No description available.

The phenomenon of cell type-specific DNA methylation has received much attention in recent years and a number of DNA methylation differences have been described between cells of the immune system. Of particular interest when studying DNA methylation are CpG islands (CGIs) which are distinct from the rest of the genome due to their elevated CpG content, generally unmethylated state and promoter association. In the instances when they become methylated this is associated with gene repression although it is unclear the extent to which differential methylation corresponds to differential gene expression. I have used an immune system model to assess the role of CGI methylation and the role of the methylation reader MBD2 in regulation of gene expression. A relatively small number of DNA methylation differences were seen between immune cell types with the most developmentally related cells showing the fewest methylation differences. Interestingly, the vast majority of CGI-associated cellspecific methylation occurred at intragenic CGIs located, not at transcription start sites, but in the gene body. Increased intragenic CGI methylation tended to associate with gene repression, although the precise reason for this remains unclear. Most differentially methylated CGIs were depleted for the active chromatin mark H3K4me3 regardless of their methylation state but some of these were associated with the silencing mark H3K27me3 when unmethylated. These findings suggest that intragenic CGIs are a distinct class of genomic element particularly susceptible to cell type-specific methylation. I also looked at the effect of removing the methyl- CpG binding domain protein MBD2 from immune system cells. Immune cells from Mbd2-/- mice showed a number of previously uncharacterised phenotypes as well as a number of differences in gene expression compared to wild-type animals. Most of these genes increased their expression in the absence of MBD2 consistent with MBD2’s role as a transcriptional repressor and Mbd2-/- Th1 cells showed increases in histone H3 acetylation compared to wild-type Th1 cells. This work provides an insight into the role played by cell-specific CGI methylation and MBD2 in regulating gene expression.

After almost two decades of research on direct repression by p53, I provide evidence that the transcription factor p53 solely acts as an activator of transcription. I evaluate the prominent models of transcriptional regulation by p53 based on a computational meta-analysis of genome-wide data. With this tool at hand, the major contradiction how p53 binding can result in activation of one target gene and repression of another is resolved. In contrast to most current models, solely genes activated by p53 are found to be enriched for p53 binding. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and does not support models of direct repression. Consequently, as supported by experimental data, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors are also not supported by the meta-analysis. As an alternative to these models, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21- DREAM/RB pathway. Thus, results of the meta-analysis support only two models, namely activation by direct binding of p53 to target genes and repression through activating the p53-p21-DREAM/RB pathway.

Lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) are known to cooperate with the glucocorticoid receptor (GR) to regulate transcription. The current model of GR-mediated transcription classifies KATs as coactivators as they acetylate histones to form an open chromatin conformation and casts KDACs as corepressors that deacetylate histones and condense chromatin. Our recent studies have challenged this long-standing model. In the current study, we show that KDACs act as versatile coregulators, facilitating both the onset and maintenance of GC-induced transcriptional activation and repression. Through siRNA depletion studies, we define KDAC1 as the predominant Class I KDAC for efficient transactivation of a majority of the GR-target genes tested. KDACs 1 and 2 co-operate with each other to activate and repress a few target genes, however KDAC2 alone is not sufficient for activation or repression of the genes, thus questioning the functional redundancy of KDACs 1 and 2. Additionally, we found that there is a unique population of KDAC2 that does not associate with KDAC1 in our cell line. Through a series of siRNA depletion studies, steroid receptor coactivator proteins (SRCs) were shown to be dispensable for GC-induced gene activation and SRC2 was not required for Dex-induced transcriptional repression. We performed ChIP assays to address the mechanism by which Class I KDACs facilitate transactivation and transrepression. At GC-activated genes we found that KDACs are constitutively present at the gene enhancers and that KDAC inhibition does not affect the binding of GR or SRC proteins to chromatin. However, KDACs do influence the histone methylation status of H3K4 at GREs of activated genes and TSSs of repressed genes. To explain the change in the methylation status of this marker, we depleted LSD1, the specific demethylase for mono- and demethylation of H3K4, and found that LSD1 action is required for GC-mediated transrepression. However it is unlikely that KDAC inhibition impairs GR transactivation through effects on LSD1. Glucocorticoid signaling regulates multiple vital biological processes. Glucocorticoids play a major role in regulating carbohydrate, protein and lipid metabolism. They increase hepatic gluconeogenesis to maintain blood glucose concentration in the fasting state. GCs also act as potent anti-inflammatory molecules, stimulate lung maturation in the developing fetus, and affect bone metabolism. Additionally, excess or deficiency of GCs can lead to a variety of psychological abnormalities, indicating their role in CNS functions. Our results indicate that pharmaceutical modulation of KDACs may impair proper glucocorticoid signaling and disrupt vital biological processes. Other steroid hormone receptors function similarly to GR in regulating gene expression and could also be impacted by KDAC inhibition, thus suggesting serious physiological implications in patients. Therefore, the possibility of endocrine modulation should be taken into account when using KDAC inhibitors in the clinic.

