La plus grosse sous-unité (Rpb1) de l'ARN polymérase II est caractérisée par une structure unique et flexible au niveau du domaine C-terminal (CTD) qui consiste en une répétition en tandem d'une séquence consensus heptapeptidique Y1-S2-P3-T4-S5-P6-S7. Le CTD est essentiel pour pour la viabilité cellulaire et est requis pour d'importantes activités associées avec la transcription par l'ARN Pol II, dont la régulation de la synthèse de l'ARN et des événements de maturation co-transcriptionnels (mise en place de la coiffe 5', épissage, terminaison en 3'... etc). Forts d'un système permettant l'expression conditionnelle de mutants du CTD, nous disséquons le CTD afin de comprendre l'implication de résidus/répétitions spécifiques sur la transcription dans des cellules mammifères. Nos résultats montrent que le CTD est crucial pour le contrôle de la transcription pervasive et indiquent une implication inédite des complexes Mediateur et Integrateur dans le processus de terminaison de la transcription. / The largest subunit (Rpb1) of RNA polymerase II has a unique and flexible structure at its C-terminal domain (CTD) that consists of tandem repeats with the consensus heptad sequence Y1-S2-P3-T4-S5-P6-S7. The CTD is essential for cellular viability and is required for important activities associated with RNA pol II transcription, including the regulation of RNA synthesis and co-transcriptional processing events (5’ capping, splicing, 3’ termination…etc). Using a conditional CTD mutant expression system, we dissect the importance of specific residues/repeats on transcription in mammalian cells. Our results indicate the importance of the CTD in the control of pervasive transcription and hints to novel roles of the Mediator and Integrator complexes in transcription termination processes.

RNA polymerase II (Pol II) is responsible for the transcription of all protein-coding and some non-coding genes in eukaryotes. Its largest subunit, Rpb1, contains a unique C-terminal domain (CTD) which consists of repeats of the heptad YSPTSPS. It acts as a binding platform for proteins that control the different stages of transcription and their recruitment is regulated mainly by differential phosphorylation of residues contained within the CTD. Previous studies could unveil proteins containing a CTD-interacting domain (CID) as important players that specifically bind to certain phosphorylation types of the CTD. More precisely, they were shown to be important for the last step of transcription, termination. Despite extensive research over the past 30 years, the exact mechanism of how these proteins facilitate the dislodgement of Pol II from the DNA template, still remains unknown. The work presented here contains detailed studies of the CID-containing protein Seb1 from the fission yeast Schizosaccharomyces pombe, revealing an unexpectedly broad role of this protein in transcription termination. In addition to a CID, Seb1 also contains an RNA recognition motif (RRM) which allows direct binding to RNA. Here, I present high-resolution crystal structures of both domains of Seb1. While the CID has a very conserved fold, the RNA binding regions contains an unusual arrangement of a canonical RRM intertwined with a second domain that are both important for RNA binding. Structure-based mutations were introduced and a combination of in vitro and genome-wide in vivo studies uncover Seb1 as an essential player in transcription termination. Importantly, both domains are required to promote the full function of Seb1. Despite its homology to the well-studied budding yeast protein Nrd1, the role of Seb1 in fission yeast is quite different. This thesis therefore provides important insight into the mechanisms that underlie eukaryotic transcription termination.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / RNA Polymerase II (Pol II) is the primary actor in the transcription of mRNA from genes. Pol II is a complex composed of twelve protein subunits. This study focused on the changes in the interactome of Rbp3 in S. cerevisiae when the Pol II subunit Rpb9 is removed. Rpb3 is one of the core subunits of Pol II, and any significant changes to the Rpb3 incteractome due to the loss of Rpb9 can be used to infer new information about Rpb9’s role in the Pol II complex. Rpb3 was pulled down using FLAG purification from both wild type and rpb9Δ S. cerevisiae cultures. Rpb3 and the proteins complexed with it were then analyzed using multi-dimensional protein identification technology (MudPIT), a form of liquid chromatography-mass spectrometry (LC-MS). This data was searched using the SEQUEST database search algorithm, and the results were further analyzed for likelihood of interaction using Significance Analysis of INTeractome (SAINT), as well as for post-translational phosphorylation. Deletion of rpb9 did not present any changes in Pol II phosphorylation however it did cause several changes in the interaction network. The rpb9Δ strain showed new interactions with Rtr1, Sen1, Vtc4, Pyc1, Tgl4, Sec61, Tfb2, Hfd1, Erv25, Rib4, Sla1, Ubp15, Bbc1, and Hxk1. The most prominent of these hits are Rtr1, an Rpb1 C-terminal domain phosphatase linked to transcription termination, and Sen1, an RNA/DNA nuclease that terminates transcription. In addition, this mutant showed no interaction with Mtd1, an interaction that is present in the wild type. In all cases, these hits should be considered fuel for future research, rather than conclusive evidence of novel interactions.

