1
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Boulanger C, Haidara N, Yague-Sanz C, Larochelle M, Jacques PÉ, Hermand D, Bachand F. Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation. Nucleic Acids Res 2024; 52:7572-7589. [PMID: 38801067 PMCID: PMC11260464 DOI: 10.1093/nar/gkae436] [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: 03/23/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The RNA polymerase II carboxy-terminal domain (CTD) consists of conserved heptapeptide repeats that can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although CTD-associated proteins have been identified, phospho-dependent CTD interactions have remained elusive. Proximity-dependent biotinylation (PDB) has recently emerged as an alternative approach to identify protein-protein associations in the native cellular environment. In this study, we present a PDB-based map of the fission yeast RNAPII CTD interactome in living cells and identify phospho-dependent CTD interactions by using a mutant in which Ser2 was replaced by alanine in every repeat of the fission yeast CTD. This approach revealed that CTD Ser2 phosphorylation is critical for the association between RNAPII and the histone methyltransferase Set2 during transcription elongation, but is not required for 3' end processing and transcription termination. Accordingly, loss of CTD Ser2 phosphorylation causes a global increase in antisense transcription, correlating with elevated histone acetylation in gene bodies. Our findings reveal that the fundamental role of CTD Ser2 phosphorylation is to establish a chromatin-based repressive state that prevents cryptic intragenic transcription initiation.
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Affiliation(s)
- Cédric Boulanger
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Nouhou Haidara
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Carlo Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Marc Larochelle
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | | | - Damien Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Francois Bachand
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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2
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Velychko T, Mohammad E, Ferrer-Vicens I, Parfentev I, Werner M, Studniarek C, Schwalb B, Urlaub H, Murphy S, Cramer P, Lidschreiber M. CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release. Mol Cell 2024; 84:2287-2303.e10. [PMID: 38821049 DOI: 10.1016/j.molcel.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/01/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]
Abstract
Cyclin-dependent kinase 7 (CDK7), part of the general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (RNA Pol II). Here, we combine rapid CDK7 kinase inhibition with multi-omics analysis to unravel the direct functions of CDK7 in human cells. CDK7 inhibition causes RNA Pol II retention at promoters, leading to decreased RNA Pol II initiation and immediate global downregulation of transcript synthesis. Elongation, termination, and recruitment of co-transcriptional factors are not directly affected. Although RNA Pol II, initiation factors, and Mediator accumulate at promoters, RNA Pol II complexes can also proceed into gene bodies without promoter-proximal pausing while retaining initiation factors and Mediator. Further downstream, RNA Pol II phosphorylation increases and initiation factors and Mediator are released, allowing recruitment of elongation factors and an increase in RNA Pol II elongation velocity. Collectively, CDK7 kinase activity promotes the release of initiation factors and Mediator from RNA Pol II, facilitating RNA Pol II escape from the promoter.
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Affiliation(s)
- Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eusra Mohammad
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ivan Ferrer-Vicens
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marcel Werner
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cecilia Studniarek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
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3
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Borao S, Vega M, Boronat S, Hidalgo E, Hümmer S, Ayté J. A systematic screen identifies Saf5 as a link between splicing and transcription in fission yeast. PLoS Genet 2024; 20:e1011316. [PMID: 38833506 PMCID: PMC11178228 DOI: 10.1371/journal.pgen.1011316] [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: 01/11/2024] [Revised: 06/14/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Splicing is an important step of gene expression regulation in eukaryotes, as there are many mRNA precursors that can be alternatively spliced in different tissues, at different cell cycle phases or under different external stimuli. We have developed several integrated fluorescence-based in vivo splicing reporter constructs that allow the quantification of fission yeast splicing in vivo on intact cells, and we have compared their splicing efficiency in a wild type strain and in a prp2-1 (U2AF65) genetic background, showing a clear dependency between Prp2 and a consensus signal at 5' splicing site (5'SS). To isolate novel genes involved in regulated splicing, we have crossed the reporter showing more intron retention with the Schizosaccharomyces pombe knock out collection. Among the candidate genes involved in the regulation of splicing, we have detected strong splicing defects in two of the mutants -Δcwf12, a member of the NineTeen Complex (NTC) and Δsaf5, a methylosome subunit that acts together with the survival motor neuron (SMN) complex in small nuclear ribonucleoproteins (snRNP) biogenesis. We have identified that strains with mutations in cwf12 have inefficient splicing, mainly when the 5'SS differs from the consensus. However, although Δsaf5 cells also have some dependency on 5'SS sequence, we noticed that when one intron of a given pre-mRNA was affected, the rest of the introns of the same pre-mRNA had high probabilities of being also affected. This observation points Saf5 as a link between transcription rate and splicing.
