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Zhang Q, Chen Y, Teng Z, Lin Z, Liu H. CDK11 facilitates centromeric transcription to maintain centromeric cohesion during mitosis. Mol Biol Cell 2024; 35:ar18. [PMID: 38019613 PMCID: PMC10881149 DOI: 10.1091/mbc.e23-08-0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Actively-transcribing RNA polymerase (RNAP)II is remained on centromeres to maintain centromeric cohesion during mitosis, although it is largely released from chromosome arms. This pool of RNAPII plays an important role in centromere functions. However, the mechanism of RNAPII retention on mitotic centromeres is poorly understood. We here demonstrate that Cyclin-dependent kinase (Cdk)11 is involved in RNAPII regulation on mitotic centromeres. Consistently, we show that Cdk11 knockdown induces centromeric cohesion defects and decreases Bub1 on kinetochores, but the centromeric cohesion defects are partially attributed to Bub1. Furthermore, Cdk11 knockdown and the expression of its kinase-dead version significantly reduce both RNAPII and elongating RNAPII (pSer2) levels on centromeres and decrease centromeric transcription. Importantly, the overexpression of centromeric α-satellite RNAs fully rescues Cdk11-knockdown defects. These results suggest that the maintenance of centromeric cohesion requires Cdk11-facilitated centromeric transcription. Mechanistically, Cdk11 localizes on centromeres where it binds and phosphorylates RNAPII to promote transcription. Remarkably, mitosis-specific degradation of G2/M Cdk11-p58 recapitulates Cdk11-knockdown defects. Altogether, our findings establish Cdk11 as an important regulator of centromeric transcription and as part of the mechanism for retaining RNAPII on centromeres during mitosis.
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Affiliation(s)
- Qian Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Yujue Chen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Teng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Hong Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA 70112
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2
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Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y. Structural visualization of transcription initiation in action. Science 2023; 382:eadi5120. [PMID: 38127763 DOI: 10.1126/science.adi5120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
Abstract
Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuechun Qu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
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3
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Funke K, Düster R, Wilson PDG, Arévalo L, Geyer M, Schorle H. Transcriptional CDK Inhibitors as Potential Treatment Option for Testicular Germ Cell Tumors. Cancers (Basel) 2022; 14:cancers14071690. [PMID: 35406461 PMCID: PMC8997165 DOI: 10.3390/cancers14071690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Type II testicular germ cell tumors are a severe type of cancer in young men demanding alternative treatment options to conventional chemotherapy with less side effects. In particular, patients with chemotherapy-resistant tumors face a bad prognosis and low survival rates. In other tumor entities, transcriptional cyclin-dependent kinases (7/8/9/12/13) have been demonstrated to be effective targets. Here, we studied the effects of transcriptional cyclin-dependent kinase inhibitors on a cellular and molecular level. We found several inhibitors to be highly cytotoxic for certain testicular germ cell tumor cell lines while leaving a somatic (fibroblast) control cell line unaffected. This opens up a novel field for effective and specified treatment of type II testicular germ cell tumors. Abstract Type II testicular germ cell tumors (TGCT) are the most frequently diagnosed solid malignancy in young men. Up to 15% of patients with metastatic non-seminomas show cisplatin resistance and a very poor survival rate due to lacking treatment options. Transcriptional cyclin-dependent kinases (CDK) have been shown to be effective targets in the treatment of different types of cancer. Here, we investigated the effects of the CDK inhibitors dinaciclib, flavopiridol, YKL-5-124, THZ1, NVP2, SY0351 and THZ531. An XTT viability assay revealed a strong cytotoxic impact of CDK7/12/13 inhibitor SY0351 and CDK9 inhibitor NVP2 on the TGCT wild-type cell lines (2102EP, NCCIT, TCam2) and the cisplatin-resistant cell lines (2102EP-R, NCCIT-R). The CDK7 inhibitor YKL-5-124 showed a strong impact on 2102EP, 2102EP-R, NCCIT and NCCIT-R cell lines, leaving the MPAF control cell line mostly unaffected. FACS-based analysis revealed mild effects on the cell cycle of 2102EP and TCam2 cells after SY0351, YKL-5-124 or NVP2 treatment. Molecular analysis showed a cell-line-specific response for SY0351 and NVP2 inhibition while YKL-5-124 induced similar molecular changes in 2102EP, TCam2 and MPAF cells. Thus, after TGCT subtype determination, CDK inhibitors might be a potential alternative for optimized and individualized therapy independent of chemotherapy sensitivity.
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Affiliation(s)
- Kai Funke
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
| | - Robert Düster
- The Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany; (R.D.); (M.G.)
| | - Prince De-Graft Wilson
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
| | - Lena Arévalo
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
| | - Matthias Geyer
- The Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany; (R.D.); (M.G.)
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (K.F.); (P.D.-G.W.); (L.A.)
- Correspondence:
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4
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Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Colón JJG, Steimle S, Garcia BA, Kaplan CD, Murakami K. Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol Cell 2022; 82:660-676.e9. [PMID: 35051353 PMCID: PMC8818039 DOI: 10.1016/j.molcel.2021.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/04/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023]
Abstract
Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
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Affiliation(s)
- Chun Yang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Rina Fujiwara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA,Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Pratik Basnet
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yunye Zhu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jose J. Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Craig D. Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.,Lead contact,Correspondence to:
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5
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Li N, Zheng S, Xue Z, Xiong Z, Zou Y, Tang Y, Wei WD, Yang L. Expression and prognostic value of transcription-associated cyclin-dependent kinases in human breast cancer. Aging (Albany NY) 2021; 13:8095-8114. [PMID: 33686962 PMCID: PMC8034920 DOI: 10.18632/aging.202595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/14/2021] [Indexed: 12/24/2022]
Abstract
The expression and prognostic significance of transcription-associated cyclin-dependent kinases (TA-CDKs) in breast cancer have not been systematically investigated. Using Oncomine, GEPIA2, the Human Protein Atlas, the Kaplan-Meier Plotter, cBioPortal, Metascape, and DAVID 6.8, we profiled the expression of TA-CDKs in breast cancer, inferred their biological functions, and assessed their effect on prognosis. The expression of CDK7/10/13/19 mRNAs in breast cancer tissues was significantly higher than in normal breast tissues. Survival analysis of breast cancer patients revealed that increased CDK8 expression was associated with inferior overall survival (OS), higher expression of CDK7 or CDK8 was associated with inferior relapse-free survival (RFS), but higher expression of CDK13 was associated with favorable RFS and OS. In addition, a high genetic alteration rate (56%) in TA-CDKs was associated with shorter OS. On functional enrichment analysis, top GO enrichment items for TA-CDKs and their neighboring genes included cyclin-dependent protein serine/threonine kinase activity and transferase complex. The top KEGG pathways included cell cycle and mismatch repair. These results suggest that CDK7/8/13 are potential prognostic biomarkers for breast cancer patients and provide novel insight for future studies examining their usefulness as therapeutic targets.
