Thesis (Ph.D. in Molecular Biology) -- University of Colorado at Denver and Health Sciences Center, 2005. / Typescript. Includes bibliographical references (leaves 130-152). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

Deformed epidermal autoregulatory factor 1 (DEAF1) is a transcription factor that binds to (T/C)TCG(G/T) half-sites and has been shown to be involved in human diseases of cancer, diabetes, depression and intellectual disorders. We used chromatin immunoprecipitation assays to assess endogenous levels of DEAF1 and RNA polymerase II occupancy on the promoter and 5'UTR of the DEAF1 gene. In exponentially growing HEK293 cells, low levels of DEAF1 bind to sequences between -718 and +232, with +1 marking the start of translation. Within 0.5 hr of treating the cells with 500 µM H2O2, DEAF1 occupancy is increased between 7-18 fold at B (-718/-569), -577/-444, C (-432/-299), D (-205/-112) and E(-97/17). There were no statistically significant changes in either RNA polymerase II phospho-serine 5 (RNA PolII pS5) or RNA polymerase II phospho-serine 2 (RNA PolII pS2) binding with H2O2 treatment compared to control. With media change, there is an increase in RNA PolII pS2 and pS5 occupancy at both a distal site -1462/-1326 and in the coding region at 133/232, while no significant change in DEAF1 occupancy was detected. DEAF1 occupancy at the DEAF1 promoter and 5'UTR are inversely correlated with RNA polymerase II occupancy, however, there were no measurable differences in DEAF1 RNA levels at 0.5 hr and 1 hr time points. In summary, these data indicate that there is increased occupancy of DEAF1 at its own promoter following stress, which inversely affects occupancy of RNA polymerase at proximal promoter and 5'UTR sites of the DEAF1 gene.

Microsatellite repeats are a phenomenon found in DNA where a short sequence, usually 1-6bps, is repeated dozens to hundreds of times. Microsatellite repeats that are able to be transcribed are termed expanded tandem repeat-containing RNA (xtrRNA) [1]. xtrRNA have been associated with many diseases, such as Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD), which are both caused by a repeat in the C9ORF72 gene. Recent research has been focused on trying to provide treatments for patients with these diseases. This study focuses on creating a drug screening process for therapeutics targeting transcription by stopping or slowing the transcription of C9ORF72 repeat expansions. One project has focused on interrupting the interaction of two transcription factors, SUPT5H and SUPT4H1, to slow transcription. Another project has focused on slowing transcription by using transcriptional inhibitors or nucleoside analogs at low concentrations. Our hypothesis is that if transcription rates are slowed enough, pausing or arrest of RNA polymerase will be induced at complex sequences, including GC-rich regions and repeats. This should reduce synthesis of xtrRNA and provide a starting point for therapeutic development.

Indiana University-Purdue University Indianapolis (IUPUI) / Ssu72, an RNA Pol II CTD phosphatase that is conserved across eukaryotes, has been reported to have a wide array of genetic and physical associations with transcription factors and complexes in RNA transcription. Catalytic mutants of Ssu72 are lethal across many eukaryotes, and mutations to non-catalytic sites in SSU72 phosphatase have been shown to lower function. One spontaneous mutation of the SSU72 gene in Saccharomyces cerevisiae (A to C nucleotide mutation resulting in an L84F mutation in the coded protein) was shown to have transcription termination deficiency (termination override or TOV). This SSU72 mutation was suggested by Loya et al. to cause a lowering of the phosphatase activity of the protein and consequently affect proper termination. In research reported herein, an investigation was completed through in-vitro and ex-vivo approaches with the goal of understanding the impact of the SSU72 TOV mutation on the observed phenotype in S. cerevisiae. It can be concluded from work presented in this report that the SSU72 TOV mutation does not cause a decrease in in-vitro phosphatase activity as compared to wild type. Evidence presented even suggests an increase in phosphatase activity as compared to wild type Ssu72. One model for the observed responses in transcription termination is that the phenylalanine substitution in Ssu72 leads to cooperative interactions with proline residues in the CTD. It is proposed that the corresponding increase in Ssu72 phosphatase activity limits RNA Pol II CTD association with termination factors, such as Nrd1, thus causing deficient transcription termination.

