horses. In the first part of the thesis, I focused on an intronic mutation leading to more muscle growth and less fat deposition in domestic pigs to identify a transcription factor (TF) that binds to the regulatory element overlapping with the mutation. The aim has been to further study the function of the previously unknown TF in mouse myoblast cells and in insulin-producing cells (Paper I-III). We discovered a new TF ZBED6 binding to intron 3 of the IGF2 gene, in which a single nucleotide substitution in pigs abrogates the binding and causes increased leanness in domestic pigs. Silencing of ZBED6 expression in mouse myoblasts increased Igf2 expression, cell proliferation and migration, and myotube formation. This result is in line with the increased leanness phenotype in mutant pigs. Chromatin Immunoprecipitation-sequencing (ChIP-seq) using an anti-ZBED6 antibody identified 1200 ZBED6 target genes besides IGF2 and many are TFs controlling fundamental biological processes. In the first follow-up study we found ZBED6 mainly affected the expression of muscle protein genes by directly regulating Igf2 and Twist2 expression, in agreement with our previous observation of faster myotube formation in ZBED6-silenced cells. ChIP-seq with antibodies against six different histone modifications revealed that ZBED6 preferentially binds to active promoters and modulates transcriptional activity by a novel mechanism rather than by recruiting repressive histone modifications. The second follow-up study revealed that ZBED6 affects the morphology and insulin content and release in pancreatic ß cells. In the second part (Paper IV), we investigate the functional significance of an intronic duplication in the Syntaxin 17 (STX17) gene causing hair greying and melanoma in horses. We found two Microphtalmia-associated transcription factor (MITF) binding sites within the duplication and showed that the duplicated sequence up-regulates reporter gene expression in a melanocyte-specific manner both by reporter assays in mouse melanocytes and in transgenic zebrafish. These results established that the intronic duplication acts as a melanocyte-specific enhancer that becomes much stronger when it is duplicated.

The recent advances in molecular and computational biology have made possible the study of complicated transcriptional regulatory networks that control a wide range of biological processes and phenotypic traits. In this thesis, several approaches were combined including next generation sequencing, gene expression profiling, chromatin and RNA immunoprecipitation, bioinformatics and genome editing methods in order to characterize the biological significance of the ZBED6 and ZC3H11A genes. A mutation in the binding site of ZBED6, located in an intron of IGF2, disrupts the binding and leads to 3-fold upregulation of IGF2 mRNA in pig muscle tissues. The first part of the thesis presents a detailed functional characterization of ZBED6. Transient silencing of ZBED6 expression in mouse myoblasts led to increased Igf2 expression (~2-fold). ChIP-seq analysis of ZBED6 and histone modifications showed that ZBED6 preferentially binds active promoters and modulates their transcriptional activities (paper I). In the follow-up studies using CRISPR/Cas9 we showed that either the deletion of ZBED6 or its binding site in Igf2 (Igf2ΔGGCT) led to more than 30-fold up-regulation of Igf2 expression in myoblasts. Differentiation of these genetically engineered cells resulted in hypertrophic myotubes. Transcriptome analysis revealed ~30% overlap between the differentially expressed genes in Zbed6-/- and Igf2ΔGGCT myotubes, with significant enrichment of muscle-specific genes. ZBED6-overexpression in myoblasts led to cell cycle arrest, reduced cell viability, reduced mitochondrial activities and impaired the differentiation of myoblasts (paper II). Further studies on cancer cells showed that ZBED6 influences the growth of colorectal cancer cells with dramatic changes in the transcription of hundreds of cancer-related genes (paper III). The phenotypic characterization of Zbed6-/- and Igf2pA/mG mouse models showed that the ZBED6-Igf2 axis has a major effect on regulating muscle growth and the growth of internal organs. Transcriptome analysis demonstrated a massive up-regulation of Igf2 expression (~30-fold) in adult tissues, but not in fetal tissues, of transgenic mice (paper IV). In the second part of the thesis we investigated the cellular function of Zc3h11a, the gene harboring ZBED6 in one of its first introns. The function of the ZC3H11A protein is so far poorly characterized. We show that ZC3H11A is a novel stress-induced protein that is required for efficient mRNA export from the nucleus. The inactivation of ZC3H11A inhibited the growth of multiple viruses including HIV, influenza, HSV and adenoviruses (paper V).

Upon fertilization the paternal and maternal genomes unite, giving rise to the embryo, with its unique genetic code. All cells in the human body are derived from the fertilized ovum: hence they all contain (with a few exceptions) the same genetic composition. However, by selective processes, genes are turned on and off in an adaptable, and cell type-specific, manner. The aim of this thesis is to investigate how signals coming from outside the cell and epigenetic factors residing in the cell nucleus, cooperate to control gene expression. The transforming growth factor-β (TGF-β) superfamily consists of around 30 cytokines, which are essential for accurate gene regulation during embryonic development and adult life. Among these are the ligands TGF-β1 and bone morphogenetic (BMP) -7, which interact with diverse plasma membrane receptors, but signal via partly the same Smad proteins. Smad4 is essential to achieve TGF-β-dependent responses. We observed that by regulating transcription factors such as Id2 and Id3 in a specific manner, TGF-β1 and BMP-7 achieve distinct physiological responses. Moreover, we demonstrate that CTCF, an insulator protein regulating higher order chromatin conformation, is able to direct transcription by recruiting RNA polymerase II to its target sites. This is the first mechanistic explanation of how an insulator protein can direct transcription, and reveals a link between epigenetic modifications and classical regulators of transcription. We also detected that DNA loci occupied by CTCF replicate late. The timing of replication is a crucial determinant of gene activity. Genes replicating early tend to be active, whereas genes replicating late often are silenced. Thus, CTCF can regulate transcription at several levels. Finally, we detected a substantial cross-talk between CTCF and TGF-β signaling. This is the first time that a direct interplay between a signal transduction pathway and the chromatin insulator CTCF is demonstrated.