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Affiliation(s)
- Ning Li
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shaoquan Zheng
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhicheng Xue
- Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhenchong Xiong
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yutian Zou
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yuhui Tang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wei-Dong Wei
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lu Yang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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6
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Dhar S, Datta A, Brosh RM. DNA helicases and their roles in cancer. DNA Repair (Amst) 2020; 96:102994. [PMID: 33137625 DOI: 10.1016/j.dnarep.2020.102994] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
DNA helicases, known for their fundamentally important roles in genomic stability, are high profile players in cancer. Not only are there monogenic helicase disorders with a strong disposition to cancer, it is well appreciated that helicase variants are associated with specific cancers (e.g., breast cancer). Flipping the coin, DNA helicases are frequently overexpressed in cancerous tissues and reduction in helicase gene expression results in reduced proliferation and growth capacity, as well as DNA damage induction and apoptosis of cancer cells. The seminal roles of helicases in the DNA damage and replication stress responses, as well as DNA repair pathways, validate their vital importance in cancer biology and suggest their potential values as targets in anti-cancer therapy. In recent years, many laboratories have characterized the specialized roles of helicase to resolve transcription-replication conflicts, maintain telomeres, mediate cell cycle checkpoints, remodel stalled replication forks, and regulate transcription. In vivo models, particularly mice, have been used to interrogate helicase function and serve as a bridge for preclinical studies that may lead to novel therapeutic approaches. In this review, we will summarize our current knowledge of DNA helicases and their roles in cancer, emphasizing the latest developments.
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Affiliation(s)
- Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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7
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Epstein-Barr virus co-opts TFIIH component XPB to specifically activate essential viral lytic promoters. Proc Natl Acad Sci U S A 2020; 117:13044-13055. [PMID: 32434920 DOI: 10.1073/pnas.2000625117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is associated with epithelial and lymphoid malignancies, establishes latent infection in memory B cells, and intermittently produces infectious virions through lytic replication. Released virions play a key role in latent reservoir maintenance and transmission. Lytic EBV transcription differs from cellular transcription in requiring a virus-encoded preinitiation complex that binds to TATT motifs unique to EBV late lytic promoters. Expression of 15 late lytic genes that are important for virion production and infectivity is particularly dependent on the EBV SM protein, a nuclear protein expressed early during lytic reactivation that binds to viral RNAs and enhances RNA stability. We recently discovered that spironolactone blocks EBV virion production by inhibiting EBV SM function. Since spironolactone causes degradation of xeroderma pigmentosum group B-complementing protein (XPB), a component of human transcription factor TFIIH, in both B lymphocytes and epithelial cells, we hypothesized that SM utilizes XPB to specifically activate transcription of SM target promoters. While EBV SM has been thought to act posttranscriptionally, we provide evidence that SM also facilitates EBV gene transcription. We demonstrate that SM binds and recruits XPB to EBV promoters during lytic replication. Depletion of XPB protein, by spironolactone treatment or by siRNA transfection, inhibits SM-dependent late lytic gene transcription but not transcription of other EBV genes or cellular genes. These data indicate that SM acts as a transcriptional activator that has co-opted XPB to specifically target 15 EBV promoters that have uniquely evolved to require XPB for activity, providing an additional mechanism to differentially regulate EBV gene expression.
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8
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Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A. Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy. Cancer Discov 2020; 10:351-370. [DOI: 10.1158/2159-8290.cd-19-0528] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022]
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9
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Zhou Y, Lu L, Jiang G, Chen Z, Li J, An P, Chen L, Du J, Wang H. Targeting CDK7 increases the stability of Snail to promote the dissemination of colorectal cancer. Cell Death Differ 2018; 26:1442-1452. [PMID: 30451989 DOI: 10.1038/s41418-018-0222-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/09/2018] [Accepted: 10/08/2018] [Indexed: 12/20/2022] Open
Abstract
Targeted inhibition of cyclin-dependent kinase 7 (CDK7) via its covalent inhibitor THZ1 can suppress the growth of various cancers, while its roles on colorectal cancer (CRC) remain obscure. Here we report that the expression of CDK7 is upregulated in CRC cells and tissues. THZ1 exhibits high potency and selectivity against CRC cells both in vitro and in vivo via induction of cell apoptosis rather than cell cycle disruption. Intriguingly, THZ1 treatment increases the ability of epithelial mesenchymal transition (EMT) and in vivo metastasis to liver of CRC cells. Mechanistical studies reveal that THZ1 increases the expression of Snail, while not other EMT-transcription factors, via enhancing its protein stability rather than mRNA expression or translation. By screening Snail stability related factors via qRT-PCR, results indicate THZ1 and si-CDK7 decrease the expression of protein kinase D1 (PKD1) in CRC cells. Down regulation of PKD1 mediates THZ1 up regulated Snail via dephosphorylation of Snail Ser 11 and prevention of proteasome mediated degradation. Clinical analysis confirms that CDK7 is significantly (p < 0.05) negatively correlated with the expression of mesenchymal markers including FN1, VIM, and MMP2. CRC patients whose tumors expressing less CDK7/SNAI1 or PKD1/SNAI1 showed significant (p < 0.05) poorer overall survival (OS) rate as compared with those with greater levels. Collectively, our data suggest that targeted inhibition of CDK7 can trigger the metastasis of CRC during cancer development via PKD1/Snail axis, which imposes great challenge that inhibition of CDK7 is a potential approach for cancer treatment.
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Affiliation(s)
- Yan Zhou
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Linlin Lu
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Guanmin Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.,Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Jiexin Li
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Panpan An
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Likun Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Jun Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hongsheng Wang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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10
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Rimel JK, Taatjes DJ. The essential and multifunctional TFIIH complex. Protein Sci 2018; 27:1018-1037. [PMID: 29664212 PMCID: PMC5980561 DOI: 10.1002/pro.3424] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022]
Abstract
TFIIH is a 10‐subunit complex that regulates RNA polymerase II (pol II) transcription but also serves other important biological roles. Although much remains unknown about TFIIH function in eukaryotic cells, much progress has been made even in just the past few years, due in part to technological advances (e.g. cryoEM and single molecule methods) and the development of chemical inhibitors of TFIIH enzymes. This review focuses on the major cellular roles for TFIIH, with an emphasis on TFIIH function as a regulator of pol II transcription. We describe the structure of TFIIH and its roles in pol II initiation, promoter‐proximal pausing, elongation, and termination. We also discuss cellular roles for TFIIH beyond transcription (e.g. DNA repair, cell cycle regulation) and summarize small molecule inhibitors of TFIIH and diseases associated with defects in TFIIH structure and function.