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Affiliation(s)
- Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Susanna Boronat
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
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4
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Düster R, Anand K, Binder SC, Schmitz M, Gatterdam K, Fisher RP, Geyer M. Structural basis of Cdk7 activation by dual T-loop phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580246. [PMID: 38405971 PMCID: PMC10888979 DOI: 10.1101/2024.02.14.580246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Cyclin-dependent kinase 7 (Cdk7) occupies a central position in cell-cycle and transcriptional regulation owing to its function as both a CDK-activating kinase (CAK) and part of the general transcription factor TFIIH. Cdk7 forms an active complex upon association with Cyclin H and Mat1, and its catalytic activity is regulated by two phosphorylations in the activation segment (T loop): the canonical activating modification at T170 and another at S164. Here we report the crystal structure of the fully activated human Cdk7/Cyclin H/Mat1 complex containing both T-loop phosphorylations. Whereas pT170 coordinates a set of basic residues conserved in other CDKs, pS164 nucleates an arginine network involving all three subunits that is unique to the ternary Cdk7 complex. We identify differential dependencies of kinase activity and substrate recognition on individual phosphorylations within the Cdk7 T loop. The CAK function of Cdk7 is not affected by T-loop phosphorylation, whereas activity towards non-CDK substrates is increased several-fold by phosphorylation at T170. Moreover, dual T-loop phosphorylation at both T170 and S164 stimulates multi-site phosphorylation of transcriptional substrates-the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and the SPT5 carboxy-terminal repeat (CTR) region. In human cells, Cdk7-regulatory phosphorylation is a two-step process in which phosphorylation of S164 precedes, and may prime, T170 phosphorylation. Thus, dual T-loop phosphorylation can regulate Cdk7 through multiple mechanisms, with pS164 supporting tripartite complex formation and possibly influencing Cdk7 processivity, while the canonical pT170 enhances kinase activity towards critical substrates involved in transcription.
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Affiliation(s)
- Robert Düster
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kanchan Anand
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Sophie C. Binder
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Maximilian Schmitz
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Robert P. Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
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5
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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6
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DeBerardine M, Booth GT, Versluis PP, Lis JT. The NELF pausing checkpoint mediates the functional divergence of Cdk9. Nat Commun 2023; 14:2762. [PMID: 37179384 PMCID: PMC10182999 DOI: 10.1038/s41467-023-38359-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Promoter-proximal pausing by RNA Pol II is a rate-determining step in gene transcription that is hypothesized to be a prominent point at which regulatory factors act. The pausing factor NELF is known to induce and stabilize pausing, but not all kinds of pausing are NELF-mediated. Here, we find that NELF-depleted Drosophila melanogaster cells functionally recapitulate the NELF-independent pausing we previously observed in fission yeast (which lack NELF). Critically, only NELF-mediated pausing establishes a strict requirement for Cdk9 kinase activity for the release of paused Pol II into productive elongation. Upon inhibition of Cdk9, cells with NELF efficiently shutdown gene transcription, while in NELF-depleted cells, defective, non-productive transcription continues unabated. By introducing a strict checkpoint for Cdk9, the evolution of NELF was likely critical to enable increased regulation of Cdk9 in higher eukaryotes, as Cdk9 availability can be restricted to limit gene transcription without inducing wasteful, non-productive transcription.