No description available.

After almost two decades of research on direct repression by p53, I provide evidence that the transcription factor p53 solely acts as an activator of transcription. I evaluate the prominent models of transcriptional regulation by p53 based on a computational meta-analysis of genome-wide data. With this tool at hand, the major contradiction how p53 binding can result in activation of one target gene and repression of another is resolved. In contrast to most current models, solely genes activated by p53 are found to be enriched for p53 binding. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and does not support models of direct repression. Consequently, as supported by experimental data, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors are also not supported by the meta-analysis. As an alternative to these models, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21- DREAM/RB pathway. Thus, results of the meta-analysis support only two models, namely activation by direct binding of p53 to target genes and repression through activating the p53-p21-DREAM/RB pathway.

Listeria monocytogenes transporte le cellobiose principalement via le PTS (PEP:carbohydrate phosphotransferase system). La croissance sur cellobiose induit l'expression des opérons celBCA1, celBA2 ainsi que du gène lmrg_01989, qui codent respectivement le composant soluble EIIACel1, le transporteur EIICCel1, le composant soluble EIIBCel1, les protéines EIIBCel2 et EIIACel2, et une seconde EIICCel. La croissance sur glucose réprime fortement l'expression de ces gènes. La délétion de celC1 codant l'EIICCel1 ou des deux gènes, celA1 et celA2, ralentit considérablement la consommation cellobiose. L'expression des trois unités de transcription induite par le cellobiose dépend de CelR. CelR, qui code un régulateur transcriptionnel LevR- like, est situé en aval de l'opéron bicistronique celBA2. CelR est activé par phosphorylation par EI et HPr de l'His550. En revanche, la phosphorylation de l'His823, catalysée par P~EIIBCel1 et P~EIIBCel2, inhibe l'activité de CelR. Le remplacement de l'His823 par une Ala empêchant cette phosphorylation ou la délétion des deux gènes codants les EIIAsCel ou EIIBsCel entraîne l'expression constitutive des trois unités de transcription contrôlées par CelR. Comme le glucose, le cellobiose inhibe fortement l'activité de PrfA, l'activateur des gènes de virulence. Nous avons donc cherché à tester si l'un des composants PTSCel pouvait être impliqué dans la répression de gènes de virulence. Les mutants consommant faiblement le cellobiose, présentaient une levée de la répression des gènes de virulence par le cellobiose, alors que le glucose et les autres sucres-PTS les réprimaient toujours. De manière surprenante, la délétion du gène monocistronique lmrg_00557, qui code un autre composant EIIBCel du PTS, induisait la levée de la répression des gènes de virulence médiée par toutes les sources de carbone mais n'avait aucun effet sur la consommation de glucose ou de cellobiose. Ce gène lmrg_00557 a été appelé vgiB (virulence gene inhibitor B) et la protéine correspondante, qui semble jouer un rôle majeur dans la régulation de l'activité de PrfA, EIIBVir. Cette protéine est phosphorylée par le PEP et les composants PTS EI, HPr et EIIACel2 sur le résidu cystéine-8. La complémentation du mutant ΔvgiB avec l'allèle sauvage, mais également avec l'allèle Cys8Ala, restaurait le mécanisme général de répression des gènes de virulence par les sucres, suggérant ainsi que la forme non phosphorylée de EIIBVir inhibe l'activité de PrfA. / Listeria monocytogenes transports cellobiose mainly via a PEP:carbohydrate phosphotranseferase system (PTS). Growth on cellobiose induces the expression of the celBCA1 and celBA2 operons as well as lmrG01989, which encode the soluble EIIA Cel1 and EIIB Cel1 components, the transporter EIIC Cel1 , the EIIA Cel2 and EIIB Cel2 proteins, and a second EIIC Cel , respectively. Growth on lucose strongly repressed the expression of these genes. Deletion of the EIIC Cel1 –encoding celC1 or of both, celA1 and celA2, significantly slowed cellobiose consumption. The bicistronic operon celBA2 is located downstream from celR, which codes for a LevR-like transcription activator. Expression of the three cellobiose-induced transcription units depends on CelR. The gene encoding CelR is located upstream from the bicistronic operon celBA2. CelR itself is activated via phosphorylation by EI and HPr at His550. In contrast, phosphorylation at His823, which is catalyzed by both, P~EIIB Cel1 and P~EIIB Cel2 , inhibits CelR activity. Preventing this phosphorylation by replacing His823 with Ala or deleting the two EIIA Cel – or EIIB Cel -encoding genes caused constitutive expression of all three CelR-controlled transcription units. Similar to glucose, cellobiose strongly inhibits the activity of the virulence gene activator PrfA. We therefore tested whether one of the PTS Cel components might be involved in virulence gene repression. Mutants, that exhibit slow cellobiose consumption, were relieved from cellobiose-mediated virulence gene repression, whereas glucose and other PTS-sugars still repressed them. Strikingly, deletion of the presumed monocistronic lmrg_00557, which codes for another EIIB Cel -like PTS component, caused a general relief from carbon source-mediated virulence gene repression, but had no effect on cellobiose or glucose consumption. The gene lmrg_00557 was named vgiB (virulence gene inhibitor B) and the encoded protein, which seems to play a major role in PrfA regulation, was called EIIB Vir . It becomes phosphorylated by PEP and the PTS components enzyme I, HPr and EIIA Cel2 at cysteine-8. Complementation of the ΔvgiB mutant with wild-type vgiB, but also with the Cys8Ala allele restored general virulence gene repression, thus suggesting that it is the unphosphorylated form of EIIB Vir , which inhibits the activity of PrfA.