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Affiliation(s)
- Jenna K Rimel
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
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11
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TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning. Nat Struct Mol Biol 2017; 24:1139-1145. [PMID: 29106413 PMCID: PMC5741190 DOI: 10.1038/nsmb.3500] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/09/2017] [Indexed: 12/23/2022]
Abstract
Eukaryotic mRNA transcription initiation is directed by the formation of the megaDalton-sized pre-initiation complex (PIC). After PIC formation, double-stranded DNA is unwound to form a single-stranded DNA bubble and the template strand is loaded into the polymerase active site. DNA opening is catalyzed by Ssl2(XPB), the dsDNA translocase subunit of the basal transcription factor TFIIH. In yeast, transcription initiation proceeds through a scanning phase where downstream DNA is searched for optimal start-sites. Here, to test models for initial DNA opening and start-site scanning, we measure the DNA bubble sizes generated by Saccharomyces cerevisiae PICs in real time using single-molecule magnetic tweezers. We show that ATP hydrolysis by Ssl2 opens a 6 base-pair (bp) bubble that grows to 13 bp in the presence of NTPs. These observations support a two-step model wherein ATP-dependent Ssl2 translocation leads to a 6 bp open complex which RNA polymerase II expands via NTP-dependent RNA transcription.
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12
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Bahleda R, Grilley-Olson JE, Govindan R, Barlesi F, Greillier L, Perol M, Ray-Coquard I, Strumberg D, Schultheis B, Dy GK, Zalcman G, Weiss GJ, Walter AO, Kornacker M, Rajagopalan P, Henderson D, Nogai H, Ocker M, Soria JC. Phase I dose-escalation studies of roniciclib, a pan-cyclin-dependent kinase inhibitor, in advanced malignancies. Br J Cancer 2017; 116:1505-1512. [PMID: 28463960 PMCID: PMC5518866 DOI: 10.1038/bjc.2017.92] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 03/01/2017] [Accepted: 03/05/2017] [Indexed: 02/06/2023] Open
Abstract
Background: To evaluate safety, pharmacokinetics, and maximum tolerated dose of roniciclib in patients with advanced malignancies, with dose expansion to evaluate clinical benefit at the recommended phase II dose (RP2D). Methods: Two phase I dose-escalation studies evaluated two roniciclib dosing schedules: 3 days on/4 days off or 4 weeks on/2 weeks off. The expansion phase included patients with small-cell lung cancer (SCLC), ovarian cancer, or tumour mutations involving the CDK signalling pathway. Results: Ten patients were evaluable in the 4 weeks on/2 weeks off schedule (terminated following limited tolerability) and 47 in the 3 days on/4 days off schedule dose-escalation cohorts. On the 3 days on/4 days off schedule, RP2D was 5 mg twice daily in solid tumours (n=40); undetermined in lymphoid malignancies (n=7). Common roniciclib-related adverse events included nausea (76.6%), fatigue (65.8%), diarrhoea (63.1%), and vomiting (57.7%). Roniciclib demonstrated rapid absorption and dose-proportional increase in exposure. One partial response (1.0%) was observed. In RP2D expansion cohorts, the disease control rate (DCR) was 40.9% for patients with ovarian cancer (n=25), 17.4% for patients with SCLC (n=33), and 33.3% for patients with CDK-related tumour mutations (n=6). Conclusions: Roniciclib demonstrated an acceptable safety profile and moderate DCR in 3 days on/4 days off schedule.
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Affiliation(s)
- Rastislav Bahleda
- Drug Development Department, Gustave Roussy, 114, rue Édouard-Vaillant, Paris 94805, France
| | - Juneko E Grilley-Olson
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, 170 Manning Drive, Chapel Hill, NC 27514, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University Medical School, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Fabrice Barlesi
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille University, Assistance Publique Hôpitaux de Marseille, Centre Essais Précoces en Cancérologie de Marseille CLIP, 80, rue Brochier, Marseille 13005, France
| | - Laurent Greillier
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille University, Assistance Publique Hôpitaux de Marseille, Centre Essais Précoces en Cancérologie de Marseille CLIP, 80, rue Brochier, Marseille 13005, France
| | - Maurice Perol
- Department of Medical Oncology, Cancer Research Centre Léon Bérard and Claude Bernard University, 28, Prom. Léa et Napoléon Bullukian, Lyon 69008, France
| | - Isabelle Ray-Coquard
- Department of Medical Oncology, Cancer Research Centre Léon Bérard and Claude Bernard University, 28, Prom. Léa et Napoléon Bullukian, Lyon 69008, France
| | - Dirk Strumberg
- Department of Internal Medicine, Oncology and Haematology, Marienhospital Herne, Ruhr-University Bochum, Bochum Süd, Universitätsstraße 150, Bochum 44801, Germany
| | - Beate Schultheis
- Department of Internal Medicine, Oncology and Haematology, Marienhospital Herne, Ruhr-University Bochum, Bochum Süd, Universitätsstraße 150, Bochum 44801, Germany
| | - Grace K Dy
- Department of Medicine, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Gérard Zalcman
- Pulmonology and Thoracic Oncology Department, Clinical Research Center, University Hospital, Avenue de la Côte de Nacre, Caen 14033, France
| | - Glen J Weiss
- Virginia G. Piper Cancer Center Clinical Trials at Scottsdale Healthcare/TGen, 10510 North 92nd Street, Suite 200, Scottsdale, AZ 85258, USA.,Cancer Treatment Centers of America, 14200 Celebrate Life Way, Goodyear, AZ 85338, USA
| | | | | | - Prabhu Rajagopalan
- Bayer HealthCare Pharmaceuticals, Inc., 100 Bayer Boulevard, Whippany, NJ 07981, USA
| | | | | | | | - Jean-Charles Soria
- Drug Development Department, Gustave Roussy, 114, rue Édouard-Vaillant, Paris 94805, France
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13
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Zhang Y, Najmi SM, Schneider DA. Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:246-255. [PMID: 27989933 DOI: 10.1016/j.bbagrm.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, nuclear RNA synthesis is accomplished by at least three unique, multisubunit RNA polymerases. The roles of these enzymes are generally partitioned into the synthesis of the three major classes of RNA: rRNA, mRNA, and tRNA for RNA polymerases I, II, and III respectively. Consistent with their unique cellular roles, each enzyme has a complement of specialized transcription factors and enzymatic properties. However, not all transcription factors have evolved to affect only one eukaryotic RNA polymerase. In fact, many factors have been shown to influence the activities of multiple nuclear RNA polymerases. This review focuses on a subset of these factors, specifically addressing the mechanisms by which these proteins influence RNA polymerases I and II.
