Дисертації з теми "H3K9ac"

SCA7 est une maladie génétique dont l’un des principaux symptômes est une perte progressive d’acuité visuelle pouvant aller jusqu’à la cécité. La mutation responsible de cette pathologie est une expansion instable d’un triplet CAG au sein de l’ATXN7, gene codant une sous-unité du complexe SAGA, un co-activateur de l’ARN polymerase de type II. Des études réalisées sur modèles de souris transgéniques mirent en évidence une perte d’identité des photorécepteurs au niveau morphologique, fonctionnel, et moléculaire. Au cours de ma thèse la caractérisation d’un nouveau modèle knock-in de SCA7 fut réalisée. Ce modèle, qui exprime le gène muté à un niveau endogène récapitule les atteintes rétiniennes observées dans les modèles transgéniques et chez les patients. Une étude transcriptomique (RNA-seq) et épigénomique (ChIP-seq) de ce modèle fut réalisée et mis en évidence des défauts globaux de l’acétylation des lysines 9 et 27 de l’histone H3 (H3K9 et H3K27ac). De plus une étude plus poussée des ARNs non codants mit en évidence l’existance d’ARN enhancer (eRNA) encore non répertoriés au niveau des loci de gènes uniquement exprimés dans les photorécepteurs comme Rho, ces même eRNAs sont retrouvés dérégulés chez les animaux développant la rétinopathie SCA7
SCA7 is a genetic disorder whose one of its main symptoms is a progressive loss of visual acuity which can ultimately lead to blindness. The mutation responsible for this disease is an unstable CAG expansion within ATXN7, a gene encoding a subunit of the SAGA complex, a co-activator of the RNA polymerase II. Previous studies performed on transgenic mouse models highlighted a neuronal identity loss of the photoreceptors at the morphological, functional and molecular levels. During my PhD a characterization of a new SCA7 knock-in mouse model was performed. This model, which expresses the mutated genes at endogenous level recapitulates the retinal impairments observed in transgenic models and in patients. A transcriptomic (RNA-seq) and epigenomic (ChIP-seq) analyses were performed on this model and highlight global acetylation defects on lysine 9 and 27 of histone H3 (H3K9ac and H3K27ac). Moreover, investigations on non-coding RNAs identified the presence of enhancer RNAs (eRNAs) on photoreceptor specific genes such as Rho. These eRNAs, which were never described before, undergo a downregulation in symptomatic SCA7 mice

Avec 59 000 nouveaux cas en 2017, le cancer du sein est le cancer le plus fréquemment diagnostiqué chez les femmes françaises, et pose un réel problème de santé publique en France, mais aussi au niveau mondial. Il est bien établi que la complexité de la carcinogenèse implique des modifications épigénétiques profondes qui contribuent au processus du développement tumoral. La dérégulation des marques d'histones acétylées H3 et H4 font partie de ces modifications. L'acétylation et la désacétylation des protéines sont des modifications posttraductionnelles majeures qui régulent l'expression des gènes liés au cancer et à l'activité d'une myriade d'oncoprotéines. Ainsi, une activité désacétylase aberrante peut alors favoriser ou supprimer la tumorigenèse dans différents types de cancers humains, y compris le cancer du sein. La désacétylase SIRT1 et l’acétyltransférase TIP60 sont 2 enzymes épigénétiques antagonistes qui sont impliquées dans l'apoptose, la régulation des gènes, la stabilité génomique, la réparation de l'ADN, et le développement du cancer. Dans le cadre de cette thèse, nous avons étudié la dérégulation des profils d’acétylation des histones H3 et H4 dans les différents sous-types moléculaires du cancer du sein, et investigué l’implication de SIRT1 et de TIP60 dans la progression tumorale de cancer du sein. Tout d’abord, nous avons signalé les rôles de SIRT1 et de TIP60 comme des biomarqueurs pronostiques potentiels en révélant leurs expressions différentielles en fonction de l’agressivité du cancer. Ensuite, nous avons montré leur régulation épigénétique différentielle des cibles histones en fonction du sous-type moléculaire, ainsi que leur modulation de la marque activatrice H3K4ac. En outre, l’inhibition de ces 2 enzymes par des Épidrogues s’est avérée comme une stratégie efficace dans le traitement du cancer. Ces travaux mettent en relief alors, SIRT1 et TIP60 comme des cibles thérapeutiques potentielles du cancer sporadique du sein
With 59,000 new cases in 2017, breast cancer is the most frequently diagnosed cancer among French women, and poses a real public health problem in France, but also worldwide. It is well established that the complexity of carcinogenesis involves profound epigenetic deregulations that contribute to the tumorigenesis process. Deregulated H3 and H4 acetylated histone marks are amongst those alterations. Acetylation and deacetylation are major post-translational protein modifications that regulate gene expression and the activity of a myriad of oncoproteins. Aberrant deacetylase activity can promote or suppress tumorigenesis in different types of human cancers, including breast cancer. The deacetylase SIRT1 and the acetyltransferase TIP60 are 2 antagonistic epigenetic enzymes that are well implicated in apoptosis, gene regulation, genomic stability, DNA repair, and cancer development. In this manuscript, we identified the dysregulation of the histones H3 and H4 acetylation profiles in different molecular subtypes of sporadic breast cancer, and investigated the involvement of SIRT1 and TIP60 in breast tumorigenesis. First, we highlighted the roles of SIRT1 and TIP60 as potential prognostic biomarkers by revealing their differential expression patterns depending on breast cancer aggressiveness. Then, we demonstrated their differential epigenetic regulation of histone targets according to molecular subtype, and revealed their modulation of the H3K4ac epigenetic marker. Moreover, Epi-drugs mediated inhibition of these 2 enzymes has proven to be an effective strategy in the treatment of cancer. Thus, this work highlights the potential use of SIRT1 and TIP60 as epigenetic therapeutic targets for sporadic breast cancer

In most eukaryotes methylation of histone H3 on lysine 9 (H3K9me) is the key post-translational modification required for the assembly of constitutive heterochromatin at centromeres and other chromosomal regions. H3K9me is bound by the chromodomain proteins HP1/Swi6 and the Suv39/Clr4 H3K9 methyltransferase itself suggesting that, once established, H3K9me might act as an epigenetic mark that can transmit the chromatin state independently of the initiator signal. However, it has not been demonstrated that H3K9me does indeed act as an epigenetic mark. Fission yeast represents an excellent system to address this question since S. pombe lacks DNA methylation and H3K9me is catalysed by the unique, non-essential H3K9 methyltransferase Clr4. To determine whether H3K9me carries epigenetic properties it is important to uncouple H3K9me from genomic domains that have the intrinsic ability to recruit the heterochromatin machinery. One way to solve this problem is to isolate H3K9me from its original context and investigate whether at an ectopic site H3K9me can self-propagate through cell division. To accomplish this, we tethered regulatable TetR-Clr4 fusion protein at euchromatic loci in fission yeast. This resulted in the assembly of an extensive domain of H3K9me-dependent heterochromatin that is rapidly disassembled following TetR-Clr4 release. Strikingly, the inactivation of Epe1, a putative histone demethylase, is sufficient to maintain the silent H3K9me-dependent heterochromatin at the tethering sites through mitotic and meiotic cell divisions in absence of TetR-Clr4. These results indicate that H3K9me acts as an epigenetic mark to maintain heterochromatin domains; however, a regulatory mechanism dependent on Epe1 exists to actively remove H3K9me and thus prevent heterochromatin from being transmitted when assembled at inappropriate regions of the genome.

