Flavopridol (FVP) is a well known pharmacological inhibitor of Cyclin Dependent Kinases (CDKs), with significant selectivity for Cyclin Dependent Kinase 9 (CDK9). Treatment of cells with FVP results in inhibition of transcription elongation. CDK9 is a serine/threonine kinase that associates with T-type cyclins. These complexes are designated transcription elongation factors (P-TEFb). P-TEFb controls transcription elongation by phosphorylating the carboxyl terminal domain (CTD) of RNA polymerase II (RNAPII) and negative elongation factors. Whether P-TEFb is required for the elongation of most genes transcribed by RNAPII or fraction of them is still debatable. The aim of my Thesis is to understand the early and late effects of FVP on primary response gene expression. Two different microarray analyses with RNA probes obtained from T98G and BJ-TERT cells were performed by Drs. Graña and Garriga to determine the effect of inhibiting CDK9 on global mRNA expression using a dominant negative mutant of CDK9 (dnCDK9) and FVP. These gene profiling experiments showed that FVP and dnCDK9 downregulate the expression of several genes. However, these studies also showed upregulation of a group of primary response genes (PRGs). The goal of this thesis was to bring some light into this unexpected phenomenon. I have found that several PRGs including FOS, JUNB, EGR1 and GADD45B, are rapidly and potently downregulated before they are upregulated upon FVP treatment in exponentially growing cells. In serum starved cells restimulated with serum, FVP also inhibits the expression of these genes, but subsequently, JUNB, GADD45B and EGR1 are upregulated in the presence of FVP. Chromatin Immunoprecipitation of RNAPII revealed that EGR1 and GADD45B are apparently transcribed at the FVP-treatment time points where their corresponding mRNAs accumulate. These results suggest a possible stress response triggered by CDK9 inhibition. I also show that serum starvation does not affect the localization of RNAPII immediately downstream of the promoter of a PRG where RNAPII remains paused in the absence of mitogenic stimulation, suggesting that initiation is not rate limiting for transcription of at least certain PRGs in the absence of mitogens and remains dependent on transcription elongation. In sum, I have shown that certain PRG/IRGs are transcribed in the presence of FVP and their transcription might be independent of CDK9 suggesting a possible alternative mechanism of their transcription. I also determined that transcription initiation is not affected by serum starvation, as paused RNAPII appears to remain bound downstream of a PRG promoter in quiescent cells independently of the length of mitogenic starvation. / Molecular Biology and Genetics

As CDKs 9 e 11 fazem parte da subfamília de CDKs transcricionais, e portanto desempenham papéis de controle na dinâmica atividade de síntese e processamento do RNA mensageiro pela RNA Polimerase II. Devido à sua capacidade de modular individualmente a atividade dos complexos de transcrição da RNAP II, estas quinases assumem uma grande importância para a regulação da expressão gênica em células eucarióticas. Casos de desregulação da atividade de CDKs transcricionais têm sido frequentemente relacionados a diversas patologias humanas graves, incluindo vários tipos de câncer e também a AIDS (em razão do papel essencial desempenhado pela CDK9 na replicação do HIV. O objetivo deste trabalho é a obtenção das CDKs humanas 9 e 11 através da expressão heteróloga em Escherichia coli, buscando o aperfeiçoamento de métodos para produzir estas enzimas em quantidade e pureza suficientes para aplicação em estudos estruturais. A utilização de um sistema bacteriano oferece muitas vantagens práticas, como a simplicidade da técnica, baixo custo, altos níveis de expressão, e elevado rendimento na purificação do produto. No entanto, a obtenção de quinases humanas ativas a partir de E. coli sempre representou um desafio experimental, devido aos problemas comumente associados à expressão heteróloga. Os resultados apresentados aqui demonstram a possibilidade de se obter a CDK9 humana enzimaticamente ativa pelo reenovelamento in vitro da proteína expressa pela bactéria na forma de corpos de inclusão, após etapas de solubilização e purificação em condições