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Affiliation(s)
- Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Saman M Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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14
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Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, Przytycka TM, Kouzine F, Lewis BA, Zhao K, Levens D. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell 2016; 165:357-71. [PMID: 27058666 DOI: 10.1016/j.cell.2016.02.036] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 12/01/2015] [Accepted: 02/17/2016] [Indexed: 11/24/2022]
Abstract
We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using chromatin immunoprecipitation sequencing (ChIP-seq) versus TOP1 activity using topoisomerase 1 sequencing (TOP1-seq), a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. TOP1 stimulation is strongly dependent on the kinase activity of BRD4, a protein that phosphorylates Ser2-CTD and regulates RNAPII pause-release. Thus the coordinated action of BRD4 and TOP1 overcame the torsional stress opposing transcription as RNAPII commenced elongation but preserved negative supercoiling that assists promoter melting at start sites. This nexus between transcription and DNA topology promises to elicit new strategies to intercept pathological gene expression.
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Affiliation(s)
| | | | - Kairong Cui
- Systems Biology Center, NHLBI/NIH, Bethesda, MD 20892, USA
| | | | - Hye-Jung Chung
- Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA
| | - Ka Yim Chan-Salis
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Kelli Wilson
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Hongliang Zhang
- Development Therapeutics Branch and Laboratory of Molecular Pharmacology, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Craig J Thomas
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Dinah S Singer
- Experimental Immunology Branch, NCI/NIH, Bethesda, MD 20892, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yves Pommier
- Development Therapeutics Branch and Laboratory of Molecular Pharmacology, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Fedor Kouzine
- Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA
| | - Brian A Lewis
- Lymphoid Malignancies Branch, NCI/NIH, Bethesda, MD 20892, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI/NIH, Bethesda, MD 20892, USA.
| | - David Levens
- Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA.
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15
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Tripartite DNA Lesion Recognition and Verification by XPC, TFIIH, and XPA in Nucleotide Excision Repair. Mol Cell 2015; 59:1025-34. [PMID: 26384665 DOI: 10.1016/j.molcel.2015.08.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 07/09/2015] [Accepted: 08/17/2015] [Indexed: 11/23/2022]
Abstract
Transcription factor IIH (TFIIH) is essential for both transcription and nucleotide excision repair (NER). DNA lesions are initially detected by NER factors XPC and XPE or stalled RNA polymerases, but only bulky lesions are preferentially repaired by NER. To elucidate substrate specificity in NER, we have prepared homogeneous human ten-subunit TFIIH and its seven-subunit core (Core7) without the CAK module and show that bulky lesions in DNA inhibit the ATPase and helicase activities of both XPB and XPD in Core7 to promote NER, whereas non-genuine NER substrates have no such effect. Moreover, the NER factor XPA activates unwinding of normal DNA by Core7, but inhibits the Core7 helicase activity in the presence of bulky lesions. Finally, the CAK module inhibits DNA binding by TFIIH and thereby enhances XPC-dependent specific recruitment of TFIIH. Our results support a tripartite lesion verification mechanism involving XPC, TFIIH, and XPA for efficient NER.
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16
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Abstract
The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.
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17
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Fazal FM, Meng CA, Murakami K, Kornberg RD, Block SM. Real-time observation of the initiation of RNA polymerase II transcription. Nature 2015; 525:274-7. [PMID: 26331540 PMCID: PMC4624315 DOI: 10.1038/nature14882] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/03/2015] [Indexed: 01/22/2023]
Abstract
Biochemical and structural studies have shown that the initiation of RNA polymerase II (pol II) transcription proceeds in the following stages: assembly of pol II with general transcription factors (GTFs) and promoter DNA in a “closed” preinitiation complex (PIC)1,2; unwinding about 15 bp of the promoter DNA to form an “open” complex3,4; scanning downstream to a transcription start site; synthesis of a short transcript, believed to be about 10 nucleotides; and promoter escape. We have assembled a 32-protein, 1.5 megadalton PIC5 derived from Saccharomyces cerevisiae and observed subsequent initiation processes in real time with optical tweezers6. Contrary to expectation, scanning driven by transcription factor IIH (TFIIH)7-12 entailed the rapid opening of an extended bubble, averaging 85 bp, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.
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Affiliation(s)
- Furqan M Fazal
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Cong A Meng
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Kenji Murakami
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA.,Department of Biology, Stanford University, Stanford, California 94305, USA
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18
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Uncoupling Promoter Opening from Start-Site Scanning. Mol Cell 2015; 59:133-8. [PMID: 26073544 DOI: 10.1016/j.molcel.2015.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/08/2015] [Accepted: 05/08/2015] [Indexed: 01/24/2023]
Abstract
Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp downstream of the TATA box in metazoans, TSSs are located 40-120 bp downstream in S. cerevisiae. Promoter melting begins about 12 bp downstream in all eukaryotes, so Pol II is presumed to "scan" further downstream before starting transcription in yeast. Here we report that removal of the kinase complex TFIIK from TFIIH shifts the TSS in a yeast system upstream to the location observed in metazoans. Conversely, moving the normal TSS to an upstream location enables a high level of TFIIK-independent transcription in the yeast system. We distinguish two stages of the transcription initiation process: bubble formation by TFIIH, which fills the Pol II active center with single-stranded DNA, and subsequent scanning downstream, also driven by TFIIH, which requires displacement of the initial bubble. Omission of TFIIK uncouples the two stages of the process.