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Affiliation(s)
- Michael DeBerardine
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Kanvas Biosciences, Monmouth Junction, NJ, USA
| | - Philip P Versluis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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7
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Ohtsuka H, Sakata H, Kitazaki Y, Tada M, Shimasaki T, Otsubo Y, Maekawa Y, Kobayashi M, Imada K, Yamashita A, Aiba H. The ecl family gene ecl3+ is induced by phosphate starvation and contributes to sexual differentiation in fission yeast. J Cell Sci 2023; 136:287015. [PMID: 36779416 PMCID: PMC10038150 DOI: 10.1242/jcs.260759] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/07/2023] [Indexed: 02/14/2023] Open
Abstract
In Schizosaccharomyces pombe, ecl family genes are induced by several signals, such as starvation of various nutrients, including sulfur, amino acids and Mg2+, and environmental stress, including heat or oxidative stress. These genes mediate appropriate cellular responses and contribute to the maintenance of cell viability and induction of sexual differentiation. Although this yeast has three ecl family genes with overlapping functions, any environmental conditions that induce ecl3+ remain unidentified. We demonstrate that ecl3+ is induced by phosphate starvation, similar to its chromosomally neighboring genes, pho1+ and pho84+, which respectively encode an extracellular acid phosphatase and an inorganic phosphate transporter. ecl3+ expression was induced by the transcription factor Pho7 and affected by the cyclin-dependent kinase (CDK)-activating kinase Csk1. Phosphate starvation induced G1 arrest and sexual differentiation via ecl family genes. Biochemical analyses suggested that this G1 arrest was mediated by the stabilization of the CDK inhibitor Rum1, which was dependent on ecl family genes. This study shows that ecl family genes are required for appropriate responses to phosphate starvation and provides novel insights into the diversity and similarity of starvation responses.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Hiroki Sakata
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuto Kitazaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masanobu Tada
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi 444-858, Japan
- National Institute for Fusion Science, Toki, Gifu 509-5292, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mikuto Kobayashi
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Imada
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi 444-858, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Aichi 464-8603, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
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8
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You KS, Yi YW, Cho J, Park JS, Seong YS. Potentiating Therapeutic Effects of Epidermal Growth Factor Receptor Inhibition in Triple-Negative Breast Cancer. Pharmaceuticals (Basel) 2021; 14:589. [PMID: 34207383 PMCID: PMC8233743 DOI: 10.3390/ph14060589] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subset of breast cancer with aggressive characteristics and few therapeutic options. The lack of an appropriate therapeutic target is a challenging issue in treating TNBC. Although a high level expression of epidermal growth factor receptor (EGFR) has been associated with a poor prognosis among patients with TNBC, targeted anti-EGFR therapies have demonstrated limited efficacy for TNBC treatment in both clinical and preclinical settings. However, with the advantage of a number of clinically approved EGFR inhibitors (EGFRis), combination strategies have been explored as a promising approach to overcome the intrinsic resistance of TNBC to EGFRis. In this review, we analyzed the literature on the combination of EGFRis with other molecularly targeted therapeutics or conventional chemotherapeutics to understand the current knowledge and to provide potential therapeutic options for TNBC treatment.
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Affiliation(s)
- Kyu Sic You
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea;
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 3116, Chungcheongnam-do, Korea
| | - Yong Weon Yi
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (J.C.)
| | - Jeonghee Cho
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (J.C.)
| | - Jeong-Soo Park
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea;
| | - Yeon-Sun Seong
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea;
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 3116, Chungcheongnam-do, Korea
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (J.C.)
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9
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Cossa G, Parua PK, Eilers M, Fisher RP. Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets. Genes Dev 2021; 35:658-676. [PMID: 33888562 PMCID: PMC8091971 DOI: 10.1101/gad.348315.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, Cossa et al. discuss the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle. The transcription cycle of RNA polymerase II (RNAPII) is governed at multiple points by opposing actions of cyclin-dependent kinases (CDKs) and protein phosphatases, in a process with similarities to the cell division cycle. While important roles of the kinases have been established, phosphatases have emerged more slowly as key players in transcription, and large gaps remain in understanding of their precise functions and targets. Much of the earlier work focused on the roles and regulation of sui generis and often atypical phosphatases—FCP1, Rtr1/RPAP2, and SSU72—with seemingly dedicated functions in RNAPII transcription. Decisive roles in the transcription cycle have now been uncovered for members of the major phosphoprotein phosphatase (PPP) family, including PP1, PP2A, and PP4—abundant enzymes with pleiotropic roles in cellular signaling pathways. These phosphatases appear to act principally at the transitions between transcription cycle phases, ensuring fine control of elongation and termination. Much is still unknown, however, about the division of labor among the PPP family members, and their possible regulation by or of the transcriptional kinases. CDKs active in transcription have recently drawn attention as potential therapeutic targets in cancer and other diseases, raising the prospect that the phosphatases might also present opportunities for new drug development. Here we review the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle.