desnaturantes. Por outro lado, a CDK11 humana só pôde ser obtida em uma versão encurtada, consistindo apenas no seu domínio quinase, devido à forte inibição que um trecho N-terminal da sequência mostrou exercer sobre a expressão da proteína. Assim, este trabalho fornece exemplos de como é possível superar algumas das adversidades comuns da expressão heteróloga a fim de se obter CDKs humanas ativas empregando o sistema bacteriano. / CDK9 and CDK11 are members of the subfamily of transcriptional CDKs and therefore play central roles in the control of the dynamic activity of messenger RNA synthesis and processing by RNA polymerase II. Because of their ability to individually modulate the activity of RNAP II transcription complexes, these kinases are of great importance for the regulation of gene expression in eukaryotic cells. Several cases of deregulation of the transcriptional CDKs have been linked to important human diseases, including various types of cancer and also AIDS (due to the essential role of CDK9 in HIV replication). The objective of this work is to obtain human CDK9 and CDK11 heterologously expressed in Escherichia coli, seeking improved methods to produce these enzymes in quantity and purity suitable for structural studies. A bacterial system offers many practical advantages to protein production, such as technical simplicity, low costs, high levels of expression and high purification yield. However, it has always been an experimental challenge to obtain active human kinases from E. coli, because of the problems commonly associated with heterologous expression. The results presented here demonstrate the possibility of obtaining the enzymatically active human CDK9 by in vitro refolding of the protein expressed as bacterial inclusion bodies, after its solubilization and purification under denaturing conditions. Human CDK11, on the other hand, could only be obtained in a shortened form consisting just of its kinase domain, due to the strong inhibition that an N-terminal stretch exerts on the protein\'s own expression. Therefore, this work provides examples of how it is possible to overcome some of the common adversities of heterologous expression in order to obtain active human CDKs through the bacterial system.

The radiosensitivity of tumour cells depends mainly on their capacity to maintain genomic integrity. This requires efficient repair of radiation-induced DNA double strand breaks, a process governed by the cell cycle. Based on their functions in cell cycle regulation and DNA damage repair, we hypothesised that targeting of CDK2 and CDK9 modifies cancer cell response to radiotherapy. Therefore, we evaluated the significance of CDK2 and CDK9 for the cellular radiation response in a panel of human head and neck squamous cell carcinoma (HNSCC) cell lines. In order to achieve our goal, we performed a series of experiments to measure several key parameters such as clonogenic radiation survival, cell cycling, DNA damage repair and apoptosis. We found that loss of CDK2 radiosensitises mouse embryonic fibroblasts (MEFs) as well as HNSCC two dimensional (2D) cell cultures. However, under more physiological three dimensional (3D) growth conditions in laminin-rich extracellular matrix, targeting of CDK2 failed to modulate the radiosensitivity of HNSCC cells. Moreover, CDK2 attenuated the repair of radiogenic double strand breaks (DSBs) in MEFs as well as SAS and FaDu HNSCC cells indicating a possible role of CDK2 in DNA damage repair. However, we found that CDK2 is dispensable for cell cycle and checkpoint regulation in response to irradiation in SAS and FaDu cells. Taken together, our results suggest that targeting of CDK2 may not provide a therapeutic benefit to overcome HNSCC cell resistance to radiotherapy. We also showed that depletion of CDK9 clearly enhances the radiosensitivity of HNSCC cultures. In addition, the ectopic expression of CDK9 has a radioprotective effect. These findings suggest a potential role of CDK9 in the radiation response of HNSCC cells. Moreover, our study indicates a possible role of CDK9 in the DNA damage repair response and cell cycling of HNSCC cells. Conclusively, on the basis of these data, targeting of CDK9 in addition to conventional radiotherapy might be a viable strategy to overcome cancer cell resistance.