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19
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Asghar U, Witkiewicz AK, Turner NC, Knudsen ES. The history and future of targeting cyclin-dependent kinases in cancer therapy. Nat Rev Drug Discov 2015; 14:130-46. [PMID: 25633797 PMCID: PMC4480421 DOI: 10.1038/nrd4504] [Citation(s) in RCA: 1210] [Impact Index Per Article: 134.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cancer represents a pathological manifestation of uncontrolled cell division; therefore, it has long been anticipated that our understanding of the basic principles of cell cycle control would result in effective cancer therapies. In particular, cyclin-dependent kinases (CDKs) that promote transition through the cell cycle were expected to be key therapeutic targets because many tumorigenic events ultimately drive proliferation by impinging on CDK4 or CDK6 complexes in the G1 phase of the cell cycle. Moreover, perturbations in chromosomal stability and aspects of S phase and G2/M control mediated by CDK2 and CDK1 are pivotal tumorigenic events. Translating this knowledge into successful clinical development of CDK inhibitors has historically been challenging, and numerous CDK inhibitors have demonstrated disappointing results in clinical trials. Here, we review the biology of CDKs, the rationale for therapeutically targeting discrete kinase complexes and historical clinical results of CDK inhibitors. We also discuss how CDK inhibitors with high selectivity (particularly for both CDK4 and CDK6), in combination with patient stratification, have resulted in more substantial clinical activity.
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Affiliation(s)
- Uzma Asghar
- Breakthrough Breast Cancer Research Centre, Chester Beatty Laboratories, Institute of Cancer Research, London, SW3 6JB, UK
| | - Agnieszka K Witkiewicz
- Simmons Cancer Center and Department of Pathology, University of Texas Southwestern, Dallas, USA
| | - Nicholas C Turner
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust Breast Cancer Unit, London, SW3 6JJ, UK
| | - Erik S Knudsen
- Simmons Cancer Center and Department of Pathology, University of Texas Southwestern, Dallas, USA
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20
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Abstract
Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified. Among the factors we describe are the pausing factors--NELF (negative elongation factor) and DSIF (DRB sensitivity-inducing factor)--and P-TEFb (positive elongation factor b), which is the key player in pause release. We also describe the high-resolution view of Pol II pausing and propose nonexclusive models for how pausing is achieved. We then discuss Pol II elongation through the bodies of genes and the roles of FACT and SPT6, factors that allow Pol II to move through nucleosomes.
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Affiliation(s)
- Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703; ,
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21
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Nagore LI, Nadeau RJ, Guo Q, Jadhav YLA, Jarrett HW, Haskins WE. Purification and characterization of transcription factors. MASS SPECTROMETRY REVIEWS 2013; 32:386-398. [PMID: 23832591 PMCID: PMC3758410 DOI: 10.1002/mas.21369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 11/19/2012] [Accepted: 11/19/2012] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA-protein complex on solid supports. Additional methods for improving dynamic range include two- and three-dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome.
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Affiliation(s)
- LI Nagore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
| | - RJ Nadeau
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Q Guo
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - YLA Jadhav
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - HW Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
| | - WE Haskins
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Biology, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
- Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
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22
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Murakami K, Calero G, Brown CR, Liu X, Davis RE, Boeger H, Kornberg RD. Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. J Biol Chem 2013; 288:6325-32. [PMID: 23303183 DOI: 10.1074/jbc.m112.433623] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Whereas individual RNA polymerase II (pol II)-general transcription factor (GTF) complexes are unstable, an assembly of pol II with six GTFs and promoter DNA could be isolated in abundant homogeneous form. The resulting complete pol II transcription preinitiation complex (PIC) contained equimolar amounts of all 31 protein components. An intermediate in assembly, consisting of four GTFs and promoter DNA, could be isolated and supplemented with the remaining components for formation of the PIC. Nuclease digestion and psoralen cross-linking mapped the PIC between positions -70 and -9, centered on the TATA box. Addition of ATP to the PIC resulted in quantitative conversion to an open complex, which retained all 31 proteins, contrary to expectation from previous studies. Addition of the remaining NTPs resulted in run-off transcription, with an efficiency that was promoter-dependent and was as great as 17.5% with the promoters tested.
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Affiliation(s)
- Kenji Murakami
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA
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23
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Abstract
Structures of complete 10-subunit yeast TFIIH and of a nested set of subcomplexes, containing 5, 6, and 7 subunits, have been determined by electron microscopy (EM) and 3D reconstruction. Consistency among all the structures establishes the location of the "minimal core" subunits (Ssl1, Tfb1, Tfb2, Tfb4, and Tfb5), and additional densities can be specifically attributed to Rad3, Ssl2, and the TFIIK trimer. These results can be further interpreted by placement of previous X-ray structures into the additional densities to give a preliminary picture of the RNA polymerase II preinitiation complex. In this picture, the key catalytic components of TFIIH, the Ssl2 ATPase/helicase and the Kin28 protein kinase are in proximity to their targets, downstream promoter DNA and the RNA polymerase C-terminal domain.
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24
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Biswas T, Pero JM, Joseph CG, Tsodikov OV. DNA-Dependent ATPase Activity of Bacterial XPB Helicases. Biochemistry 2009; 48:2839-48. [DOI: 10.1021/bi8022416] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tapan Biswas
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Jessica M. Pero
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Caleb G. Joseph
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Oleg V. Tsodikov
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
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25
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Stevens M, De Clercq E, Balzarini J. The regulation of HIV-1 transcription: molecular targets for chemotherapeutic intervention. Med Res Rev 2006; 26:595-625. [PMID: 16838299 PMCID: PMC7168390 DOI: 10.1002/med.20081] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The regulation of transcription of the human immunodeficiency virus (HIV) is a complex event that requires the cooperative action of both viral and cellular components. In latently infected resting CD4(+) T cells HIV-1 transcription seems to be repressed by deacetylation events mediated by histone deacetylases (HDACs). Upon reactivation of HIV-1 from latency, HDACs are displaced in response to the recruitment of histone acetyltransferases (HATs) by NF-kappaB or the viral transcriptional activator Tat and result in multiple acetylation events. Following chromatin remodeling of the viral promoter region, transcription is initiated and leads to the formation of the TAR element. The complex of Tat with p-TEFb then binds the loop structures of TAR RNA thereby positioning CDK9 to phosphorylate the cellular RNA polymerase II. The Tat-TAR-dependent phosphorylation of RNA polymerase II plays an important role in transcriptional elongation as well as in other post-transcriptional events. As such, targeting of Tat protein (and/or cellular cofactors) provide an interesting perspective for therapeutic intervention in the HIV replicative cycle and may afford lifetime control of the HIV infection.