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Affiliation(s)
- Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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10
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Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription. Proc Natl Acad Sci U S A 2020; 117:32348-32357. [PMID: 33293419 DOI: 10.1073/pnas.2011224117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In eukaryotes, RNA polymerase II (RNApII) transcribes messenger RNA from template DNA. Decades of experiments have identified the proteins needed for transcription activation, initiation complex assembly, and productive elongation. However, the dynamics of recruitment of these proteins to transcription complexes, and of the transitions between these steps, are poorly understood. We used multiwavelength single-molecule fluorescence microscopy to directly image and quantitate these dynamics in a budding yeast nuclear extract that reconstitutes activator-dependent transcription in vitro. A strong activator (Gal4-VP16) greatly stimulated reversible binding of individual RNApII molecules to template DNA. Binding of labeled elongation factor Spt4/5 to DNA typically followed RNApII binding, was NTP dependent, and was correlated with association of mRNA binding protein Hek2, demonstrating specificity of Spt4/5 binding to elongation complexes. Quantitative kinetic modeling shows that only a fraction of RNApII binding events are productive and implies a rate-limiting step, probably associated with recruitment of general transcription factors, needed to assemble a transcription-competent preinitiation complex at the promoter. Spt4/5 association with transcription complexes was slowly reversible, with DNA-bound RNApII molecules sometimes binding and releasing Spt4/5 multiple times. The average Spt4/5 residence time was of similar magnitude to the time required to transcribe an average length yeast gene. These dynamics suggest that a single Spt4/5 molecule remains associated during a typical transcription event, yet can dissociate from RNApII to allow disassembly of abnormally long-lived (i.e., stalled) elongation complexes.
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11
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Sansó M, Parua PK, Pinto D, Svensson JP, Pagé V, Bitton DA, MacKinnon S, Garcia P, Hidalgo E, Bähler J, Tanny JC, Fisher RP. Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription. Nucleic Acids Res 2020; 48:7154-7168. [PMID: 32496538 PMCID: PMC7367204 DOI: 10.1093/nar/gkaa474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.
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Affiliation(s)
- Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Danny A Bitton
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Patricia Garcia
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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12
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Parua PK, Kalan S, Benjamin B, Sansó M, Fisher RP. Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. Nat Commun 2020; 11:4338. [PMID: 32859893 PMCID: PMC7455706 DOI: 10.1038/s41467-020-18173-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022] Open
Abstract
Reversible phosphorylation of Pol II and accessory factors helps order the transcription cycle. Here, we define two kinase-phosphatase switches that operate at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3′ and 5′ ends of genes, respectively, and have overlapping but distinct specificities for Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between Kyrpides-Ouzounis-Woese (KOW) motifs 4 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation decreases as transcription complexes pass the cleavage and polyadenylation signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in termination first uncovered in yeast. Depletion of PP4-complex subunits increases phosphorylation of both Ser666 and the CTR, and promotes redistribution of promoter-proximally paused Pol II into gene bodies. These results suggest that switches comprising Cdk9 and either PP4 or PP1 govern pause release and the elongation-termination transition, respectively. Cdk9 (P-TEFb) and its substrate Spt5 influence events throughout the transcription cycle. Here, the authors define two switches with the potential to regulate promoter-proximal pause release and termination, respectively containing phosphatases PP4 and PP1, which are both inhibited by Cdk9, but have different specificities for sites on Spt5 and occupy opposite ends of genes.
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Affiliation(s)
- Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Sampada Kalan
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Bradley Benjamin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA.