Cette dernière décennie a vu augmenter le nombre d’études portant sur la caractérisation des protéines JUMONJI (JMJ) et montrant leur rôle prépondérant dans la régulation des gènes et le développement des organismes. Ces protéines sont capables de déméthyler certains résidus des queues des histones et ont été organisées en groupes phylogénétiques en fonction de la conservation de leur domaine catalytique. Pour chaque clade entre un et trois substrats spécifiques ont pu être identifiés. De la sous famille KDM3, dont le résidu cible est H3K9, seul un membre, IBM1, a été caractérisé chez Arabidopsis. Cette étude montre que la mutation de JMJ24, un autre membre de ce groupe, entraine une augmentation de la taille des racines, cotylédons et organes floraux, suggérant un rôle dans le contrôle du développement à différents stades. De plus, l’analyse de l’expression tissulaire indique que JMJ24 est exprimé dans le phloème, en cohérence avec l’effet pléiotropique de sa mutation. Enfin, nos données suggèrent une interaction entre JMJ24 et d’autres protéines JMJ, telles JMJ14 et IBM1, mais aussi une interaction avec les protéines DCL, impliquées dans la régulation des gènes et des éléments transposables
Numerous studies over the last decade have reported the characterization of the JUMONJI (JMJ) proteins, showing their critical importance in regulating genes and organism’s development. These proteins are able to demethylate a subset of histone tail residues and were clustered into distinct groups using a phylogenetic analysis based on their catalytic domain conservation. Furthermore, modification of one to three specific residues has been attributed to each JMJ group. Within the KDM3 subfamily, of which target is the H3K9 residue, only one member, IBM1, was first characterized in Arabidopsis. In this report, we showed that the mutation of JMJ24, another member of this subfamily, resulted in an increase of the root length, cotyledon and floral organ size, suggesting that JMJ24 functions is needed at different developmental stage. In addition, the analysis of the tissue-specific expression of JMJ24 indicated that the gene is expressed within the phloem of all organs, correlating with the pleiotropic effect of the gene mutation. Last, our data also suggested that JMJ24 interacts with other JMJ protein like JMJ14 and IBM1, but also with the DCL proteins knowing to be involved in genes and transposable elements regulation

Les travaux épidémiologiques et expérimentaux effectués à ce jour sur le cancer du sein ont montré que les oestrogènes - comme l’eostradiole (E2) - et leur récépteur (ER) - un facteur de transcription les liants - sont fortement impliqués dans au moins 70% des cas de cancer du sein. Cette implication est d’autant plus visible que les patients, suite à une thérapie anti-oestrogénique, ont tendance à développer une résistance endocrinienne au traitement. Pendant longtemps, l’ER a été étudié en tant que facteur indépendant liant directement une séquence ADN spécifique sur le génome. Aujourd’hui le paradigme a profondément changé. Il est bien connu que ER s’associe avec de nombreux autres facteurs de transcription et protéines régulant la chromatine afin de réguler l’expression des gènes. Cependant, nos connaissances concernant la fonction de modifications épigénétiques suite à l’activation de ER - notamment la méthylation de l’ADN et l’acétylation des histones - sont encore limitées. Dans cette étude, j’ai mis en place un protocole de culture cellulaire adapté à l’étude de la privation et à la re-stimulation d’E2 stricto sensu. Dans un premier temps, ce protocole a été évalué à l’aide de la toute dernière technologie de puce permettant la lecture du méthylome et couvrant la liste complète des éléments amplificateurs. Dans un deuxième temps, j’ai mesuré le transcriptome et les profiles d’acétylation de l’histone H3 (H3K27ac) afin de déterminer la capacité de ER à réguler l’expression des gènes J’ai découvert que, suite à la privation de E2, les niveaux de méthylation de l’ADN et de H3K27ac changent et que ces changements s’accentuent avec le temps, en particulier au niveau des éléments amplificateurs. Une analyse d’enrichissement des facteurs de transcription et des séquences de liaison spécifiques a révélé que les facteurs de transcriptions des familles AP-1 et FOX sont des intermédiaires favorisants la liaison de ER aux éléments amplificateurs. Finalement, la re-stimulation des cellules par de l’E2 a montré que la majorité des changements épigénétiques observé sont réversibles mais que certains éléments amplificateurs restent hyperméthylés et déacétylés. Ceci pourrait indiquer que les traitements anti-oestrogéniques sont efficaces mais pourrait également indiquer un marqueur de résistance endocrinienne. Cette étude apporte des informations nouvelles quant aux effets de l’inhibition et l’activation de ER sur la méthylation de l’ADN et l’acétylation de l’histone H3 à l’échelle du génome et renforce l’importance du rôle d’autres facteurs au niveau des amplificateurs
Previous epidemiological and experimental studies have strongly implicated estrogens in breast cancer risk and Estrogen Receptor (ER), the transcription factor to which estrogen binds, is considered as the major molecular driver of around 70% breast cancers. The importance of the deregulated estrogen signalling is further highlighted by increasing evidence that current chemopreventive and therapeutic strategies that target hormonally responsive breast cancers frequently result in the development of resistance to anti-estrogens and metastatic progression, highlighting the need for understanding the molecular underlying mechanisms. While until recently, ER was believed to act as a stand-alone transcription factor, which can directly bind its motifs in DNA, it is now accepted that ER activity is a complex and dynamic process that requires highly concerted actions of a dozen transcriptional cofactors and various chromatin regulators at DNA. Recent studies focused on characterising ER-associated cofactors and their role in opening the chromatin provided a remarkable insight into transcriptional regulation mediated by ER. However DNA methylation and histone acetylation are poorly understood in the context of ER’s dynamic binding. In this thesis, I combined a cell culture protocol adapted for studying estradiol (E2) deprivation and re-stimulation in stricto sensu in ER-positive breast cancer cells with the latest methylation array, that allowed a genome-wide interrogation of DNA methylation (including a comprehensive panel of enhancers). I further investigated histone acetylation (ChIP-seq) and transcriptome (RNA-seq) after E2 deprivation and re-stimulation to better characterise the ability of ER to coordinate gene regulation. I found that E2 deprivation and re-stimulation result in time-dependent DNA methylation changes and in histone acetylation across diverse genomic regions, many of which overlap with enhancers. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER tethering mainly through two partner TF families, AP-1 and FOX, in the proximity of enhancers that are differentially methylated and acetylated. This is the first study that comprehensively characterized DNA methylation at enhancers in response to inhibition and activation of ER signalling. The transcriptome and genome occupancy data further reinforced the notion that ER activity may orchestrate a broad transcriptional programme through regulating a limited panel of critical enhancers. Finally, the E2 re-stimulation experiments revealed that although the majority of the observed epigenetic changes induced by E2 deprivation could be largely reversed when the cells were re-stimulated we show that DNA hypermethylation and H3K27 acetylation at enhancers as well as several gene expression changes are selectively retained. The partial reversibility can be interpreted as a sign of treatment efficiency but also as a mechanism by which ER activity may contribute to endocrine resistance. This study provides entirely new information that constitutes a major advance in our understanding of the events by which ER and its cofactors mediate changes in DNA methylation and chromatin states at enhancers. These findings should open new avenues for studying role of the deregulated estrogen signalling in the mechanism underlying the “roots” of endocrine resistance that commonly develops in response to anti-estrogen therapy