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Affiliation(s)
- Miguel Stevens
- Rega Institute for Medical Research, Minderbroedersstraat 10, B‐3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Minderbroedersstraat 10, B‐3000 Leuven, Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research, Minderbroedersstraat 10, B‐3000 Leuven, Belgium
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26
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Pal M, Ponticelli AS, Luse DS. The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II. Mol Cell 2005; 19:101-10. [PMID: 15989968 DOI: 10.1016/j.molcel.2005.05.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2004] [Revised: 04/20/2005] [Accepted: 05/19/2005] [Indexed: 11/27/2022]
Abstract
We have studied promoter clearance at a series of RNA polymerase II promoters with varying spacing of the TATA box and start site. We find that regardless of promoter spacing, the upstream edge of the transcription bubble forms 20 bp from TATA. The bubble expands downstream until 18 bases are unwound and the RNA is at least 7 nt long, at which point the upstream approximately 8 bases of the bubble abruptly reanneal (bubble collapse). If either bubble size or transcript length is insufficient, bubble collapse cannot occur. Bubble collapse coincides with the end of the requirement for the TFIIH helicase for efficient transcript elongation. We also provide evidence that bubble collapse suppresses pausing at +7 to +9 caused by the presence of the B finger segment of TFIIB within the complex. Our results indicate that bubble collapse defines the RNA polymerase II promoter clearance transition.
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Affiliation(s)
- Mahadeb Pal
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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27
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Lin YC, Choi WS, Gralla JD. TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape. Nat Struct Mol Biol 2005; 12:603-7. [PMID: 15937491 DOI: 10.1038/nsmb949] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Accepted: 05/10/2005] [Indexed: 11/08/2022]
Abstract
DNA helicases open the duplex during DNA replication, repair and transcription. However, RNA polymerase II is the only member of its family with this requirement; RNA polymerases I and III and bacterial RNA polymerases open DNA without a helicase. In this report, characterization of XPB mutants indicates that its helicase activity is not used for RNA polymerase II promoter opening, which is instead driven by its ATPase activity. The mutants have parallels in sigma(54) bacterial transcription and this suggests a similar mode of opening DNA for both RNA polymerases, involving ATP-dependent enzyme conformational changes. Promoter escape is defective in these XPB mutants, suggesting that the XPB helicase acts as an ATP-driven motor to reorganize the tightly wrapped multiprotein eukaryotic preinitiation complex during the remodeling that precedes elongation and the coupling to RNA processing events.
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Affiliation(s)
- Yin Chun Lin
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, PO Box 951569, Los Angeles, California 90095-1569, USA
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28
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Lin YC, Gralla JD. Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE. Nucleic Acids Res 2005; 33:3072-81. [PMID: 15917439 PMCID: PMC1140373 DOI: 10.1093/nar/gki623] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 05/11/2005] [Accepted: 05/11/2005] [Indexed: 11/13/2022] Open
Abstract
TFIIE and TFIIH are essential for the promoter opening and escape that occurs as RNA polymerase II transits into early elongation. XPB, a subunit of TFIIH, contains an ATP-dependent helicase activity that is used in both of these processes. Here, we show that the smaller beta subunit of TFIIE stimulates the XPB helicase and ATPase activities. The larger alpha subunit can use its known inhibitory activity to moderate the stimulation by the beta subunit. Regions of TFIIE beta required for the helicase stimulation were identified. Mutants were constructed that are defective in stimulating the XPB helicase but still allow intact TFIIE to bind and recruit XPB and TFIIH to form the pre-initiation complex. In a test for the functional significance of the stimulatory effect of TFIIE beta, these mutant forms of TFIIE were shown to be defective in a transcription assay on linear DNA. The data suggest that the beta subunit of TFIIE is an ATPase and helicase co-factor that can assist the XPB subunit of TFIIH during transcription initiation and the transition to early elongation, enhancing the potential diversity of regulatory targets.
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Affiliation(s)
- Yin C. Lin
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California Los AngelesLos Angeles, CA 90095-1569, USA
| | - Jay D. Gralla
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California Los AngelesLos Angeles, CA 90095-1569, USA
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29
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Weber A, Liu J, Collins I, Levens D. TFIIH operates through an expanded proximal promoter to fine-tune c-myc expression. Mol Cell Biol 2005; 25:147-61. [PMID: 15601838 PMCID: PMC538784 DOI: 10.1128/mcb.25.1.147-161.2005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A continuous stream of activating and repressing signals is processed by the transcription complex paused at the promoter of the c-myc proto-oncogene. The general transcription factor IIH (TFIIH) is held at promoters prior to promoter escape and so is well situated to channel the input of activators and repressors to modulate c-myc expression. We have compared cells expressing only a mutated p89 (xeroderma pigmentosum complementation group B [XPB]), the largest TFIIH subunit, with the same cells functionally complemented with the wild-type protein (XPB/wt-p89). Here, we show structural, compositional, and functional differences in transcription complexes between XPB and XPB/wt-89 cells at the native c-myc promoter. Remarkably, although the mean levels of c-Myc are only modestly elevated in XPB compared to those in XPB/wt-p89 cells, the range of expression and the cell-to-cell variation of c-Myc are markedly increased. Our modeling indicates that the data can be explained if TFIIH integrates inputs from multiple signals, regulating transcription at multiple kinetically equivalent steps between initiation and promoter escape. This helps to suppress the intrinsic noise of transcription and to ensure the steady transcriptional output of c-myc necessary for cellular homeostasis.
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Affiliation(s)
- Achim Weber
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute/NIH, Bldg. 10, Rm. 2N106, Bethesda, MD 20892-1500, USA
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30
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Cabart P, Chew HK, Murphy S. BRCA1 cooperates with NUFIP and P-TEFb to activate transcription by RNA polymerase II. Oncogene 2004; 23:5316-29. [PMID: 15107825 DOI: 10.1038/sj.onc.1207684] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The tumor suppressor gene product BRCA1 is a component of the RNA polymerase II (pol II) holoenzyme that is involved, through binding to various regulatory proteins, in either activation or repression of transcription. Using a yeast two-hybrid screen, we have identified a human zinc-finger-containing protein NUFIP that interacts with BRCA1. The ubiquitous, stably expressed, nuclear protein NUFIP specifically stimulates activator-independent pol II transcription in vitro and in vivo. Immunodepletion of the endogenous NUFIP causes a marked decrease of pol II transcription, which is then shown to be restored by stable complex of ectopically produced NUFIP and associated factors. NUFIP not only interacts with BRCA1 but also associates with the positive elongation factor P-TEFb through interaction with the regulatory Cyclin T1 subunit. Cyclin T1 is required for BRCA1- and NUFIP-dependent synergistic activation of pol II transcription in 293 cells. Mutation of the zinc-finger domain abolishes the NUFIP-mediated transcriptional activation. We show that NUFIP is associated with preinitiation complexes, open transcription complexes, and elongation complexes. In addition, NUFIP facilitates ATP-dependent dissociation of hyperphosphorylated pol II from open transcription complexes in vitro.