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13
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Dissecting the Pol II transcription cycle and derailing cancer with CDK inhibitors. Nat Chem Biol 2020; 16:716-724. [PMID: 32572259 DOI: 10.1038/s41589-020-0563-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 05/07/2020] [Indexed: 12/16/2022]
Abstract
Largely non-overlapping sets of cyclin-dependent kinases (CDKs) regulate cell division and RNA polymerase II (Pol II)-dependent transcription. Here we review the molecular mechanisms by which specific CDKs are thought to act at discrete steps in the transcription cycle and describe the recent emergence of transcriptional CDKs as promising drug targets in cancer. We emphasize recent advances in understanding the transcriptional CDK network that were facilitated by development and deployment of small-molecule inhibitors with increased selectivity for individual CDKs. Unexpectedly, several of these compounds have also shown selectivity in killing cancer cells, despite the seemingly universal involvement of their target CDKs during transcription in all cells. Finally, we describe remaining and emerging challenges in defining functions of individual CDKs in transcription and co-transcriptional processes and in leveraging CDK inhibition for therapeutic purposes.
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14
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Ding L, Cao J, Lin W, Chen H, Xiong X, Ao H, Yu M, Lin J, Cui Q. The Roles of Cyclin-Dependent Kinases in Cell-Cycle Progression and Therapeutic Strategies in Human Breast Cancer. Int J Mol Sci 2020; 21:ijms21061960. [PMID: 32183020 PMCID: PMC7139603 DOI: 10.3390/ijms21061960] [Citation(s) in RCA: 250] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are serine/threonine kinases whose catalytic activities are regulated by interactions with cyclins and CDK inhibitors (CKIs). CDKs are key regulatory enzymes involved in cell proliferation through regulating cell-cycle checkpoints and transcriptional events in response to extracellular and intracellular signals. Not surprisingly, the dysregulation of CDKs is a hallmark of cancers, and inhibition of specific members is considered an attractive target in cancer therapy. In breast cancer (BC), dual CDK4/6 inhibitors, palbociclib, ribociclib, and abemaciclib, combined with other agents, were approved by the Food and Drug Administration (FDA) recently for the treatment of hormone receptor positive (HR+) advanced or metastatic breast cancer (A/MBC), as well as other sub-types of breast cancer. Furthermore, ongoing studies identified more selective CDK inhibitors as promising clinical targets. In this review, we focus on the roles of CDKs in driving cell-cycle progression, cell-cycle checkpoints, and transcriptional regulation, a highlight of dysregulated CDK activation in BC. We also discuss the most relevant CDK inhibitors currently in clinical BC trials, with special emphasis on CDK4/6 inhibitors used for the treatment of estrogen receptor-positive (ER+)/human epidermal growth factor 2-negative (HER2−) M/ABC patients, as well as more emerging precise therapeutic strategies, such as combination therapies and microRNA (miRNA) therapy.
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Affiliation(s)
- Lei Ding
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Jiaqi Cao
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Wen Lin
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Hongjian Chen
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Xianhui Xiong
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Hongshun Ao
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Min Yu
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Jie Lin
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Qinghua Cui
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
- Correspondence:
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15
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Duan J, Liu Q, Su S, Cha J, Zhou Y, Tang R, Liu X, Wang Y, Liu Y, He Q. The Neurospora RNA polymerase II kinase CTK negatively regulates catalase expression in a chromatin context-dependent manner. Environ Microbiol 2019; 22:76-90. [PMID: 31599077 DOI: 10.1111/1462-2920.14821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/25/2019] [Accepted: 10/02/2019] [Indexed: 01/15/2023]
Abstract
Clearance and adaptation to reactive oxygen species (ROS) are crucial for cell survival. As in other eukaryotes, the Neurospora catalases are the main enzymes responsible for ROS clearance and their expression are tightly regulated by the growth and environmental conditions. The RNA polymerase II carboxyl terminal domain (RNAPII CTD) kinase complex (CTK complex) is known as a positive elongation factor for many inducible genes by releasing paused RNAPII near the transcription start site and promoting transcription elongation. However, here we show that deletion of CTK complex components in Neurospora led to high CAT-3 expression level and resistance to H2 O2 -induced ROS stress. The catalytic activity of CTK-1 is required for such a response. On the other hand, CTK-1 overexpression led to decreased expression of CAT-3. ChIP assays shows that CTK-1 phosphorylates the RNAPII CTD at Ser2 residues in the cat-3 ORF region during transcription elongation and deletion of CTK-1 led to dramatic decreases of SET-2 recruitment and H3K36me3 modification. As a result, histones at the cat-3 locus become hyperacetylated to promote its transcription. Together, these results demonstrate that the CTK complex is negative regulator of cat-3 expression by affecting its chromatin structure.