Transcription is a fundamental process catalyzed by DNA-dependent RNA polymerases (DdRPs). Interestingly, some DdRPs can use both DNA and RNA as templates for transcription. This RNA-dependent RNA polymerase (RdRP) activity of DdRPs is used by RNA-based pathogens such as viroids and hepatitis delta virus for replication. In addition, RdRP activity of DdRPs widely occurs in various organisms to regulate gene transcription. Despite the importance of this intrinsic RdRP activity of DdRPs, associated factors and mechanisms are in their infancy stage. We employed potato spindle tuber viroid (PSTVd) as a model to study RNA-templated transcription. Here, we present evidence showing that circular PSTVd templates are critical for the synthesis of longer-than-unit-length (-) strand products. Further, we show transcription factor IIS is dispensable for PSTVd replication supporting de novo transcription on PSTVd RNA templates. The absence of canonical general transcription factor, TFIIS from PSTVd-templated transcription complex led to the hypothesis that RNA-templated transcription has a distinct organization on the RNA template. To test this hypothesis, we used our well-established in vitro transcription (IVT) system and demonstrated that RNA polymerase II (Pol II) accepts minus-strand for transcription. In addition, transcription factor TFIIIA-7ZF is needed to aid Pol II transcription activity. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed that the first three zinc finger domains are pivotal for template binding. Notably, we identified a remodeled Pol II complex for viroid transcription that is missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9. General transcription factors for DNA-templated transcription are also absent in the transcription complex on the RNA template. This remodeled Pol II complex still possesses the transcription activity on PSTVd RNA template. Collectively, our data illustrate a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.

Les protéines Hox sont des facteurs de transcription à homéodomaine, dont les propriétés de liaison à l’ADN contrastent avec leur spécificité fonctionnelle in vivo. Ils interagissent avec les cofacteurs PBC (Extradenticle (Exd) chez la drosophile) formant des complexes multimériques dont la spécificité fonctionnelle est accrue. Cette interaction repose sur le motif l’hexapeptide (HX), conservé dans la plupart des protéines Hox. Récemment, nous avons identifié le domaine UbdA (UA), spécifique aux protéines Hox de classe centrale Ultrabithorax (Ubx) et AbdominalA (Abd-A), comme un nouveau motif d'interaction avec la protéine Exd. Des analyses in vivo de la contribution de l’HX et de UbdA dans l’activité des protéines Ubx et Abd-A ont indiqué que les protéines Ubx et Abd-A partagent des fonctions (Exd dépendantes et indépendantes), qui ne sont pas médiées par une utilisation identique des motifs protéiques HX et UA.L’objectif de ces travaux est d’analyser les mécanismes moléculaires qui sous-tendent une utilisation ciblée/sélective des motifs protéiques HX et UA de Ubx et de Abd-A en absence du cofacteur connu Exd. Pour cela, des lignées cellulaires S2 DRSC exprimant les protéines Ubx sauvages et mutantes sur les motifs HX et UA, ont été générées et analysées par des expériences de ChIP-Seq. Nos données comparées à celles obtenues précédemment dans l’équipe pour la protéine Abd-A posent les bases permettant d’appréhender la contribution fonctionnelle et l’utilisation sélective des motifs protéiques HX et UA, au-delà de leurs fonctions dans la médiation de l'interaction avec le cofacteur Exd. / Hox proteins are homeodomain-containing transcription factors, whose poor DNA-binding properties contrast with their functional specificity in vivo. They interact with PBC cofactors (Extradenticle (Exd) in Drosophila), forming multimeric complexes with increased functional specificity. This interaction involve a conserved motif called the hexapeptide (HX), found in most Hox proteins. Recently, we the UbdA domain (UA), specific to the central class Hox proteins Ultrabithorax (Ubx) and Abdominal-A (Abd-A), as a novel interaction motif with the Exd protein. In vivo analysis of the HX and UA contributions to Ubx and Abd-A protein activity indicated Ubx and Abd-A shared functions (Exd dependent or independent) do not necessarily rely on a similar use of the HX or UA protein motifs. The aim of this work was to investigate the molecular mechanisms underlying the targeted/selective use of the HX and UA protein motifs in Ubx and Abd-A in the absence of the usual Hox Exd cofactor. For this, S2 DSRC cell lines stably expressing the Ubx protein, as well as HX or UA variants have been generated and analysed by ChiP-Seq experiments. Our data, compared to those previously obtained for Abd-A in the laboratory, set bases for apprehending the functional contribution and selective use of the HX and UA protein motifs, outside their established function in mediating interaction with the Exd cofactor.