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Affiliation(s)
- Pavel Cabart
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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31
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Moon WJ, Apostol JA, McBride AJ, Shukla LI, Dvir A, Burton ZF. Efficient production of recombinant human transcription factor IIE. Protein Expr Purif 2004; 34:317-23. [PMID: 15003267 DOI: 10.1016/j.pep.2003.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2003] [Revised: 12/10/2003] [Indexed: 11/17/2022]
Abstract
Transcription factor IIE (TFIIE) is a general initiation and promoter escape factor for RNA polymerase II composed of p56 (TFIIE-alpha) and p34 (TFIIE-beta) subunits. Our laboratories experienced difficulty producing adequate quantities of recombinant human TFIIE-alpha for in vitro studies using available clones. We therefore re-engineered the TFIIE subunit production vectors and tested various Escherichia coli host strains to optimize expression. We report a much-improved system for production of pure, soluble, and active TFIIE complex for in vitro studies.
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Affiliation(s)
- Woo J Moon
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
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32
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Forget D, Langelier MF, Thérien C, Trinh V, Coulombe B. Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms. Mol Cell Biol 2004; 24:1122-31. [PMID: 14729958 PMCID: PMC321454 DOI: 10.1128/mcb.24.3.1122-1131.2004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2003] [Accepted: 11/03/2003] [Indexed: 11/20/2022] Open
Abstract
The topological organization of a TATA binding protein-TFIIB-TFIIF-RNA polymerase II (RNAP II)-TFIIE-promoter complex was analyzed using site-specific protein-DNA photo-cross-linking of gel-purified complexes. The cross-linking results for the subunits of RNAP II were used to determine the path of promoter DNA against the structure of the enzyme. The results indicate that promoter DNA wraps around the mobile clamp of RNAP II. Cross-linking of TFIIF and TFIIE both upstream of the TATA element and downstream of the transcription start site suggests that both factors associate with the RNAP II mobile clamp. TFIIE alpha closely approaches promoter DNA at nucleotide -10, a position immediately upstream of the transcription bubble in the open complex. Increased stimulation of transcription initiation by TFIIE alpha is obtained when the DNA template is artificially premelted in the -11/-1 region, suggesting that TFIIE alpha facilitates open complex formation, possibly through its interaction with the upstream end of the partially opened transcription bubble. These results support the central roles of the mobile clamp of RNAP II and TFIIE in transcription initiation.
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Affiliation(s)
- Diane Forget
- Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada H2W 1R7
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33
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Riedl T, Hanaoka F, Egly JM. The comings and goings of nucleotide excision repair factors on damaged DNA. EMBO J 2003; 22:5293-303. [PMID: 14517266 PMCID: PMC204472 DOI: 10.1093/emboj/cdg489] [Citation(s) in RCA: 337] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To understand the mechanism of nucleotide excision repair (NER), one of the major human DNA repair pathways, we have set up a DNA repair system in which a linear damaged DNA substrate is immobilized by its terminus. By isolating functionally active intermediate complexes, our data dissect the ordered arrival and displacement of NER factors in the progress of the dual incision step. We describe (i) the role of ATP in remodelling the NER-initiating complex of XPC/TFIIH/damaged DNA as a prerequisite for the recruitment of the next NER factors; (ii) the coordination between damage removal and DNA resynthesis and the release of XPC-HR23B, TFIIH and XPA upon arrival of XPG and XPF-ERCC1, respectively; (iii) how RPA remains associated with the excised DNA initiating the assembly of resynthesis factors such as PCNA; (iv) the recycling of XPC-HR23B, TFIIH and XPA in the NER; and the shuttling of TFIIH between NER and transcription. Thus, our findings define multiple functions of NER factors to explain the molecular basis of human NER disorders.
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Affiliation(s)
- Thilo Riedl
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, B.P. 10142, 67404 Illkirch, C.U. de Strasbourg, France
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34
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Wang X, Spangler L, Dvir A. Promoter escape by RNA polymerase II. Downstream promoter DNA is required during multiple steps of early transcription. J Biol Chem 2003; 278:10250-6. [PMID: 12527757 DOI: 10.1074/jbc.m210848200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent evidence, obtained in a reconstituted RNA polymerase II transcription system, indicated that the promoter escape stage of transcription requires template DNA located downstream of the elongating polymerase. In the absence of downstream DNA, very early elongation complexes are unable to synthesize transcripts longer than approximately 10-14 nucleotides. In contrast, once transcripts longer than approximately 15 nucleotides have been synthesized, an extended region of downstream DNA is no longer required (Dvir, A., Tan, S., Conaway, J. W., and Conaway, R. C. (1997) J. Biol. Chem. 272, 28175-28178). In this work, we sought to define precisely when, during the synthesis of the first 10-15 phosphodiester bonds, downstream DNA is required. We report that, for complete promoter escape, downstream DNA extending to position 40/42 is required. The polymerase can be forced to arrest at several points prior to the completion of promoter escape by removing downstream DNA proximally to positions 40/42. The positions at which the polymerase arrests appear to be determined by the length of available downstream DNA, with arrest occurring at a relatively fixed position of approximately 28 nucleotides to the distal end of the template. A similar requirement is observed for transcription initiation, i.e. the formation of the first phosphodiester bond of nascent transcripts. In addition, we show that the requirement for a downstream region is independent of downstream DNA sequence, suggesting that the requirement reflects a general mechanism. Taken together, our results indicate (i) that downstream DNA is required continuously through the synthesis of the first 14-15 phosphodiester bonds of nascent transcripts, and (ii) that a major conformational change in the transcription complex likely occurs only after the completion of promoter escape.
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Affiliation(s)
- Xiaoxue Wang
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309, USA
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35
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Jona G, Livi LL, Gileadi O. Mutations in the RING domain of TFB3, a subunit of yeast transcription factor IIH, reveal a role in cell cycle progression. J Biol Chem 2002; 277:39409-16. [PMID: 12176978 DOI: 10.1074/jbc.m202733200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase II general transcription factor TFIIH is composed of 9 known subunits and possesses DNA helicase and protein kinase activities. The kinase subunits of TFIIH in animal cells, Cdk7, cyclin H, and MAT1, were independently isolated as an activity termed CAK (Cdk-activating kinase), which phosphorylates and activates cell cycle kinases. However, CAK activity of TFIIH subunits could not be demonstrated in budding yeast. TFB3, the 38-kDa subunit of yeast TFIIH, is the homolog of mammalian MAT1. By random mutagenesis we have isolated a temperature-sensitive mutation in the conserved RING domain. The mutant Tfb3 protein associates less efficiently with the kinase moiety of TFIIH than the wild type protein. In contrast to lethal mutants in other subunits of TFIIH, this mutation does not impair general transcription. Transcription of CLB2, and possibly other genes, is reduced in the mutant. At the restrictive temperature, the cells display a defect in cell cycle progression, which is manifest at more than one phase of the cycle. To conclude, in the present study we bring another demonstration of the multifunctional nature of TFIIH.