Chez les eucaryotes, l’expression des gènes dépend en partie du degré de compaction de la chromatine. La structure chromatinienne est régulée par des marques dites épigénétiques,telles que les modifications post-traductionnelles des protéines structurelles de la chromatine, les histones. Ainsi, la méthylation de la lysine 9 de l’histone H3 (H3K9) sur le promoteur des gènes est essentiellement associée à la répression de la transcription. H3K9 est méthylée par différentes enzymes appelées lysine méthyltransférases (KMTs). L’objectif principal de mon projet de thèse a été de mieux comprendre le rôle de principales KMTs de H3K9, que sontG9a, GLP, Suv39h1 et SETDB1, dans la régulation de l’équilibre entre prolifération et différenciation terminale. Pour cela, j’ai utilisé le modèle de différenciation terminale de cellules du muscle squelettique. En effet, durant la différenciation terminale, les myoblastes arrêtent de proliférer et fusionnent entre eux pour former de longues cellules multi nucléées que sont les myotubes. Ce processus implique, d’une part, l’expression des gènes de différenciation musculaire et, d’autre part, la répression irréversible des gènes associés à la prolifération cellulaire. L’introduction bibliographique de ce travail de thèse est séparée en trois chapitres. Le premier chapitre porte sur la chromatine et ses modifications post-traductionnelles. Le second s’attache à décrire les rôles de la méthylation de H3K9 et, en particulier, des quatre KMTs sur lesquelles j’ai travaillé durant ma thèse : G9a, GLP, SETDB1 et Suv39h1. Dans le troisième chapitre, je présente le modèle de la différenciation terminale du muscle squelettique. Dans la partie "Résultats", je décris deux des principales études que j’ai menées durant ma thèse. La première porte sur les rôles antagonistes de G9a et GLP. La seconde porte sur le rôle de SETDB1 durant la différenciation musculaire. Les résultats que j’ai obtenus sont discutés dans cette partie. Je conclus ce manuscrit en discutant mes résultats de manière plus générale et en proposant des perspectives à long terme. Enfin, une annexe présentera les autres articles de recherche auxquels j’ai participé pendant ma thèse
In eukaryotes, gene expression partly relies on chromatin compaction degree. Chromatin status is controlled by epigenetic marks, such as histones (chromatin structural proteins) posttranslational modifications. As an example, histone H3 lysine 9 (H3K9) methylation on gene promoters is mainly associated with transcriptional repression. H3K9 is methylated by several enzymes called lysine methyltransferases (KMTs). The aim of my thesis project was to understand the role of the H3K9 KMTs, G9a, GLP, Suv39h1 and SETDB1 in regulating the balance between proliferation and terminal differentiation. For this purpose, I used skeletal muscle terminal differentiation as model. Upon muscle terminal differentiation, myoblasts exit, in an irreversible way, from the cell cycle and under go differentiation where cells fusion and form myotubes. During this process, cell cycle genes are permanently silenced and muscle specific genes are activated. Thesis introduction is divided into three chapters. The first chapter focuses on chromatin and post-translational modifications. The second chapter describes H3K9 methylation characteristics and the role of the four KMTs that I studied during my thesis project: G9a,GLP, Suv39h1 and SETDB1. In the third chapter, the skeletal muscle terminal differentiation model is described in details. Results section reports my two major studies outcomes and their discussion. The first concerns the antagonistic roles of G9a and GLP regarding the muscle terminal differentiation and the second focuses on the role of SETDB1 during muscle differentiation. Finally, I conclude this manuscript by a plainer discussion followed by long term perspectives and an appendix presents other research articles, in which I collaborated during my PhD

During development, intrinsic genetic programs give rise to distinct cellular lineages through the establishment of cell type specific chromatin states. These distinct chromatin states instruct gene expression primarily through the genome-wide demarcation of enhancers. In addition to maintaining cellular identity, the chromatin state of a cell provides a platform for transcriptional responses to environmental signals. However, relatively little is known about the influence of extracellular stimuli on chromatin state at enhancers, and it is not clear which enhancers among the tens of thousands that have been recently identified function to drive stimulus-responsive transcription. In the nervous system, the chromatin state of terminally differentiated neurons not only maintains neuronal identity but also provides a platform for sensory experience-dependent gene expression, which plays a critical role in the development and refinement of neural circuits and in long-lasting changes in neuronal function that underlie learning, memory, and behavior. Using chromatin-immunoprecipitation followed by high through put sequencing (ChIP-Seq), we determined the effects of neuronal stimuli on the active chromatin landscape of mouse cortical neurons. We discover that stimulation with neuronal activity and brain derived neurotrophic factor (BDNF) cause rapid, widespread, and distinct changes in the acetylation of histone H3 lysine 27 (H3K27Ac) at thousands of enhancers throughout the neuronal genome. We find that functional stimulus-responsive enhancers can be identified by stimulus- inducible H3K27Ac, and we use this dynamic chromatin signature to discover neuronal enhancers that respond to neuronal activity, BDNF, or both stimuli. Finally, we investigate the transcriptional mechanisms underlying the function of stimulus responsive enhancers. We show that a subset of stimulus-responsive enhancers in the nervous system require the coordinated action of the stimulus-general transcription factor activator protein 1 (AP1) with additional stimulus-specific factors. Our studies reveal the genome-wide basis for transcriptional specificity in response to distinct neuronal stimuli. Furthermore, the comprehensive identification of neuronal activity and BDNF-dependent enhancers in cortical neurons provides a critical resource for elucidating the role of stimulus-responsive transcription in synaptic plasticity, learning and memory, behavior, and disease. Finally, the epigenetic signature of stimulus-inducible H3K27Ac may aid in the identification and study of stimulus- regulated enhancers in other tissues.

Endogenous retroviruses (ERVs) are found in genomes of all higher eukaryotes. As retrotransposition is deleterious, pathways have evolved to repress these retroelements. While DNA methylation transcriptionally represses ERVs in differentiated cells, this epigenetic mark is dispensable for maintaining proviral silencing during early stages of mouse embryogenesis and in embryonic stem cells (mESCs). Studies in diverse species have found histone H3K9 methylation and DNA methylation to function together to repress retrotransposons. However, until recently, little was known about the role of this histone modification in proviral silencing in mESCs. Interestingly, our analysis of mESCs lacking G9a, an H3K9-specific lysine methyltransferase (KMTase) revealed that although ERVs lost H3K9 di-methylation (me2) and DNA methylation, they remained silent. Strikingly, the levels of H3K9 tri-methylation (me3) remained unaltered, suggesting that this mark may instead be responsible for maintaining these parasitic elements transcriptionally inactive. The first stage of my research focused on identifying the enzyme depositing H3K9me3 at ERVs and on determining its role in proviral silencing. I discovered that Setdb1, another H3K9-specific KMTase, was indeed depositing H3K9me3 at a subset of ERVs and was required for maintaining transcriptional repression. Interestingly, this silencing pathway operated independently of DNA methylation. Through collaboration, we also discovered that this pathway played a diminished role in differentiated cells. Taken together, these findings indicate the existence of a DNA methylation-independent proviral silencing pathway in mESCs. The second stage of my research focused on the establishment of transcriptional repression of newly integrated proviruses. By employing an exogenous retroviral construct, I discovered a dramatic silencing defect in mESCs lacking G9a, which phenocopied cells depleted of the de novo DNA methyltransferases. Furthermore, efficient DNA methylation of proviruses required G9a-mediated H3K9me2. These findings reveal that histone modifications and DNA methylation function in concert to defend the genome against invading retroviral elements in mESCs. Taken together with discoveries regarding the mechanism of DNA demethylation in early embryos, I propose that cells undergoing DNA methylation reprogramming predominantly employ histone modification-based pathways to maintain these parasitic elements in a silent state; however, the establishment of transcriptional repression for newly integrated elements also requires de novo DNA methylation.