As CDKs 9 e 11 fazem parte da subfamília de CDKs transcricionais, e portanto desempenham papéis de controle na dinâmica atividade de síntese e processamento do RNA mensageiro pela RNA Polimerase II. Devido à sua capacidade de modular individualmente a atividade dos complexos de transcrição da RNAP II, estas quinases assumem uma grande importância para a regulação da expressão gênica em células eucarióticas. Casos de desregulação da atividade de CDKs transcricionais têm sido frequentemente relacionados a diversas patologias humanas graves, incluindo vários tipos de câncer e também a AIDS (em razão do papel essencial desempenhado pela CDK9 na replicação do HIV. O objetivo deste trabalho é a obtenção das CDKs humanas 9 e 11 através da expressão heteróloga em Escherichia coli, buscando o aperfeiçoamento de métodos para produzir estas enzimas em quantidade e pureza suficientes para aplicação em estudos estruturais. A utilização de um sistema bacteriano oferece muitas vantagens práticas, como a simplicidade da técnica, baixo custo, altos níveis de expressão, e elevado rendimento na purificação do produto. No entanto, a obtenção de quinases humanas ativas a partir de E. coli sempre representou um desafio experimental, devido aos problemas comumente associados à expressão heteróloga. Os resultados apresentados aqui demonstram a possibilidade de se obter a CDK9 humana enzimaticamente ativa pelo reenovelamento in vitro da proteína expressa pela bactéria na forma de corpos de inclusão, após etapas de solubilização e purificação em condições desnaturantes. Por outro lado, a CDK11 humana só pôde ser obtida em uma versão encurtada, consistindo apenas no seu domínio quinase, devido à forte inibição que um trecho N-terminal da sequência mostrou exercer sobre a expressão da proteína. Assim, este trabalho fornece exemplos de como é possível superar algumas das adversidades comuns da expressão heteróloga a fim de se obter CDKs humanas ativas empregando o sistema bacteriano. / CDK9 and CDK11 are members of the subfamily of transcriptional CDKs and therefore play central roles in the control of the dynamic activity of messenger RNA synthesis and processing by RNA polymerase II. Because of their ability to individually modulate the activity of RNAP II transcription complexes, these kinases are of great importance for the regulation of gene expression in eukaryotic cells. Several cases of deregulation of the transcriptional CDKs have been linked to important human diseases, including various types of cancer and also AIDS (due to the essential role of CDK9 in HIV replication). The objective of this work is to obtain human CDK9 and CDK11 heterologously expressed in Escherichia coli, seeking improved methods to produce these enzymes in quantity and purity suitable for structural studies. A bacterial system offers many practical advantages to protein production, such as technical simplicity, low costs, high levels of expression and high purification yield. However, it has always been an experimental challenge to obtain active human kinases from E. coli, because of the problems commonly associated with heterologous expression. The results presented here demonstrate the possibility of obtaining the enzymatically active human CDK9 by in vitro refolding of the protein expressed as bacterial inclusion bodies, after its solubilization and purification under denaturing conditions. Human CDK11, on the other hand, could only be obtained in a shortened form consisting just of its kinase domain, due to the strong inhibition that an N-terminal stretch exerts on the protein\'s own expression. Therefore, this work provides examples of how it is possible to overcome some of the common adversities of heterologous expression in order to obtain active human CDKs through the bacterial system.

Skeletal myogenesis is under the control of a combinatorial network of transcription factors. It has been shown that the homeobox protein Six1 is required for embryonic myogenesis. Using functional genomics approaches, I determined that Six1 is required for myoblasts differentiation through direct binding to a cluster of genes that are related to muscle function and muscle structure during my Master’s studies. However, it was still not fully understood how Six1 selects its genomic targets and whether Six1 regulates the expression of Myod directly. I devoted my PhD work to study three central aspects of Six1 function: through what DNA motif it binds to DNA, how it regulates the expression of the myogenic regulatory factor MyoD, and how it might regulate chromatin structure at the enhancer regions of muscle genes. A more degenerate MEF3-like DNA sequence consensus has been identified from Six1 ChIP-on-chip experiments. This MEF3 motif was further optimized using bioinformatic methods and was proved to discover Six1 binding sites with improved specificity and sensitivity. Myod, a member of myogenic regulatory factors (MRFs), is a master regulator in the myogenic lineage. Multiple MEF3 sites were identified on the regulatory regions of Myod, including two MEF3 sites within its core enhancer region (CER). Six1 was able to bind to the CER directly through these two MEF3 sites and regulated the Myod expression in cultured primary myoblasts. Previous work has suggested that the CER is also bound by Myod in myoblasts. I demonstrated that the binding of Myod to the CER depended on the presence of Six1. Six1 was also involved in maintaining a relatively ‘open’ chromatin structure at the CER, suggesting that Six1 may play a direct or indirect role in chromatin remodeling. During my Master’s studies, I demonstrated a synergistic regulation by the Six and MRF families. This synergistic function gains potential importance by the fact that ~25% of Six1 genomic targets are also bound by Myod. I decided to study whether the co-occupancy of Six1 and Myod was essential to maintain the proper global chromatin structure at these loci. Six1 and Myod co-bound genomic regions correlated with more accessible chromatin, which was detected by the formaldehyde-assisted isolation of regulatory elements (FAIRE) assay followed by DNA deep sequencing (FAIRE-seq). When combined with small interfering RNA-mediated gene knockdown of Six1 or Myod, FAIRE-seq data suggested that Six1, but not Myod, was involved in regulating the chromatin accessibility at these co-bound DNA loci. To shed light on the mechanism by which Six1 functions, proteomics approaches were used and revealed that proteins involved in “regulation of transcription” and “chromatin organization” were enriched among Six1-bound proteins. Cdk9 and its partner cyclin T have been shown to stimulate gene expression by releasing RNA polymerase II from transcriptional pause, but they can also function at gene enhancers. I determined that Six1 and Cdk9 participated in the same protein complex, and that the Cdk9 activity appeared to mediate the effect of Six1 on the chromatin accessibility at the CER to regulate the Myod expression. Taken together, these results demonstrate that Six1 regulates the expression of Myod through its direct binding on the CER which facilitates transcriptional elongation.