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Affiliation(s)
- Ghil Jona
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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36
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Abstract
Transcription of protein-coding genes is one of the most fundamental processes that underlies all life and is a primary mechanism of biological regulation. In eukaryotic cells, transcription depends on the formation of a complex at the promoter region of the gene that minimally includes RNA polymerase II and several auxiliary proteins known as the general transcription factors. Transcription initiation follows at the promoter site given the availability of nucleoside triphosphates and ATP. Soon after the polymerase begins the synthesis of the nascent mRNA chain, it enters a critical stage, referred to as promoter escape, that is characterized by physical and functional instability of the transcription complex. These include formation of abortive transcripts, strong dependence on ATP cofactor, the general transcription factor TFIIH and downstream template. These criteria are no longer in effect when the nascent RNA reaches a length of 14-15 nucleotides. Towards the end of promoter escape, disruption or adjustment of protein-protein and protein-DNA interactions, including the release of some of the general transcription factors from the early transcription complex is to be expected, allowing the transition to the elongation stage of transcription. In this review, we examine the experimental evidence that defines promoter escape as a distinct stage in transcription, and point out areas where critical information is missing.
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MESH Headings
- HeLa Cells
- Humans
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/physiology
- RNA Polymerase II/chemistry
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/metabolism
- Sarcosine/analogs & derivatives
- Sarcosine/pharmacology
- Transcription Factor TFIIH
- Transcription Factors, General/chemistry
- Transcription Factors, General/metabolism
- Transcription Factors, TFII/genetics
- Transcription Factors, TFII/metabolism
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
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Affiliation(s)
- Arik Dvir
- Department of Biological Sciences, Oakland University, Rochester, MI 48309-4401, USA.
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37
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Abstract
The Saccharomyces cerevisiae Paf1-RNA polymerase II (Pol II) complex is biochemically and functionally distinct from the Srb-mediator form of Pol II holoenzyme and is required for full expression of a subset of genes. In this work we have used tandem affinity purification tags to isolate the Paf1 complex and mass spectrometry to identify additional components. We have established that Ctr9, Rtf1, and Leo1 are factors that associate with Paf1, Cdc73, and Pol II, but not with the Srb-mediator. Deletion of either PAF1 or CTR9 leads to similar severe pleiotropic phenotypes, which are unaltered when the two mutations are combined. In contrast, we found that deletion of LEO1 or RTF1 leads to few obvious phenotypes, although mutation of RTF1 suppresses mutations in TATA-binding protein, alters transcriptional start sites, and affects elongation. Remarkably, deletion of LEO1 or RTF1 suppresses many paf1Delta phenotypes. In particular, an rtf1Delta paf1Delta double mutant grew faster, was less temperature sensitive, and was more resistant to caffeine and hydroxyurea than a paf1Delta single mutant. In addition, expression of the G(1) cyclin CLN1, reduced nearly threefold in paf1Delta, is restored to wild-type levels in the rtf1Delta paf1Delta double mutant. We suggest that lack of Paf1 results in a defective complex and a block in transcription, which is relieved by removal of Leo1 or Rtf1.
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Affiliation(s)
- Cherie L Mueller
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
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38
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Oelgeschläger T. Regulation of RNA polymerase II activity by CTD phosphorylation and cell cycle control. J Cell Physiol 2002; 190:160-9. [PMID: 11807820 DOI: 10.1002/jcp.10058] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The carboxyl-terminal domain (CTD) of the largest subunit of mammalian RNA polymerase II (RNAP II) consists of 52 repeats of a consensus heptapeptide and is subject to phosphorylation and dephosphorylation events during each round of transcription. RNAP II activity is regulated during the cell cycle and cell cycle-dependend changes in RNAP II activity correlate well with CTD phosphorylation. In addition, global changes in the CTD phosphorylation status are observed in response to mitogenic or cytostatic signals such as growth factors, mitogens and DNA-damaging agents. Several CTD kinases are members of the cyclin-dependent kinase (CDK) superfamily and associate with transcription initiation complexes. Other CTD kinases implicated in cell cycle regulation include the mitogen-activated protein kinases ERK-1/2 and the c-Abl tyrosine kinase. These observations suggest that reversible RNAP II CTD phosphorylation may play a key role in linking cell cycle regulatory events to coordinated changes in transcription.
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Affiliation(s)
- Thomas Oelgeschläger
- Eukaryotic Gene Regulation Laboratory, Marie Curie Research Institute, The Chart, Oxted, Surrey, United Kingdom.
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39
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Zhou M, Nekhai S, Bharucha DC, Kumar A, Ge H, Price DH, Egly JM, Brady JN. TFIIH inhibits CDK9 phosphorylation during human immunodeficiency virus type 1 transcription. J Biol Chem 2001; 276:44633-40. [PMID: 11572868 DOI: 10.1074/jbc.m107466200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tat stimulates human immunodeficiency virus, type 1 (HIV-1), transcription elongation by recruitment of the human transcription elongation factor P-TEFb, consisting of CDK9 and cyclin T1, to the TAR RNA structure. It has been demonstrated further that CDK9 phosphorylation is required for high affinity binding of Tat/P-TEFb to the TAR RNA structure and that the state of P-TEFb phosphorylation may regulate Tat transactivation. We now demonstrate that CDK9 phosphorylation is uniquely regulated in the HIV-1 preinitiation and elongation complexes. The presence of TFIIH in the HIV-1 preinitiation complex inhibits CDK9 phosphorylation. As TFIIH is released from the elongation complex between +14 and +36, CDK9 phosphorylation is observed. In contrast to the activity in the "soluble" complex, phosphorylation of CDK9 is increased by the presence of Tat in the transcription complexes. Consistent with these observations, we have demonstrated that purified TFIIH directly inhibits CDK9 autophosphorylation. By using recombinant TFIIH subcomplexes, our results suggest that the XPB subunit of TFIIH is responsible for this inhibition of CDK9 phosphorylation. Interestingly, our results further suggest that the phosphorylated form of CDK9 is the active kinase for RNA polymerase II carboxyl-terminal domain phosphorylation.
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Affiliation(s)
- M Zhou
- Virus Tumor Biology Section, Basic Research Laboratory, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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