Le lymphome à cellules du manteau (LCM) est un cancer lymphoïde agressif caractérisé par des rechutes itératives et un mauvais pronostique. Le LCM est associé à une génétique complexe et à des dérégulations de gènes tissu-spécifiques, potentiellement liées à des perturbations de la marque épigénétique H3K9me3. En criblant les niveaux d’H3K9me3 dans une cohorte de 120 cas de LCM, nous avons montré une perte de cette marque dans 30% des cas. Cette perte d’H3K9me3 a été reliée à une diminution de l’expression ou de l’activité des histones methyltransferases SUV39H1 et SETDB1, et à l’expression différentielle de programmes d’expression génique associés aux cellules souches embryonnaires ou hématopoïétiques, à la différentiation B et la réponse aux dommages à l’ADN. Un séquençage à haut-débit ciblé n’a pas permis de mettre en évidence de mutations associées à cette perturbation épigénétique.Nous avons également montré qu’une invalidation de l’expression de SUV39H1 causait une augmentation du volume tumoral dans un modèle de xénogreffe et qu’une perte de SETDB1 induisait un arrêt du cycle cellulaire en phase G1/S, associé à une reprogrammation cellulaire vers un phénotype pré-B. L’ensemble de ces données suggère une convergence des voies de signalisation associées à H3K9me3 vers des cibles essentielles à la pathogénèse du LCM. Les mécanismes épigénétiques associées à la régulation de ces cibles sont actuellement étudiés par immunoprécipitation de la chromatine associée à H3K9me3. Des analyses de survie dans le cadre d’un essai clinique prospectif permettront également d’établir l’impact pronostique des pertes d’H3K9me3 dans le LCM
Mantle cell lymphoma (MCL) is an aggressive lymphoid cancer characterised by iterative clinical relapses and short survival. MCL displays complex genetics and hallmarks of misregulated expression of lineage specific genes. We have hypothesized that the latter might result from corruption of H3 lysine 9 trimethylation signaling. By screening for H3K9me3 levels across a cohort of 120 MCL cases, we found global reductions in H3K9me3 in 1/3 of cases. H3K9me3 depletion was linked to underexpression / attenuated activity of SUV39H1 and SETDB1 histone methylases, respectively, and to differential expression of key cancer signatures relating to embryonic/hematopoietic stem cell function, B cell differentiation, and DNA damage response. Targeted deep sequencing did not reveal association to mutations in known epigenetic modifiers, indicating a new, previously-unsuspected role for H3K9me3 in MCL pathogenesis. In keeping with this, knockdown of SUV39H1 increased tumour growth in MCL xenografts while SETDB1 depletion induced G1/S arrest coincident to reprogramming to a pre-B cell phenotype. Taken together this identifies convergence of H3K9me3 signaling pathways to essential targets for MCL disease pathogenesis. These are currently under investigation by H3K9me3 ChIP-seq. Survival analyses in the setting of a prospective clinical trial will establish the prognostic impact of H3K9me3 in MCL

Central to the control of virtually all cellular activity is the regulation of gene expression. In eukaryotes, this regulation is greatly influenced by chromatin structure, which is itself regulated by numerous chromatin-remodeling complexes. These are typically large protein complexes with interchangeable subunits that allow for highly specialized functions in different cell types. Moreover, additional specificity can be gained through complexes formed from different subunit isoforms. Histone modifications also regulate chromatin by recruiting remodeling complexes to particular genomic regions. In this thesis we characterize MBD3C, an isoform of the Nucleosome Remodeling and Deacetylase (NuRD) complex subunit MBD3. MBD3 is essential for pluripotency and development, but MBD3C appears to be expressed only in embryonic stem cells (ESCs), and whether it forms a distinct NuRD complex, how its expression is regulated, and its precise function(s) remain unknown. We show that MBD3C forms a complete NuRD complex that functions redundantly with the other MBD3 isoforms in ESC gene regulation. Furthermore, MBD3C binds the SET/MLL complex subunit WDR5 through a conserved motif within its unique N-terminal region, and this interaction is necessary for the regulation of >2,000 ESC genes. Together, these findings indicate that ESCs can utilize isoforms of the same protein to achieve similar functions through diverse mechanisms. The second part of this thesis focuses on the role of the histone modification H3.3K56ac in pluripotency and differentiation. Although H3K56ac is well-studied in yeast, in mammalian cells it is far less abundant and its functions are largely unknown. Our data indicate that the H3.3K56R mutant is largely normal for ESC maintenance and loss of pluripotency markers during differentiation, but H3.3K56ac is necessary for proper lineage commitment. Ongoing studies will characterize the H3.3K56Q phospho-mimetic mutant during differentiation, and examine H3.3K56ac function at lineage-specific genes.

Central to the control of virtually all cellular activity is the regulation of gene expression. In eukaryotes, this regulation is greatly influenced by chromatin structure, which is itself regulated by numerous chromatin-remodeling complexes. These are typically large protein complexes with interchangeable subunits that allow for highly specialized functions in different cell types. Moreover, additional specificity can be gained through complexes formed from different subunit isoforms. Histone modifications also regulate chromatin by recruiting remodeling complexes to particular genomic regions. In this thesis we characterize MBD3C, an isoform of the Nucleosome Remodeling and Deacetylase (NuRD) complex subunit MBD3. MBD3 is essential for pluripotency and development, but MBD3C appears to be expressed only in embryonic stem cells (ESCs), and whether it forms a distinct NuRD complex, how its expression is regulated, and its precise function(s) remain unknown. We show that MBD3C forms a complete NuRD complex that functions redundantly with the other MBD3 isoforms in ESC gene regulation. Furthermore, MBD3C binds the SET/MLL complex subunit WDR5 through a conserved motif within its unique N-terminal region, and this interaction is necessary for the regulation of >2,000 ESC genes. Together, these findings indicate that ESCs can utilize isoforms of the same protein to achieve similar functions through diverse mechanisms. The second part of this thesis focuses on the role of the histone modification H3.3K56ac in pluripotency and differentiation. Although H3K56ac is well-studied in yeast, in mammalian cells it is far less abundant and its functions are largely unknown. Our data indicate that the H3.3K56R mutant is largely normal for ESC maintenance and loss of pluripotency markers during differentiation, but H3.3K56ac is necessary for proper lineage commitment. Ongoing studies will characterize the H3.3K56Q phospho-mimetic mutant during differentiation, and examine H3.3K56ac function at lineage-specific genes.