HYAL-1 (hyaluronidase-1) appartient à la famille des hyaluronidases connues pour leur rôle dans la dégradation de l’acide hyaluronique. L’expression de HYAL-1 est élevée dans de nombreux type de cancers, notamment dans le cancer de la prostate, de la vessie, des reins et du sein où il est impliqué dans la croissance tumorale et les métastases. Récemment notre laboratoire a aussi démontré une expression élevée de HYAL-1 dans le cancer épithélial de l’ovaire (CEO) de type mucineux et à cellules claires, expression qui est inversement corrélée à celle du récepteur de l’oestrogène alpha (REα). Cependant, malgré le fait que le rôle de HYAL-1 dans le cancer soit bien établit, le mécanisme de sa régulation reste encore inconnu. Le REα est un facteur de transcription qui suite à sa liaison avec son ligand va réguler l’expression de plusieurs gènes. Le REα ainsi stimulé par l’hormone va activer la transcription de ces gènes cibles mais il est connu maintenant qu’une grande partie des gènes régulés par le REα sont en réalité réprimés par ce récepteur. Dans ce travail nous proposons d’étudier le mécanisme de la régulation du gène HYAL-1 par le REα dans le CEO à cellules claires et dans le cancer du sein. L’expression ectopique du REα dans la lignée TOV21G (RE-) de même que le traitement de la lignée MCF-7 (RE+) avec de l’oestrogène a induit une diminution du niveau d’expression de l’ARN m de HYAL-1. Ces résultats nous ont permis de confirmer que HYAL-1 est un gène cible du REα. Il est aussi connu que le REα peut exercer son action par différents mécanismes d’action, entre autres en interagissant avec une séquence d’ADN appelée élément de réponse à l’oestrogène (ERE), retrouvé sur le promoteur des gènes cibles ou bien indirectement par des interactions protéine-protéine en se liant à d’autres facteur de transcription tels que Sp1. Après avoir identifiés de telles séquences sur le promoteur proximal de HYAL-1, (1 ERE proximal à -900 pb, 3 distaux à -32350 pb, 48430, -50130 pb du site d’initiation de la transcription) en plus des 2 Sp1 connus (-60 et – 1020pb), nous avons démontrés par immunoprécipitation de la chromatine que le REα est recruté sur le promoteur de HYAL-1 au niveau de l’ERE proximal -900 pb et du distal -32350 pb de même que sur le site Sp1 -1020 pb. De plus, l’activité biologique de l’ERE -900 pb et du ii Sp1-1020pb à été confirmée par des essais de gènes rapporteurs à la luciférase. Avec son rôle connu dans la tumorigenèse, l’identification de HYAL-1 comme gène cible du REα pourrait être une avenue intéressante pour le traitement des cancers hormono-indépendants. / HYAL-1 (hyaluronidase-1) belongs to the hyaluronidase family of enzymes that degrade hyaluronic acid. HYAL-1 expression is elevated in many types of cancers including prostate, bladder, liver and breast cancer where it is involved in tumor growth and metastasis. In accordance to these observations, our group has also demonstrated high expression of HYAL-1 in clear cell and mucinous epithelial ovarian cancer (EOC) subtypes which was inversely correlated to that of estrogen receptor alpha (ERα). However, despite the fact that the role of HYAL-1 in cancer is well established, the mechanism of its regulation is still unknown. ERα is a transcriptional factor that regulates target-gene expression following ligand binding. Upon hormone stimulation, activated ERα will upregulate transcription of many target genes. However, it has been recently well documented that a large number of ERα responsive genes are in fact repressed. In this work we propose to study the mechanism by which ERα regulates HYAL-1 expression in clear cell EOC subtype as well as in breast cancer. The ectopic expression of ERα in TOV21G cell line (ERα -) and estrogen treatment of MCF-7 cells (ERα +) decreased HYAL-1 mRNA expression and allowed us to confirm that HYAL-1 is an ERα target gene. It is also known that ERα may exert its action through different mechanisms of action including interacting with a DNA sequence called estrogen response element (ERE) found in the promoter of target genes or indirectly by protein-protein interactions by binding to other transcription factor such as Sp1. Having identified such sequences in the proximal promoter of HYAL-1, (one proximal ERE -900 bp, 3 distals at -32350, -48430, -50130 bp from the start site of transcription) in addition to the two known Sp1 (-60 and -1020pb), we have demonstrated by chromatin immunoprecipitation that ERα is recruited at the HYAL-1 promoter at the ERE sites -900 pb and -32350 pb as well as at the Sp1 site -1020. Furthermore, the biological activity of the proximal ERE -900 and Sp1 -1020 sites were further confirmed by luciferase reporter gene assay. Given its known role in tumorigenesis, identification of HYAL-1 as an ERα target may provide an interesting approach for the treatment of hormono-independent cancer.