In humans, RNA polymerase II is the sole source of messenger RNAs that are ultimately translated into proteins and its transcriptional activity is highly regulated. Mechanisms have evolved to control which, when, and to what degree genes are transcribed. Because most cells have the same genome, control of transcription is essential in maintaining cellular identity. Misregulation of Pol II transcription is a hallmark of both cancer and retroviral infection. This research investigates the regulation of Pol II transcription and related co-transcriptional mRNA capping. Chromatin immunoprecipitation experiments were used to characterize the composition of nucleosomes and Pol II, DSIF and NELF occupancies at bidirectional promoters and enhancers. In collaboration with Alberto Bosque and Vicente Planelles, sequencing experiments were performed in a primary T cell model of HIV latency and a role for sequence-specific recruitment of STAT5 was established in HIV reactivation. In contrast, analysis of Myc binding in vitro and in cells demonstrated that transcription machinery played a major role in recruiting Myc to genomic sites. A precise method was also developed to detect polymerase-associated nascent transcripts in nuclei. The roles of Cdk7, a subunit of TFIIH that phosphorylates Pol II during initiation, were characterized by treatment of nuclear extracts and cells with THZ1, a recently developed covalent inhibitor with anti-cancer properties. Inhibition of Cdk7 was demonstrated to cause defects in Pol II phosphorylation, co-transcriptional capping, promoter proximal pausing, and productive elongation. Capping of nascent RNAs was found to be spatially and temporally regulated in part by a previously undescribed THZ1-sensitive factor present in nuclear extract. THZ1 impacted pausing through a capping-independent block of DSIF and NELF loading. The P-TEFb-dependent transition into productive elongation was also inhibited by THZ1, likely due to misloading of DSIF. In vitro and sequencing methods were used to describe an extremely rapid and global transcriptional response to hydrogen peroxide. During periods of oxidative stress, termination was likely inhibited and Pol II accumulated at promoters and enhancers after as few as two minutes, and clearance of these polymerases required P-TEFb. In the presence of flavopiridol, a potent P-TEFb inhibitor, non-productive elongation was observed and a potential role for P-TEFb in termination was proposed.