Developmental processes are carefully controlled at the level of transcription to ensure that the fertilized egg develops into an adult organism. The mechanisms that controls transcription of protein-coding genes ultimately ensure that the Pol II machine synthesizes mRNA from the correct set of genes in every cell type. Transcriptional control involves Pol II recruitment as well as transcriptional elongation. Recent genome-wide studies shows that recruitment of Pol II is often followed by an intermediate step where Pol II is halted in a promoter-proximal paused configuration. The release of Pol II from promoter-proximal pausing is thus an additional and commonly occurring mechanism in metazoan gene regulation. The serine kinase P-TEFb is part of the Super Elongation Complex that regulates the release of paused Pol II into productive elongation. However, little is known about the role of P-TEFb mediated gene expression in development. We have investigated the function of P-TEFb in early Drosophila embryogenesis and find that P-TEFb and other Super Elongation Complex subunits are critical for activation of the most early expressed genes. We demonstrate an unexpected function for Super Elongation Complex in activation of genes with non-paused Pol II. Furthermore, the Super Elongation Complex shares phenotypes with subunits of the Mediator complex to control the activation of essential developmental genes. This raises the possibility that the Super Elongation Complex has an unappreciated role in the recruitment of Pol II to promoters. The unique chromatin landscape of each cell type is comprised of post-translational chromatin modifications such as histone methylations and acetylations. To study the function of histone modifications during development, we depleted the histone demethylase KDM4A in Drosophila to evaluate the role of KDM4A and histone H3 lysine 36 trimethylation (H3K36me3) in gene regulation. We find that KDM4A has a male-specific function and regulates gene expression both by catalytic-dependent and independent mechanisms. Furthermore, we used histone replacement to investigate the direct role of H3K14 acetylation in a multicellular organism. We show that H3K14 acetylation is essential for development, but is not cell lethal, suggesting that H3K14 acetylation has a critical role in developmental gene regulation. This work expands our knowledge of the mechanisms that precisely controls gene regulation and transcription, and in addition highlights the complexity of metazoan development.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Manuscript.

Trimethylation of histone H3 lysine 9 (H3K9me3) and DNA methylation mark heterochromatin, contributing to gene silencing and normal cellular functions. My research investigated the control of H3K9me3 and DNA methylation in the filamentous fungus Neurospora crassa. The H3K9 methyltransferase complex, DCDC, consists of DIM-5, DIM-7, DIM-9, DDB1, and CUL4. Each component of DCDC is required for H3K9me3. The DIM-9/DDB1/CUL4 subunits are reminiscent of known cullin E3 ubiquitin ligases. I showed that core features of CUL4-based E3 ubiquitin ligases are not required for H3K9me3 and DNA methylation in Neurospora. H3K9me3 is bound by heterochromatin protein 1 (HP1) to recruit the DIM-2 DNA methyltransferase and the HCHC histone deacetylase complex. HCHC consists of HP1, CDP-2, HDA-1, and CHAP. Both HP1 and CDP-2 harbor conserved chromodomains that bind H3K9me3, and CHAP contains two putative AT-hook domains that bind A:T-rich DNA. To test the contributions of these domains to HCHC function, I deleted the chromodomains of HP1 and CDP-2. Deletion of the HP1 chromodomain resulted in a reduction of DNA methylation, which was not exacerbated by deletion of the CDP-2 chromodomain. A strain with deletions of chap and the HP1 chromodomain showed a DNA methylation phenotype comparable to the loss of the HDA-1 catalytic subunit. These findings support a model in which recognition of H3K9me3 and A:T-rich DNA by HP1 and CHAP, respectively, are required for proper HCHC function. To examine the relationships between H3K9me3, DNA methylation, and histone acetylation, I utilized in vivo protein tethering of core heterochromatin components. The requirement of DIM-7 for native heterochromatin, previously implicated in localizing the H3K9 methyltransferase DIM-5, was not bypassed by DIM-5 tethering, indicating that DIM-7 has additional roles within the DCDC. Artificial localization of the HCHC histone deacetylase, by tethering HP1 or HDA-1, resulted in induction of H3K9me3, DNA methylation, and gene silencing, but silencing did not require H3K9me3 or DNA methylation. HCHC-mediated establishment of H3K9me3 was not required for de novo heterochromatin formation at native heterochromatic loci suggesting a role in heterochromatin spreading. Together, this work implicates HDA-1 activity as a key driver of heterochromatin spreading and silencing. This dissertation includes previously published co-authored material.

In normal embryonic development, cells generated from a fertilised oocyte lose their pluripotent status and become restricted to a particular differentiation pathway. This production of functionally distinct cell lineages is thought to be mediated by epigenetic processes that help control gene expression both temporally and spatially without any changes to the DNA sequence. These epigenetic changes consist of posttranslational modifications of the N-terminal tails of histones and differential DNA methylation. Together these act by altering local chromatin structure, which in turn directs gene transcription by regulating the accessibility of the underlying DNA. To examine the potential developmental roles of these modifications, we determined the global cellular patterns of DNA methylation, as well as histone H3 lysine 9 (H3K9) and histone H4 lysine 20 (H4K20) methylation in the developing zebrafish embryo. These modifications are seen as hallmarks of heterochromatin, which consists of DNA that is tightly packaged, gene-poor and transcriptionally silent. Thus using immunostaining techniques, we confirmed the occurrence of genome-wide DNA methylation changes during zebrafish embryogenesis, as well as observing the unique localisation of this mark around the nuclear periphery in conjunction with pericentric heterochromatin. For mono-, di- and tri-methylated H3K9, it was observed by both immunostaining and immunoblotting that these marks became apparent after the onset of zygotic transcription. Ultimately their levels increased as development progressed, in a fashion similar to that of DNA methylation, consistent with a link between these epigenetic marks. Using the same methodology, the three methylation states of H4K20 were seen to vary differentially during zebrafish development, where in particular the levels of H4K20me1 decreased in concert with a potentially sumoylated form. In contrast, the levels of H4K20me2 increased progressively during embryogenesis, while those of H4K20me3 decreased rapidly after the mid-blastula transition. Together, these findings demonstrate that both DNA and histone lysine methylation take place in a highly dynamic manner, further supporting their roles in augmenting chromatin structure and directing cellular differentiation, while also providing a valuable comparison to the developmental epigenetics of other model organisms characterised to date. Preparatory work for somatic cell nuclear transfer in zebrafish was also undertaken. In future studies, the dynamics of these marks could be compared with those of cloned embryos, so that the specific epigenetic profiles necessary for development can be elucidated. Epigenetically, a homologous process occurs within pluripotent embryonic stem cells (ESCs), which can differentiate into any cell type or undergo indefinite self-renewal. Advantageously, we were able to derive zebrafish ESC-like clusters which were morphologically similar to those derived from mice. These clusters were alkaline phosphatase-positive and expressed key ESC markers as detected by RT-PCR and immunofluorescence. In pilot studies, GFP-expressing ESC-like clusters have so far also contributed to ectodermal tissues when transplanted into wild type zebrafish embryos. Subsequently, these ESC-like clusters were epigenetically profiled using immunofluorescence, which showed that they had a similar complement of modifications to ESCs derived from mice. The derivation and initial characterisation of these ESC-like clusters from zebrafish, in addition to the development of somatic cell nuclear transfer in this species, will help pave the way for future studies involving tissue repair and regeneration, as well as opening up the potential of targeted genetic manipulation in this valuable model organism.