HYAL-1 (hyaluronidase-1) appartient à la famille des hyaluronidases connues pour leur rôle dans la dégradation de l’acide hyaluronique. L’expression de HYAL-1 est élevée dans de nombreux type de cancers, notamment dans le cancer de la prostate, de la vessie, des reins et du sein où il est impliqué dans la croissance tumorale et les métastases. Récemment notre laboratoire a aussi démontré une expression élevée de HYAL-1 dans le cancer épithélial de l’ovaire (CEO) de type mucineux et à cellules claires, expression qui est inversement corrélée à celle du récepteur de l’oestrogène alpha (REα). Cependant, malgré le fait que le rôle de HYAL-1 dans le cancer soit bien établit, le mécanisme de sa régulation reste encore inconnu. Le REα est un facteur de transcription qui suite à sa liaison avec son ligand va réguler l’expression de plusieurs gènes. Le REα ainsi stimulé par l’hormone va activer la transcription de ces gènes cibles mais il est connu maintenant qu’une grande partie des gènes régulés par le REα sont en réalité réprimés par ce récepteur. Dans ce travail nous proposons d’étudier le mécanisme de la régulation du gène HYAL-1 par le REα dans le CEO à cellules claires et dans le cancer du sein. L’expression ectopique du REα dans la lignée TOV21G (RE-) de même que le traitement de la lignée MCF-7 (RE+) avec de l’oestrogène a induit une diminution du niveau d’expression de l’ARN m de HYAL-1. Ces résultats nous ont permis de confirmer que HYAL-1 est un gène cible du REα. Il est aussi connu que le REα peut exercer son action par différents mécanismes d’action, entre autres en interagissant avec une séquence d’ADN appelée élément de réponse à l’oestrogène (ERE), retrouvé sur le promoteur des gènes cibles ou bien indirectement par des interactions protéine-protéine en se liant à d’autres facteur de transcription tels que Sp1. Après avoir identifiés de telles séquences sur le promoteur proximal de HYAL-1, (1 ERE proximal à -900 pb, 3 distaux à -32350 pb, 48430, -50130 pb du site d’initiation de la transcription) en plus des 2 Sp1 connus (-60 et – 1020pb), nous avons démontrés par immunoprécipitation de la chromatine que le REα est recruté sur le promoteur de HYAL-1 au niveau de l’ERE proximal -900 pb et du distal -32350 pb de même que sur le site Sp1 -1020 pb. De plus, l’activité biologique de l’ERE -900 pb et du ii Sp1-1020pb à été confirmée par des essais de gènes rapporteurs à la luciférase. Avec son rôle connu dans la tumorigenèse, l’identification de HYAL-1 comme gène cible du REα pourrait être une avenue intéressante pour le traitement des cancers hormono-indépendants. / HYAL-1 (hyaluronidase-1) belongs to the hyaluronidase family of enzymes that degrade hyaluronic acid. HYAL-1 expression is elevated in many types of cancers including prostate, bladder, liver and breast cancer where it is involved in tumor growth and metastasis. In accordance to these observations, our group has also demonstrated high expression of HYAL-1 in clear cell and mucinous epithelial ovarian cancer (EOC) subtypes which was inversely correlated to that of estrogen receptor alpha (ERα). However, despite the fact that the role of HYAL-1 in cancer is well established, the mechanism of its regulation is still unknown. ERα is a transcriptional factor that regulates target-gene expression following ligand binding. Upon hormone stimulation, activated ERα will upregulate transcription of many target genes. However, it has been recently well documented that a large number of ERα responsive genes are in fact repressed. In this work we propose to study the mechanism by which ERα regulates HYAL-1 expression in clear cell EOC subtype as well as in breast cancer. The ectopic expression of ERα in TOV21G cell line (ERα -) and estrogen treatment of MCF-7 cells (ERα +) decreased HYAL-1 mRNA expression and allowed us to confirm that HYAL-1 is an ERα target gene. It is also known that ERα may exert its action through different mechanisms of action including interacting with a DNA sequence called estrogen response element (ERE) found in the promoter of target genes or indirectly by protein-protein interactions by binding to other transcription factor such as Sp1. Having identified such sequences in the proximal promoter of HYAL-1, (one proximal ERE -900 bp, 3 distals at -32350, -48430, -50130 bp from the start site of transcription) in addition to the two known Sp1 (-60 and -1020pb), we have demonstrated by chromatin immunoprecipitation that ERα is recruited at the HYAL-1 promoter at the ERE sites -900 pb and -32350 pb as well as at the Sp1 site -1020. Furthermore, the biological activity of the proximal ERE -900 and Sp1 -1020 sites were further confirmed by luciferase reporter gene assay. Given its known role in tumorigenesis, identification of HYAL-1 as an ERα target may provide an interesting approach for the treatment of hormono-independent cancer.