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Affiliation(s)
- Jiabin Duan
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qingqing Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Sodgerel Su
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Joonseok Cha
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Yike Zhou
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ruiqi Tang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Wang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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16
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Pagé V, Chen JJ, Durand-Dubief M, Grabowski D, Oya E, Sansô M, Martin RD, Hébert TE, Fisher RP, Ekwall K, Tanny JC. Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast. Genetics 2019; 213:161-172. [PMID: 31345994 PMCID: PMC6727805 DOI: 10.1534/genetics.119.302499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 02/08/2023] Open
Abstract
Histone H2B monoubiquitylation (H2Bub1) is tightly linked to RNA polymerase II transcription elongation, and is also directly implicated in DNA replication and repair. Loss of H2Bub1 is associated with defects in cell cycle progression, but how these are related to its various functions, and the underlying mechanisms involved, is not understood. Here we describe a role for H2Bub1 in the regulation of replication-dependent histone genes in the fission yeast Schizosaccharomyces pombe H2Bub1 activates histone genes indirectly by suppressing antisense transcription of ams2+ -a gene encoding a GATA-type transcription factor that activates histone genes and is required for assembly of centromeric chromatin. Mutants lacking the ubiquitylation site in H2B or the H2B-specific E3 ubiquitin ligase Brl2 had elevated levels of ams2+ antisense transcripts and reduced Ams2 protein levels. These defects were reversed upon inhibition of Cdk9-an ortholog of the kinase component of positive transcription elongation factor b (P-TEFb)-indicating that they likely resulted from aberrant transcription elongation. Reduced Cdk9 activity also partially rescued chromosome segregation phenotypes of H2Bub1 mutants. In a genome-wide analysis, loss of H2Bub1 led to increased antisense transcripts at over 500 protein-coding genes in H2Bub1 mutants; for a subset of these, including several genes involved in chromosome segregation and chromatin assembly, antisense derepression was Cdk9-dependent. Our results highlight antisense suppression as a key feature of cell cycle-dependent gene regulation by H2Bub1, and suggest that aberrant transcription elongation may underlie the effects of H2Bub1 loss on cell cycle progression.
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Affiliation(s)
- Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Jennifer J Chen
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Mickael Durand-Dubief
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm 17177, Sweden
| | - David Grabowski
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Eriko Oya
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm 17177, Sweden
| | - Miriam Sansô
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, Mount Sinai School of Medicine, New York, New York 10029
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, Mount Sinai School of Medicine, New York, New York 10029
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm 17177, Sweden
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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17
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Chun Y, Joo YJ, Suh H, Batot G, Hill CP, Formosa T, Buratowski S. Selective Kinase Inhibition Shows That Bur1 (Cdk9) Phosphorylates the Rpb1 Linker In Vivo. Mol Cell Biol 2019; 39:e00602-18. [PMID: 31085683 PMCID: PMC6639251 DOI: 10.1128/mcb.00602-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/21/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
Cyclin-dependent kinases play multiple roles in RNA polymerase II transcription. Cdk7/Kin28, Cdk9/Bur1, and Cdk12/Ctk1 phosphorylate the polymerase and other factors to drive the dynamic exchange of initiation and elongation complex components over the transcription cycle. We engineered strains of the yeast Saccharomyces cerevisiae for rapid, specific inactivation of individual kinases by addition of a covalent inhibitor. While effective, the sensitized kinases can display some idiosyncrasies, and inhibition can be surprisingly transient. As expected, inhibition of Cdk7/Kin28 blocked phosphorylation of the Rpb1 C-terminal domain heptad repeats at serines 5 and 7, the known target sites. However, serine 2 phosphorylation was also abrogated, supporting an obligatory sequential phosphorylation mechanism. Consistent with our previous results using gene deletions, Cdk12/Ctk1 is the predominant kinase responsible for serine 2 phosphorylation. Phosphorylation of the Rpb1 linker enhances binding of the Spt6 tandem SH2 domain, and here we show that Bur1/Cdk9 is the kinase responsible for these modifications in vivo.