La méthylation de la lysine 9 de l’histone 3 (H3K9), établie par les lysine méthyltransférases (KMTs) SETDB1, SUV39H1, G9A et GLP, représente un mécanisme épigénétique central dans la régulation du destin cellulaire. En particulier, la methylation d’H3K9 est directement impliquée dans la formation de l’hétérochromatine et l’extinction des gènes. Notre laboratoire a montré que les principales KMTs (SETDB1, G9A, GLP et SUV39H1) spécifiques de H3K9 forment un méga-complexe impliqué dans la répression transcriptionnelle, probablement via une coopération pour établir les différents niveaux de méthylation. Néanmoins, la régulation des complexes de H3K9 KMT n’est jusqu’à présent pas bien comprise. Il est à noter que des modifications post-traductionnelles (PTM) ont été impliquées dans la régulation des fonctions des KMTs. Dans ce contexte, mon projet visait à comprendre comment la méthylation de SETDB1 régulerait son activité (incorporation dans des complexes, interaction avec ses partenaires, recrutement à la chromatine). Le but étant d’établir quel impact auraient ces modifications de SETDB1 sur la formation de l’hétérochromatine, l’expression des gènes et la régulation du destin cellulaire. SETDB1 est cruciale lors du développement et de la différençiation cellulaire. De plus, SETDB1 est essentielle pour la pluripotence et le renouvellement des cellules souches embryonnaires murines (mESC). L’inactivation génique de ou KO de Setdb1 est létal au stade préimplantatoire à 7,5 jours post-coïtum (dpc). En plus des histones, SETDB1 méthyle d’autres protéines comme UBF, ING2 et p53. Mes résultats montrent notamment, que SETDB1 s’autométhyle sur les lysines K1170 et K1178 localisées dans le domaine catalytique SET. SETDB1 et SUV39H1 coordonnent l’établissement et la maintenance de H3K9me3 dans l’hétérochromatine péricentromérique constitutive et co-régulent de nombreuses cibles génomiques dans l’hétérochromatine, dont les éléments transposables comme les Long Interspersed Nuclear Elements (LINEs) et les rétrovirus endogènes (ERVs). Comme SUV39H1 est une triméthyltransférase qui utilise H3K9me1 ou H3K9me2 comme substrat primaire, SETDB1 pourrait probablement fournir les mono- ou di-méthyl H3K9. Mes résultats suggèrent un modèle dans lequel l’auto-méthylation de SETDB1 est pré-requise à la trans-méthylation subséquente par SUV39H1. Ce mécanisme pourrait réguler non seulement l’interaction physique entre SETDB1 et SUV39H1, via le chromodomaine de SUV39H1, mais aussi leur coopération dans l’établissement et la maintenance des blocs (grands domaines) d’hétérochromatine et l’extinction des éléments transposables, au moins dans les cellules souches. Ainsi, nous souhaitons mieux comprendre comment le « dialogue » entre ces deux H3K9 KMT majeures, SETDB1 et SUV39H1, est impliqué dans leurs interactions et leurs recrutements aux loci cibles
Histone H3 lysine 9 (H3K9) methylation, which is established by the lysine methyltransferases (KMTs) SETDB1, SUV39H1, G9A and GLP, is a central epigenetic mechanism involved in cell fate regulation. In particular, H3K9 methylation is directly involved in heterochromatin formation and gene silencing. Our lab showed that the main H3K9 KMTs (SETDB1, G9A, GLP and SUV39H1) form a functional megacomplex involved in transcriptional silencing, probably via the cooperative establishment of the different H3K9 methylation levels. However, up to now, the regulation of the H3K9 KMT complexes is not fully understood. Interestingly, post-translational modifications (PTMs) have been implicated in the regulation of H3K9 KMT functions. In this, my PhD thesis aimed to decipher how methylation of SETDB1, regulates its activity (complex formation, interaction with partners, recruitment to chromatin), which ultimately could impact on heterochromatin formation, gene expression and cell fate regulation. SETDB1 is crucial during development and cellular differentiation. Moreover, SETDB1 is essential in mouse embryonic stem cells (mESCs) pluripotency and self-renewal, Setbd1 KO is lethal at the peri-implantation stage at 7.5 days postcoitum (dpc). Beside histones, SETDB1 is also able to methylate other proteins (e.g. UBF, ING2, p53). Notably, my current data show that SETDB1 undergoes (auto)methylation on the lysines K1170 and K1178 located inside its catalytic SET domain. SETDB1 and SUV39H1 coordinate the establishment and maintenance of H3K9me3 at constitutive pericentromeric heterochromatin and co-regulate many genomic targets within heterochromatin, including transposable elements, such as long interspersed nuclear elements (LINEs) and endogenous retroviruses (ERVs). Since SUV39H1 is a H3K9 tri-methyltransferase that uses H3K9me1 or H3K9me2 as a primary substrate, SETDB1 could probably provide mono- or di-methylated H3K9. Interestingly, my results point to a model in which SETDB1 auto-methylation paves the path to a subsequent trans-methylation by SUV39H1. This mechanism could regulate not only the SETDB1/SUV39H1 physical interaction (via the SUV39H1 chromodomain), but also cooperation in the establishment and maintenance of both heterochromatin blocks (large domains) and transposable elements (TEs) silencing, at least in ES cells. Thus, we would like to better understand how the crosstalk between these two key H3K9 KMTs, SETDB1 and SUV39H1, occurs in terms of interaction and recruitment to target loci

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.

Cette dernière décennie a vu augmenter le nombre d'études portant sur la caractérisation des protéines JUMONJI (JMJ) et montrant leur rôle prépondérant dans la régulation des gènes et le développement des organismes. Ces protéines sont capables de déméthyler certains résidus des queues des histones et ont été organisées en groupes phylogénétiques en fonction de la conservation de leur domaine catalytique. Pour chaque clade entre un et trois substrats spécifiques ont pu être identifiés. De la sous famille KDM3, dont le résidu cible est H3K9, seul un membre, IBM1, a été caractérisé chez Arabidopsis. Cette étude montre que la mutation de JMJ24, un autre membre de ce groupe, entraine une augmentation de la taille des racines, cotylédons et organes floraux, suggérant un rôle dans le contrôle du développement à différents stades. De plus, l'analyse de l'expression tissulaire indique que JMJ24 est exprimé dans le phloème, en cohérence avec l'effet pléiotropique de sa mutation. Enfin, nos données suggèrent une interaction entre JMJ24 et d'autres protéines JMJ, telles JMJ14 et IBM1, mais aussi une interaction avec les protéines DCL, impliquées dans la régulation des gènes et des éléments transposables.