京都大学 / 0048 / 新制・論文博士 / 博士(医科学) / 乙第13169号 / 論医科博第4号 / 新制||医科||6(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 萩原 正敏, 教授 近藤 玄, 教授 高田 穣 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

La synthèse d’ARN au cours de la différenciation des ovocytes est essentielle à la fécondation et à l'initiation du développement précoce. La nature de la machinerie basale de transcription pendant la croissance ovocytaire n'est pas connue mais la protéine TBP est remplacée par une protéine semblable spécifique des vertébrés, TBP2. Pour comprendre le rôle de TBP2 dans l'initiation de la transcription, nous avons effectué un RNA-seq à partir d'ovocytes contrôles et Tbp2-/- et montré que l'expression des gènes les plus transcrits ainsi celle des éléments rétroviraux endogènes de type MaLR est diminuée. Par immunoprécipitation couplée à la spectrométrie de masse à partir d'ovaires, nous avons montré que TBP2 ne forme pas un complexe TFIID, mais est associé à TFIIA dans les ovocytes. Globalement nos données montrent qu’une machinerie d'initiation de la transcription spécifique différente du complexe canonique TFIID contrôle la transcription dans les ovocytes de souris. / Mammalian oocytes go through consecutive differentiation process, during which the synthesis and accumulation of RNAs are essential for oocyte growth, maturation, fertilization and early embryogenesis. Little is known about the nature and function of the oocyte Pol II transcription machinery. During oocyte growth TBP is replaced by a vertebrate specific paralog, TBP2, and Tbp2-/- females are sterile. To understand whether and how TBP2 is controlling transcription initiation during oogenesis, we carried out RNA-seq analyses from wild-type and Tbp2-/- oocytes from primary and secondary follicles. These analyses show a main decrease in the expression of the most abundant genes as well as specific down-regulation of the expression of the MaLR-type endogenous retroviral elements. To identify the nature of the complex associated with TBP2 in the oocytes, we carried out immunoprecipitation followed by mass spectrometry. We demonstrate that, in the oocytes, TBP2 associates with TFIIA, but does not assemble into a TFIID-type complex. Altogether, our data show that a specific TBP2-TFIIA-containing transcription machinery, different from canonical TFIID, drives transcription in mouse oocytes.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2009. / Härtill 4 uppsatser.