<p>The yeast Mediator complex is required for transcriptional regulation both in vivo and in vitro and the identification of similar complexes from metazoans indicates that its function is conserved through evolution. Mediator subunit composition and structure is well characterized both by biochemical, genetic and biophysical methods. In contrast, little is known about the mechanisms by which Mediator operates and how the complex is regulated. The aim of my thesis was to elucidate how Mediator functions at the molecular level and to investigate functional interactions within Mediator. </p><p> It is possible to recruit RNA polymerase II to a target promoter and thus to activate transcription by fusing Mediator subunits to a DNA binding domain. In order to investigate functional interactions within Mediator, we made such fusion proteins where different Mediator subunits were fused to the DNA binding domain of lexA. The expression of a reporter gene containing binding sites for lexA was subsequently measured in both a wild type strain and in strains where genes encoding specific Mediator subunits had been disrupted. We found that lexA-Med2 and lexA-Gal11 are strong activators that function independently of all Mediator subunits tested. On the other hand, lexA-Srb10 is a weak activator that depends on Srb8 and Srb11 and lexA-Med1 and lexA-Srb7 are both cryptic activators that become active in the absence of Srb8, Srb10, Srb11, or Sin4. Both lexA-Med1 and lexA-Srb7 proteins showed a stable association with the Mediator subunits Med4 and Med8 in wild type cells and in all deletion strains tested, indicating that they were functionally incorporated into the Mediator complex. We also showed that both Med4 and Med8 exist in two forms that differed in electrophoretic mobility and that these forms differed in their ability to associate with Mediator immuno-purified from the LEXA-SRB7 and LEXA-MED1 strains. Dephosphorylation assays of purified Mediator indicated that the two mobility forms of Med4 corresponded to the phosphorylated and unphosphorylated forms of the Med4 protein respectively. </p><p> Some of the data presented in this study as well as previous genetic and biochemical data obtained in our lab suggested a functional link between the Med1, Med2, Srb10 and Srb11 proteins. We extended these findings by showing that the Srb10 kinase phosphorylates the Med2 protein at residue serine 208, both in vitro and in vivo. We also showed that a point mutation of the single phosphorylation site to an alanine or to an aspartic acid residue altered the gene expression of a specific set of genes. Taken together, these data indicate that posttranslational modification of Mediator subunits is a so far uncharacterized mechanism for regulation of gene expression. </p><p> In order to study the function of the Srb7 subunit of Mediator, we isolated a temperature sensitive strain where the amino acids 2 to 8 of srb7 were deleted. The Mediator subunits Nut2 and Med7 were isolated as high copy suppressor of srb7-∆(2-8) and we were also able to show that Srb7 interacted with Nut2 and Med7 both in a 2-hybrid system and in co-immuno precipitation experiments using recombinantly expressed proteins. Interestingly, a deletion of amino acids 2 to 8 of Srb7 abolishes its interaction with both Med7 and Nut2 in vitro. Med4 also interacted with Srb7 in the 2-hybrid system and surprisingly, the first eight amino acids of Srb7 were shown to be sufficient for this interaction.</p>

The yeast Mediator complex is required for transcriptional regulation both in vivo and in vitro and the identification of similar complexes from metazoans indicates that its function is conserved through evolution. Mediator subunit composition and structure is well characterized both by biochemical, genetic and biophysical methods. In contrast, little is known about the mechanisms by which Mediator operates and how the complex is regulated. The aim of my thesis was to elucidate how Mediator functions at the molecular level and to investigate functional interactions within Mediator. It is possible to recruit RNA polymerase II to a target promoter and thus to activate transcription by fusing Mediator subunits to a DNA binding domain. In order to investigate functional interactions within Mediator, we made such fusion proteins where different Mediator subunits were fused to the DNA binding domain of lexA. The expression of a reporter gene containing binding sites for lexA was subsequently measured in both a wild type strain and in strains where genes encoding specific Mediator subunits had been disrupted. We found that lexA-Med2 and lexA-Gal11 are strong activators that function independently of all Mediator subunits tested. On the other hand, lexA-Srb10 is a weak activator that depends on Srb8 and Srb11 and lexA-Med1 and lexA-Srb7 are both cryptic activators that become active in the absence of Srb8, Srb10, Srb11, or Sin4. Both lexA-Med1 and lexA-Srb7 proteins showed a stable association with the Mediator subunits Med4 and Med8 in wild type cells and in all deletion strains tested, indicating that they were functionally incorporated into the Mediator complex. We also showed that both Med4 and Med8 exist in two forms that differed in electrophoretic mobility and that these forms differed in their ability to associate with Mediator immuno-purified from the LEXA-SRB7 and LEXA-MED1 strains. Dephosphorylation assays of purified Mediator indicated that the two mobility forms of Med4 corresponded to the phosphorylated and unphosphorylated forms of the Med4 protein respectively. Some of the data presented in this study as well as previous genetic and biochemical data obtained in our lab suggested a functional link between the Med1, Med2, Srb10 and Srb11 proteins. We extended these findings by showing that the Srb10 kinase phosphorylates the Med2 protein at residue serine 208, both in vitro and in vivo. We also showed that a point mutation of the single phosphorylation site to an alanine or to an aspartic acid residue altered the gene expression of a specific set of genes. Taken together, these data indicate that posttranslational modification of Mediator subunits is a so far uncharacterized mechanism for regulation of gene expression. In order to study the function of the Srb7 subunit of Mediator, we isolated a temperature sensitive strain where the amino acids 2 to 8 of srb7 were deleted. The Mediator subunits Nut2 and Med7 were isolated as high copy suppressor of srb7-∆(2-8) and we were also able to show that Srb7 interacted with Nut2 and Med7 both in a 2-hybrid system and in co-immuno precipitation experiments using recombinantly expressed proteins. Interestingly, a deletion of amino acids 2 to 8 of Srb7 abolishes its interaction with both Med7 and Nut2 in vitro. Med4 also interacted with Srb7 in the 2-hybrid system and surprisingly, the first eight amino acids of Srb7 were shown to be sufficient for this interaction.