Unlike characteristic HP1 proteins, the HP1c isoform of Drosophila melanogaster is a euchromatic protein. HP1c forms a complex with the zinc finger proteins ROW and WOC, which are crucial for HP1c function. In the present work, we aimed to further characterize the HP1c complex. We purified several novel factors that are associated with the complex. In particular, we characterize the ubiquitin receptor Dsk2 as an intrinsic subunit of the HP1c complex. Further, we show that the HP1c complex binds to TSS of actively transcribed genes and contributes positively to their transcription. The HP1c complex promotes an active chromatin state at target genes. We show evidence that this role involves regulation of H2Bub1 levels through Dsk2.
Al contrario de proteinas HP1 características, la isoforma HP1c de Drosophila melanogaster es una proteína eucromatica. HP1c se encuentra en un complejo con las proteínas “zinc finger” ROW y WOC, que son esenciales para la función de HP1c. En este trabajo, quisimos caracterizar el complejo HP1c en más detalle. Purificamos varios factores nuevos que se unen al complejo. En particular, caracterizamos el receptor de ubiquitina Dsk2 como una unidad principal del complejo HP1c. Además, demostramos que el complejo HP1c se une a TSS de genes que se transcriben activamente y que influye positivamente en su transcripción. El complejo HP1c favorece un estado activo de cromatina en los genes donde se encuentra. Nuestros resultados indican que este mechansimo incluye una regulación de los niveles de H2Bub1 a través de Dsk2

碩士
國立臺北大學
企業管理學系
102
Since talents are important assets of an enterprise, how to enhance job satisfaction to retain talents has become an important issue for business leaders. Previous researchers have found that Transformational Leadership has positive influences on Job Satisfaction. Perceived Organizational Support has positive influences on Job Satisfaction, too. This study investigated the effects of Transformational Leadership and Leader-Member Exchange on Job Satisfaction, and verified if there is mediating effect of Perceived Organizational Support. This study analyzed 200 valid questionnaires on these effects and the findings are as the follows: (1) Transformational Leadership is positively related to Perceived Organizational Support. (2) Leader-Member Exchange is positively related to Perceived Organizational Support. (3) Perceived Organizational Support is positively related to n Job Satisfaction. (4) Transformational Leadership is positively related to Job Satisfaction. (5) Leader-Member Exchange is positively related to Job Satisfaction. (6) Perceived Organizational Support is a mediator between Transformational Leadership and Job Satisfaction. (7) Perceived Organizational Support is a mediator between Leader-Member Exchange and Job Satisfaction. We expect the results of this study can provide a reference on the management practices for enterprises and as the bases for further academic studies.

碩士
國立清華大學
電子工程研究所
106
Light can replace the chemical effector for programming on-demand gene expression in bacteria. Existing tools for optogenetic bacterial circuits remain cumbersome and labor intensive even for simple tasks, such as measuring growth-related gene expression. We present an array of min photobioreactors that monitors the response of optogenetic bacterial circuits to light. The array enables automated, in vivo parallelizable monitoring in real-time and enable the measurement of the host circuit interaction for a synthetic optogenetic circuit, CcaS-CcaR light sensing system in Escherichia coli. Each bioreactor measures the optical density and fluorescence and applies light-source intervention of the gene expression control. The bioreactor array is demonstrated on the CcaS–CcaR light sensing system in Escherichia coli. The interdependence between microbial growth and optogenetic gene expression is confirmed in a growth experiment with three effectors of microbial growth (carbon source, oxygenation, and antibiotic drug concentration). Growth under different carbon sources and oxygenation levels can be explained in the context of resource allocation trade off picture.

Tuberous sclerosis complex (TSC) is an autosomal dominant genetic syndrome characterized by the growth of benign tumors in multiple organ systems including brain, lung, kidney, skin, and heart. Kidney angiomyolipoma (AML) are benign, slow growing renal tumors that are seen in about 80% of TSC patients, but also occur sporadically. Although heterogeneous in nature, AMLs have a relatively low somatic mutation rate compared to most other cancers, with biallelic loss of either TSC1 or TSC2 gene considered as the primary and sufficient driver for tumor development. We hypothesized that epigenetic alterations of the AML chromatin landscape change the transcriptional dynamics of the underlying genetic system that supports and gives rise to the tumor-cell phenotype. Our data have identified microphthalmia-associated transcription factor (MITF) to be an orchestrating gene in AML development, as 6 out of the top 10 differentially expressed genes in AML are putative MITF-target genes. Integrative analysis of RNA Seq (n=28), H3K27ac ChIP Seq (n=25) and MITF ChIP Seq data (n=3), obtained from fresh-frozen kidney AML specimens, has enabled us to characterize components of a tumor-specific regulatory network under the transcriptional control of MITF. This novel approach has the potential to identify a variety of therapeutic targets, as well as provide unprecedented insight into the mechanisms behind angiomyolipoma development.
2021-06-07T00:00:00Z

博士
國立臺灣大學
毒理學研究所
99
G9a is a mammalian histone methyltransferase that contributes to the epigenetic silencing of tumor suppressor genes. Emerging evidence suggests that G9a is required to maintain the malignant phenotype, but the role of G9a function in mediating tumor metastasis has not been explored. Here, we show that G9a is expressed in aggressive lung cancer cells, and its elevated expression correlates with poor prognosis. RNAi-mediated knockdown of G9a in highly invasive lung cancer cells inhibited cell migration and invasion in vitro and metastasis in vivo. Conversely, ectopic G9a expression in weakly invasive lung cancer cells increased motility and metastasis. Mechanistic investigations suggested that repression of the cell adhesion molecule Ep-CAM mediated the effects of G9a. First, RNAi-mediated knockdown of Ep-CAM partially relieved metastasis suppression imposed by G9a suppression. Second, an inverse correlation between G9a and Ep-CAM expression existed in primary lung cancer. Third, Ep-CAM repression was associated with promoter methylation and an enrichment for dimethylated histone H3K9. G9a knockdown reduced the levels of H3K9 dimethylation and decreased the recruitment of the transcriptional cofactors HP1, DNMT1, and HDAC1 to the Ep-CAM promoter. Our findings establish a functional contribution of G9a overexpression with concomitant dysregulation of epigenetic pathways in lung cancer progression. In addition, G9a may also have functions in cancer cell motility, survival and angiogenic activity. Our results underscore the utility of developing G9a inhibitors as a potentially powerful therapeutic target. We also established the HTS platform for inhibitors against the G9a.