Enhancer regulieren die Transkription ihrer Zielgene und deren Expression. Sie bieten eine Bindestelle für verschiedenste Transkriptionsfaktoren (TF) und RNA Polymerase II (RNAPII) und unterstützen die Gentranskription durch das Zustandekommen von Chromatinkontakten. Zusätzlich transkribiert RNAPII in Enhancer-Regionen kurze, non-polyadenylierte Transkripte, die man Enhancer-RNA (eRNA) nennt. Der Mechanismus der RNAPII-Rekrutierung und –Regulation an Enhancern ist bisher wenig verstanden, insbesondere wie das Vorhandensein von RNAPII-Modifikationen den Chromatinstatus, -faltung sowie die Genaktivierung beeinflusst. In dieser Arbeit wurden verschiedene Ansätze der Enhancer-Bestimmung miteinander verglichen. Während eine klare Bestimmung des besten Ansatzes sich als komplex erwies, konnte gezeigt werden, dass die Bindung von RNAPII an regulatorische Regionen in Zusammenhang mit TF eine universelle Konstante darstellte. Weiterhin wurden der Status der Enhancer-gekoppelten RNAPII-Aktivierung und deren Transkriptionsaktivität untersucht. Als Hauptergebnis ergab sich, dass der RNAPII-Status mit der Enhancer-Aktivität und daraus folgend mit veränderter Transkriptionsaktivität korreliert ist. Weiterhin konnte gezeigt werden, dass das Vorhandensein extragenischer RNAPII ein neues Werkzeug zur Identifikation von regulatorischen Regionen ist. Erfolgreich konnten regulatorische Regionen in embryonalen Stammzellen der Maus sowie während der neuronalen Differenzierung vorhergesagt und mittels Enhancer-Aktivität in-vivo bestätigt werden. Dabei zeigte sich, dass im Laufe der der neuronalen Differenzierung extragenische RNAPII-Bindung spezifische Aktivierungsmuster aufweist: ihr Transkriptionslevel wird durch Kinasen feinmaschig reguliert und es werden verschiedene Formen maturierter RNA erzeugt. Zusammenfassend konnte RNAPII als Werkzeug zur Identifikation und Charakterisierung regulatorischer Regionen in verschiedenen Zelltypen ausgemacht werden. Selbst mit minimalen RNAPII-Datensätzen ist es möglich, gleichzeitig regulatorische Regionen zu identifizieren als auch ihren eigenen Aktivierungsstatus sowie den ihrer kodierender Genpromotoren zu bestimmen. / Enhancers regulate transcription of target genes and gene expression. They act as recruitment sites for multiple transcription factors (TFs) and RNA polymerase II (RNAPII) and favour transcription of target genes through chromatin contacts. RNAPII at enhancer regions transcribes short and mostly non-polyadenylated transcripts, called enhancer RNAs (eRNAs). The mechanisms of RNAPII recruitment and regulation at enhancers remain ill understood, in particular how signalling through RNAPII modifications may influence chromatin states, looping and gene activation. In this study, I compare enhancer lists defined with different approaches and find that their relation is very complex. However, I find that RNAPII binding co-occurs with TF binding at regulatory regions, independently of the identification approach used. I characterize the state of RNAPII activation at enhancers and its transcriptional activity. I find that RNAPII state reflects enhancer activation state and correlates with different transcriptional outputs. In addition, I demonstrate that extragenic RNAPII is a novel tool to identify regulatory regions. I successfully identified putative regulatory regions in mESC and during neuronal differentiation, with enhancer activity in vivo. Extragenic RNAPII regions have specific activation patterns during neuronal differentiation, are finely regulated at the transcriptional level by kinases and transcribe differently mature RNAs. In conclusion, I establish RNAPII as a tool to identify and characterise regulatory regions in a cell type of interest. With minimal RNAPII datasets it is possible to simultaneously identify regulatory regions, infer their state of activation, and the state of activation of coding gene promoters.

Transcription termination of RNA polymerase II (Pol II) in mammals requires a functional poly(A) signal and either downstream pause sites or co-transcriptional cleavage (CoTC) sequences together with 3’transcript degradation by the nuclear 5’-3’ exonuclease Xrn2. However the molecular mechanism of pause-dependent transcriptional termination is not yet fully understood. This thesis investigates the molecular role of R-loop structures in pause-dependent transcriptional termination of mammalian genes. The results described in Chapters 3 and 4 indicate that nascent transcripts form RNA/DNA hybrid structures (R-loops) behind elongating Pol II and are especially prevalent over G-rich pause sites positioned downstream of gene poly(A) signals. Senataxin, a helicase protein and the human homologue of the yeast Sen1, acts to resolve these R-loop structures and by so doing allows access of Xrn2 at 3’ cleavage poly(A) sites. This ultimately leads to efficient Pol II termination. In effect R-loops formed over G-rich pause sites, followed by their resolution by senataxin, are required for efficient pause-dependent transcriptional termination. In addition to this, the 3’ end processing factor, Pcf11 is also involved in this process. Experiments presented in the final part of this study reveal a link between R-loops and RNAi-dependent H3K9me2 formation over G-rich termination regions. Overall my results suggest that R-loop structures and the H3K9me2 repressive mark over pause regions are important features of Pol II pause-dependent transcriptional termination of mammalian genes.