Le cancer du sein est la principale cause de mortalité par cancer chez la femme. Deux des facteurs de transcription de la famille Fos, Fra-1 et Fra-2, sont surexprimés dans les cancers du sein agressifs et contribuent au phénotype tumoral en favorisant entre autres, la prolifération, la motilité et l'invasivité. De façon surprenante, les mécanismes moléculaires via lesquels Fra-1 et Fra-2 (et plus généralement le complexe transcriptionnel AP-1 dont ils sont des constituants) gouvernent la transcription de leurs gènes cibles sont quasi-inconnus. Dans ce contexte, en combinant diverses approches (immunoprécipitation de chromatine, interférence à l'ARN…), j'ai étudié les mécanismes moléculaires par lesquels Fra-1 et Fra-2 contrôlent la transcription dérégulée du gène de l'urokinase ou uPA (sérine protéase cruciale dans la progression tumorale et l'établissement de métastases) qui est l'un des nouveaux marqueurs utilisés en clinique pour la mise en place des choix thérapeutiques. Mes travaux montrent de façon originale que (i) Fra-1 et Fra-2 agissent de façon non redondante et coopèrent pour réguler l'expression d'uPA via leur fixation sur un enhancer AP-1 localisé à -1,9 kb du site d'initiation de la transcription (TSS), (ii) Fra-2 est nécessaire au recrutement de RNA Pol II au niveau de l'enhancer, tandis que Fra-1 stimule le passage de RNA Pol II de sa forme initiatrice à sa forme élongatrice et (iii) que la polymérase recrutée à l'enhancer rejoint le TSS par un mécanisme de « tracking », très rarement décrit dans la littérature, en produisant de petits ARNs non codants, bidirectionnels et instables. / Breast cancer is the most frequent malignant disease among women. Two transcription factors, Fra-1 and Fra-2, belonging to the Fos family members, are overexpressed in aggressive breast cancers and contribute to the tumorigenic phenotype by favoring proliferation, motility and invasion. Surprisingly, the molecular mechanisms governed by Fra-1 and Fra-2 (and more generally by the AP-1 transcriptional complex, which they are components of) for the transcription of their target genes are still largely unknown. In this context, by combining different approaches (chromatin immunoprecipitation, RNA interference…), I studied the molecular mechanisms orchestrated by Fra-1 and Fra-2 for the expression of the urokinase (or uPA) gene (encoding a serine protease crucial for tumor progression and metastasis), which is one of the new diagnostic markers now taken into consideration for deciding therapeutic strategies. Interestingly, my results show that (i) Fra-1 and Fra-2 have non redundant functions and cooperate for the transcriptional regulation of uPA through their binding to AP-1 enhancer located 1.9 kb upstream of the transcriptional start site (TSS), (ii) Fra-2 is required for the recruitment of RNA Pol II on this enhancer while Fra-1 allows the conversion of RNA Pol II initiating form into its elongating form and (iii) enhancer-recruited RNA Pol II reaches the TSS by a tracking mechanism, mechanism very rarely described in the literature, during which it synthetizes small, unstable bidirectional, non coding RNAs.