The radiosensitivity of tumour cells depends mainly on their capacity to maintain genomic integrity. This requires efficient repair of radiation-induced DNA double strand breaks, a process governed by the cell cycle. Based on their functions in cell cycle regulation and DNA damage repair, we hypothesised that targeting of CDK2 and CDK9 modifies cancer cell response to radiotherapy. Therefore, we evaluated the significance of CDK2 and CDK9 for the cellular radiation response in a panel of human head and neck squamous cell carcinoma (HNSCC) cell lines. In order to achieve our goal, we performed a series of experiments to measure several key parameters such as clonogenic radiation survival, cell cycling, DNA damage repair and apoptosis. We found that loss of CDK2 radiosensitises mouse embryonic fibroblasts (MEFs) as well as HNSCC two dimensional (2D) cell cultures. However, under more physiological three dimensional (3D) growth conditions in laminin-rich extracellular matrix, targeting of CDK2 failed to modulate the radiosensitivity of HNSCC cells. Moreover, CDK2 attenuated the repair of radiogenic double strand breaks (DSBs) in MEFs as well as SAS and FaDu HNSCC cells indicating a possible role of CDK2 in DNA damage repair. However, we found that CDK2 is dispensable for cell cycle and checkpoint regulation in response to irradiation in SAS and FaDu cells. Taken together, our results suggest that targeting of CDK2 may not provide a therapeutic benefit to overcome HNSCC cell resistance to radiotherapy. We also showed that depletion of CDK9 clearly enhances the radiosensitivity of HNSCC cultures. In addition, the ectopic expression of CDK9 has a radioprotective effect. These findings suggest a potential role of CDK9 in the radiation response of HNSCC cells. Moreover, our study indicates a possible role of CDK9 in the DNA damage repair response and cell cycling of HNSCC cells. Conclusively, on the basis of these data, targeting of CDK9 in addition to conventional radiotherapy might be a viable strategy to overcome cancer cell resistance.

Cyclin-Dependent Kinase 9 (CDK9) as part of the PTEFb complex promotes transcriptional elongation by promoting RNAPII pause release. We now report that, paradoxically, CDK9 is also essential for maintaining gene silencing at heterochromatic loci. Through a live cell screen, we discovered that CDK9 inhibition reactivates epigenetically silenced genes in cancer, leading to restored tumor suppressor gene expression and cell differentiation, along with activation of endogenous retrovirus (ERV) genes. CDK9 inhibition results in dephorphorylation of the SWI/SNF protein SMARCA4 and represses HP1α expression, both of which contribute to gene reactivation. Based on gene activation, we developed the highly selective and potent CDK9 inhibitor MC180295 (IC50 =5nM) that has broad anti-cancer activity in-vitro and is effective in in-vivo cancer models. Additionally, CDK9 inhibition sensitizes with the immune checkpoint inhibitor α-PD-1 in vivo, making it an excellent target for epigenetic therapy of cancer. / Molecular Biology and Genetics

No description available.