La chromatine possède une plasticité complexe et essentielle pour répondre à différents mécanismes cellulaires fondamentaux tels la réplication, la transcription et la réparation de l’ADN. Les histones sont les constituants essentiels de la formation des nucléosomes qui assurent le bon fonctionnement cellulaire d’où l’intérêt de cette thèse d’y porter une attention particulière. Un dysfonctionnement de la chromatine est souvent associé à l’émergence du cancer. Le chapitre II de cette thèse focalise sur la répression transcriptionnelle des gènes d’histones par le complexe HIR (HIstone gene Repressor) en réponse au dommage à l'ADN chez Saccharomyces cerevisiae. Lors de dommage à l’ADN en début de phase S, les kinases du point de contrôle Mec1, Tel1 et Rad53 s’assurent de bloquer les origines tardives de réplication pour limiter le nombre de collisions potentiellement mutagéniques ou cytotoxiques entre les ADN polymérases et les lésions persistantes dans l'ADN. Lorsque la synthèse totale d’ADN est soudainement ralentie par le point de contrôle, l’accumulation d'un excès d'histones nouvellement synthétisées est néfaste pour les cellules car les histones libres se lient de manière non-spécifique aux acides nucléiques. L'un des mécanismes mis en place afin de minimiser la quantité d’histones libres consiste à réprimer la transcription des gènes d'histones lors d'une chute rapide de la synthèse d'ADN, mais les bases moléculaires de ce mécanisme étaient très mal connues. Notre étude sur la répression des gènes d’histones en réponse aux agents génotoxiques nous a permis d’identifier que les kinases du point de contrôle jouent un rôle dans la répression des gènes d’histones. Avant le début de mon projet, il était déjà connu que le complexe HIR est requis pour la répression des gènes d’histones en phase G1, G2/M et lors de dommage à l’ADN en phase S. Par contre, la régulation du complexe HIR en réponse au dommage à l'ADN n'était pas connue. Nous avons démontré par des essais de spectrométrie de masse (SM) que Rad53 régule le complexe HIR en phosphorylant directement une de ses sous-unités, Hpc2, à de multiples résidus in vivo et in vitro. La phosphorylation d’Hpc2 est essentielle pour le recrutement aux promoteurs de gènes d’histones du complexe RSC (Remodels the Structure of Chromatin) dont la présence sur les promoteurs des gènes d'histones corrèle avec leur répression. De plus, nous avons mis à jour un nouveau mécanisme de régulation du complexe HIR durant la progression normale à travers le cycle cellulaire ainsi qu'en réponse aux agents génotoxiques. En effet, durant le cycle cellulaire normal, la protéine Hpc2 est très instable durant la transition G1/S afin de permettre la transcription des gènes d’histones et la production d'un pool d'histones néo-synthétisées juste avant l'initiation de la réplication de l’ADN. Toutefois, Hpc2 n'est instable que pour une brève période de temps durant la phase S. Ces résultats suggèrent qu'Hpc2 est une protéine clef pour la régulation de l'activité du complexe HIR et la répression des gènes d’histones lors du cycle cellulaire normal ainsi qu'en réponse au dommage à l’ADN. Dans le but de poursuivre notre étude sur la régulation des histones, le chapitre III de ma thèse concerne l’analyse globale de l’acétylation des histones induite par les inhibiteurs d’histone désacétylases (HDACi) dans les cellules normales et cancéreuses. Les histones désacétylases (HDACs) sont les enzymes qui enlèvent l’acétylation sur les lysines des histones. Dans plusieurs types de cancers, les HDACs contribuent à l’oncogenèse par leur fusion aberrante avec des complexes protéiques oncogéniques. Les perturbations causées mènent souvent à un état silencieux anormal des suppresseurs de tumeurs. Les HDACs sont donc une cible de choix dans le traitement des cancers engendrés par ces protéines de fusion. Notre étude de l’effet sur l’acétylation des histones de deux inhibiteurs d'HDACs de relevance clinique, le vorinostat (SAHA) et l’entinostat (MS-275), a permis de démontrer une augmentation élevée de l’acétylation globale des histones H3 et H4, contrairement à H2A et H2B, et ce, autant chez les cellules normales que cancéreuses. Notre quantification en SM de l'acétylation des histones a révélé de façon inattendue que la stœchiométrie d'acétylation sur la lysine 56 de l’histone H3 (H3K56Ac) est de seulement 0,03% et, de manière surprenante, cette stœchiométrie n'augmente pas dans des cellules traitées avec différents HDACi. Plusieurs études de H3K56Ac chez l’humain présentes dans la littérature ont rapporté des résultats irréconciliables. Qui plus est, H3K56Ac était considéré comme un biomarqueur potentiel dans le diagnostic et pronostic de plusieurs types de cancers. C’est pourquoi nous avons porté notre attention sur la spécificité des anticorps utilisés et avons déterminé qu’une grande majorité d’anticorps utilisés dans la littérature reconnaissent d’autres sites d'acétylation de l’histone H3, notamment H3K9Ac dont la stœchiométrie d'acétylation in vivo est beaucoup plus élevée que celle d'H3K56Ac. De plus, le chapitre IV fait suite à notre étude sur l’acétylation des histones et consiste en un rapport spécial de recherche décrivant la fonction de H3K56Ac chez la levure et l’homme et comporte également une évaluation d’un anticorps supposément spécifique d'H3K56Ac en tant qu'outil diagnostic du cancer chez l’humain.
The chromatin is a complex structure and its plasticity is essential to complete different fundamental cellular processes such as DNA replication, transcription and repair. Furthermore, chromatin malfunction is often associated with cancer emergence. The focus of this thesis will be on the function and regulation of histones, as they are essential components of nucleosomes and they ensure proper chromatin formation. Chapter II of this thesis focuses on the transcriptional repression of histone genes by the HIR (HIstone gene Repressor) complex in response to DNA damage in Saccharomyces cerevisiae. When DNA damage occurs in early S phase, the DNA damage checkpoint kinases Mec1, Tel1 and Rad53 block late origins of replication to limit potentially mutagenic or cytotoxic collisions between DNA polymerases and remaining DNA lesions. When the total DNA synthesis rate drops suddenly in S- phase, following the checkpoint control activation, accumulation of newly synthesized histones becomes detrimental for the cells because free histones bind non-specifically to nucleic acids. One mechanism that contributes to a reduction in free histones at this time is the repression of histone gene transcription; however, the molecular basis of this repression was not known. Our study on histone gene repression in response to genotoxic agents allowed us to identify the checkpoint kinases as major players in the repression of histone genes. Before initiating this project, it was known that the HIR complex is required to repress histone genes in G1 and G2/M phases and during DNA damage. Nonetheless, HIR complex regulation was not well characterized. We demonstrated by mass spectrometry (MS) analyses that Rad53 regulates the HIR complex by directly phosphorylating one of its subunits, Hpc2, at many residues in vivo and in vitro. Hpc2 phosphorylation is essential to recruit the RSC complex (Remodels the Structure of Chromatin) to histone gene promoters where its presence correlates with histone gene repression. Moreover, we uncovered a novel mechanism for the HIR complex regulation during a normal cell cycle progression and in response to genotoxic agents. Indeed, during a normal cell cycle, the Hpc2 protein is very unstable at the G1/S transition to allow histone gene transcription and production of a pool of newly synthesized histones just before DNA replication initiation. These results suggest that Hpc2 is a key player in the regulation of HIR complex activity and can repress histone gene expression both during a normal cell cycle and in response to DNA damage. In order to pursue our study on histone regulation, chapter III of this thesis covers histone acetylation induced by histone deacetylase inhibitors (HDACi) in normal and cancer cells. Histone deacetylases (HDACs) are enzymes that remove acetyl groups from lysine residues on histones, condensing the chromatin and effectively repressing local transcription. Several types of cancers are characterized by epigenetic abnormalities and HDACs contribute to oncogenesis by aberrant fusion with oncogenic protein complexes. The disruptions often lead to an abnormal silent state of tumour suppressors. HDACs are then targets of interest in cancer treatment caused by those fusion proteins. Our study of the effects of two clinically relevant HDAC inhibitors, vorinostat (SAHA) and entinostat (MS-275) on acetylation of histones demonstrated an obvious increase of histones H3 and H4 acetylation, unlike histones H2A and H2B in both normal and cancer cells. Unexpectedly, our MS quantification of histone acetylation revealed that the stoichiometry of histone H3 lysine 56 acetylation (H3K56Ac) was only 0.03% and, surprisingly, this stoichiometry did not increase upon HDACi treatments. Several reported studies in the literature of H3K56Ac in humans are irreconcilable. Furthermore, H3K56Ac was considered as a potential biomarker in diagnosis and prognosis in many cancer types. Therefore we focussed on antibody specificity and determined that the majority of antibodies used in the literature recognize other acetylation sites in histone H3, especially H3K9Ac whose stoichiometry of acetylation in vivo is much higher than H3K56Ac. Additionally, chapter IV is a follow-up of our study on histone acetylation and consists of a special report describing the function of H3K56Ac in yeast and human and also contains an evaluation of a supposedly specific H3K56Ac antibody as a diagnostic tool in human cancers.