Pichia pastoris, a methylotrophic yeast is widely used for recombinant protein production. It has a well characterized methanol utilization (MUT) pathway, the enzymes of which are induced when cells are cultured in the presence of methanol. In this study, we have identified an unannotated zinc finger protein, which was subsequently named ROP (repressor of phosphoenolpyruvate carboxykinase, PEPCK) and characterized its function. ROP expression is induced in P. pastoris cells cultured in biotin depleted glucose ammonium medium as well as a medium containing methanol as the sole source of carbon. In glucose-abundant, biotin depleted cultures, ROP induces the expression of a number of genes including that encoding PEPCK. Interestingly, a strain in which the gene encoding ROP is deleted (ΔROP) exhibits biotin-independent growth. Based on a number of studies, it was proposed that the ability of ΔROP to grow in the absence of biotin is due to the activation of a pyruvate carboxylase-independent pathway of oxaloacetate biosynthesis. It was also proposed that PEPCK, which normally functions as a gluconeogenic enzyme, may act as an anaplerotic enzyme involved in the synthesis of oxaloacetate. ROP was shown to be a key regulator of methanol metabolism when P. pastoris cells are cultured in YPM medium containing yeast extract, peptone and methanol but not YNBM medium containing yeast nitrogen base and methanol. In P. pastoris cells cultured in YPM, ROP functions as a transcriptional repressor of genes encoding key enzymes of the methanol metabolism such as the alcohol oxidase I. (AOXI). Deletion of the gene encoding ROP results in enhanced expression of AOXI and growth promotion while overexpression of ROP results in repression of AOXI and retardation of growth of P. pastoris cultured in YPM medium. Subcellular localization studies indicate that ROP translocates from cytosol to nucleus in cells cultured in YPM but not YNBM. To understand the mechanism of action of ROP, we examined its DNA-binding specificity. The DNA-binding domain of ROP shares 57% amino acid identity with that of Mxr1p, a master regulator of genes of methanol metabolism. We demonstrate that the DNA-binding specificity of ROP is similar to that of Mxr1p and both proteins compete with each other for binding to AOXI promoter sequences. Thus, transcriptional interference due to competition between Mxr1p and ROP for binding to the same promoter sequences is likely to be the mechanism by which ROP represses AOXI expression in vivo. Mxr1p and ROP are examples of transcription factors which exhibit the same DNA-binding specificity but regulate gene expression in an antagonistic fashion.