Grâce à un grand nombre d’études biochimiques, génétiques et structurales effectuées dans les dernières années, des avancements considérables ont été réalisés et une nouvelle vision du processus par lequel la machinerie transcriptionnelle de l’ARN polymérase II (Pol II) décode l’information génétique a émergé. De nouveaux indices ont été apportés sur la diversité des mécanismes de régulation de la transcription, ainsi que sur le rôle des facteurs généraux de transcription (GTFs) dans cette diversification. Les travaux présentés dans cette thèse amènent de nouvelles connaissances sur le rôle des GTFs humains dans la régulation des différentes étapes de la transcription. Dans la première partie de la thèse, nous avons analysé la fonction de la Pol II et des GTFs humains, en examinant de façon systématique leur localisation génomique. Les patrons obtenus par immunoprécipitation de la chromatine (ChIP) des versions de GTFs portant une étiquette TAP (Tandem-Affinity Purification) indiquent de nouvelles fonctions in vivo pour certains composants de cette machinerie et pour des éléments structuraux de la Pol II. Nos résultats suggèrent que TFIIF et l’hétérodimère Rpb4–Rpb7 ont une fonction spécifique pendant l’étape d’élongation transcriptionnelle in vivo. De plus, notre étude amène une première image globale de la fonction des GTFs pendant la réaction transcriptionnelle dans des cellules mammifères vivantes. Deuxièmement, nous avons identifié une nouvelle fonction de TFIIS dans la régulation de CDK9, la sous-unité kinase du facteur P-TEFb (Positive Transcription Elongation Factor b). Nous avons identifié deux nouveaux partenaires d’interaction pour TFIIS, soit CDK9 et la E3 ubiquitine ligase UBR5. Nous montrons que UBR5 catalyse l’ubiquitination de CDK9 in vitro. De plus, la polyubiquitination de CDK9 dans des cellules humaines est dépendante de UBR5 et TFIIS. Nous montrons aussi que UBR5, CDK9 and TFIIS co-localisent le long du gène  fibrinogen (FBG) et que la surexpression de TFIIS augmente les niveaux d’occupation par CDK9 de régions spécifiques de ce gène, de façon dépendante de UBR5. Nous proposons que TFIIS a une nouvelle fonction dans la transition entre les étapes d’initiation et d’élongation transcriptionnelle, en régulant la stabilité des complexes CDK9-Pol II pendant les étapes précoces de la transcription. / Biochemical, genetic and structural studies made over the last years bring a new view on the RNA polymerase II (Pol II) machinery and the process by which it decodes the genetic information. They provided new insights into the diversity of the transcriptional regulation mechanisms, and on the role played by the general transcription factors (GTFs). The studies presented in this thesis provide new evidence on the role of human GTFs in the regulation of different stages of transcription. In the first part of the thesis, we investigated the function of the human Pol II and GTFs in living cells, by systematically analyzing their genomic location. The location profiles obtained by chromatin immunoprecipitation (ChIP) of TAP (tandem-affinity purification) tagged versions of these factors indicate new in vivo functions for several components of this machinery, and for structural elements of the Pol II. These results suggest that TFIIF and the heterodimer Rpb4–Rpb7 have a specific function during the elongation stage in vivo. Additionally, our study offers for the first time a general picture of GTFs function during the Pol II transcription reaction in live mammalian cells, and provides a framework to uncover new regulatory hubs. Secondly, we report on the identification of a new function of the factor TFIIS in the regulation of CDK9, the kinase subunit of the Positive Transcription Elongation Factor b (P-TEFb). We identify two interaction partners for TFIIS, namely CDK9 and the E3 ubiquitin ligase UBR5. We show that UBR5 catalyzes the ubiquitination of CDK9 in vitro. Moreover, the polyubiquitination of CDK9 in human cells is dependent upon both UBR5 and TFIIS, and does not signal its degradation. We also show that UBR5, CDK9 and TFIIS co-localize along specific regions of the  fibrinogen (FBG) gene, and that the overexpression of TFIIS increases the occupancy of CDK9 along this gene in a UBR5 dependant manner. We propose a new function of TFIIS in the transition between initiation and elongation stages, by regulating the stability of the early CDK9-Pol II transcribing complexes. Key words: chromatin immunoprecipitation, general transcription factors, tandem-affinity purification, RNA polymerase II, Rpb4–Rpb7 heterodimer, transcription factor IIF (TFIIF), transcription factor IIS (TFIIS), UBR5 ubiquitin ligase, Positive Transcription Elongation Factor b (P-TEFb), CDK9 ubiquitination.

Grâce à un grand nombre d’études biochimiques, génétiques et structurales effectuées dans les dernières années, des avancements considérables ont été réalisés et une nouvelle vision du processus par lequel la machinerie transcriptionnelle de l’ARN polymérase II (Pol II) décode l’information génétique a émergé. De nouveaux indices ont été apportés sur la diversité des mécanismes de régulation de la transcription, ainsi que sur le rôle des facteurs généraux de transcription (GTFs) dans cette diversification. Les travaux présentés dans cette thèse amènent de nouvelles connaissances sur le rôle des GTFs humains dans la régulation des différentes étapes de la transcription. Dans la première partie de la thèse, nous avons analysé la fonction de la Pol II et des GTFs humains, en examinant de façon systématique leur localisation génomique. Les patrons obtenus par immunoprécipitation de la chromatine (ChIP) des versions de GTFs portant une étiquette TAP (Tandem-Affinity Purification) indiquent de nouvelles fonctions in vivo pour certains composants de cette machinerie et pour des éléments structuraux de la Pol II. Nos résultats suggèrent que TFIIF et l’hétérodimère Rpb4–Rpb7 ont une fonction spécifique pendant l’étape d’élongation transcriptionnelle in vivo. De plus, notre étude amène une première image globale de la fonction des GTFs pendant la réaction transcriptionnelle dans des cellules mammifères vivantes. Deuxièmement, nous avons identifié une nouvelle fonction de TFIIS dans la régulation de CDK9, la sous-unité kinase du facteur P-TEFb (Positive Transcription Elongation Factor b). Nous avons identifié deux nouveaux partenaires d’interaction pour TFIIS, soit CDK9 et la E3 ubiquitine ligase UBR5. Nous montrons que UBR5 catalyse l’ubiquitination de CDK9 in vitro. De plus, la polyubiquitination de CDK9 dans des cellules humaines est dépendante de UBR5 et TFIIS. Nous montrons aussi que UBR5, CDK9 and TFIIS co-localisent le long du gène  fibrinogen (FBG) et que la surexpression de TFIIS augmente les niveaux d’occupation par CDK9 de régions spécifiques de ce gène, de façon dépendante de UBR5. Nous proposons que TFIIS a une nouvelle fonction dans la transition entre les étapes d’initiation et d’élongation transcriptionnelle, en régulant la stabilité des complexes CDK9-Pol II pendant les étapes précoces de la transcription. / Biochemical, genetic and structural studies made over the last years bring a new view on the RNA polymerase II (Pol II) machinery and the process by which it decodes the genetic information. They provided new insights into the diversity of the transcriptional regulation mechanisms, and on the role played by the general transcription factors (GTFs). The studies presented in this thesis provide new evidence on the role of human GTFs in the regulation of different stages of transcription. In the first part of the thesis, we investigated the function of the human Pol II and GTFs in living cells, by systematically analyzing their genomic location. The location profiles obtained by chromatin immunoprecipitation (ChIP) of TAP (tandem-affinity purification) tagged versions of these factors indicate new in vivo functions for several components of this machinery, and for structural elements of the Pol II. These results suggest that TFIIF and the heterodimer Rpb4–Rpb7 have a specific function during the elongation stage in vivo. Additionally, our study offers for the first time a general picture of GTFs function during the Pol II transcription reaction in live mammalian cells, and provides a framework to uncover new regulatory hubs. Secondly, we report on the identification of a new function of the factor TFIIS in the regulation of CDK9, the kinase subunit of the Positive Transcription Elongation Factor b (P-TEFb). We identify two interaction partners for TFIIS, namely CDK9 and the E3 ubiquitin ligase UBR5. We show that UBR5 catalyzes the ubiquitination of CDK9 in vitro. Moreover, the polyubiquitination of CDK9 in human cells is dependent upon both UBR5 and TFIIS, and does not signal its degradation. We also show that UBR5, CDK9 and TFIIS co-localize along specific regions of the  fibrinogen (FBG) gene, and that the overexpression of TFIIS increases the occupancy of CDK9 along this gene in a UBR5 dependant manner. We propose a new function of TFIIS in the transition between initiation and elongation stages, by regulating the stability of the early CDK9-Pol II transcribing complexes. Key words: chromatin immunoprecipitation, general transcription factors, tandem-affinity purification, RNA polymerase II, Rpb4–Rpb7 heterodimer, transcription factor IIF (TFIIF), transcription factor IIS (TFIIS), UBR5 ubiquitin ligase, Positive Transcription Elongation Factor b (P-TEFb), CDK9 ubiquitination.