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Affiliation(s)
- Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Yoo Jin Joo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Hyunsuk Suh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gaëlle Batot
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Christopher P Hill
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tim Formosa
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
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18
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McLaughlin RP, He J, van der Noord VE, Redel J, Foekens JA, Martens JWM, Smid M, Zhang Y, van de Water B. A kinase inhibitor screen identifies a dual cdc7/CDK9 inhibitor to sensitise triple-negative breast cancer to EGFR-targeted therapy. Breast Cancer Res 2019; 21:77. [PMID: 31262335 PMCID: PMC6604188 DOI: 10.1186/s13058-019-1161-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The effective treatment of triple-negative breast cancer (TNBC) remains a profound clinical challenge. Despite frequent epidermal growth factor receptor (EGFR) overexpression and reliance on downstream signalling pathways in TNBC, resistance to EGFR-tyrosine kinase inhibitors (TKIs) remains endemic. Therefore, the identification of targeted agents, which synergise with current therapeutic options, is paramount. METHODS Compound-based, high-throughput, proliferation screening was used to profile the response of TNBC cell lines to EGFR-TKIs, western blotting and siRNA transfection being used to examine the effect of inhibitors on EGFR-mediated signal transduction and cellular dependence on such pathways, respectively. A kinase inhibitor combination screen was used to identify compounds that synergised with EGFR-TKIs in TNBC, utilising sulphorhodamine B (SRB) assay as read-out for proliferation. The impact of drug combinations on cell cycle arrest, apoptosis and signal transduction was assessed using flow cytometry, automated live-cell imaging and western blotting, respectively. RNA sequencing was employed to unravel transcriptomic changes elicited by this synergistic combination and to permit identification of the signalling networks most sensitive to co-inhibition. RESULTS We demonstrate that a dual cdc7/CDK9 inhibitor, PHA-767491, synergises with multiple EGFR-TKIs (lapatinib, erlotinib and gefitinib) to overcome resistance to EGFR-targeted therapy in various TNBC cell lines. Combined inhibition of EGFR and cdc7/CDK9 resulted in reduced cell proliferation, accompanied by induction of apoptosis, G2-M cell cycle arrest, inhibition of DNA replication and abrogation of CDK9-mediated transcriptional elongation, in contrast to mono-inhibition. Moreover, high expression of cdc7 and RNA polymerase II Subunit A (POLR2A), the direct target of CDK9, is significantly correlated with poor metastasis-free survival in a cohort of breast cancer patients. RNA sequencing revealed marked downregulation of pathways governing proliferation, transcription and cell survival in TNBC cells treated with the combination of an EGFR-TKI and a dual cdc7/CDK9 inhibitor. A number of genes enriched in these downregulated pathways are associated with poor metastasis-free survival in TNBC. CONCLUSIONS Our results highlight that dual inhibition of cdc7 and CDK9 by PHA-767491 is a potential strategy for targeting TNBC resistant to EGFR-TKIs.
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Affiliation(s)
- Ronan P. McLaughlin
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jichao He
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Vera E. van der Noord
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jevin Redel
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - John A. Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yinghui Zhang
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Bob van de Water
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
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19
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Fisher RP. Cdk7: a kinase at the core of transcription and in the crosshairs of cancer drug discovery. Transcription 2019; 10:47-56. [PMID: 30488763 PMCID: PMC6602562 DOI: 10.1080/21541264.2018.1553483] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 12/22/2022] Open
Abstract
The transcription cycle of RNA polymerase II (Pol II) is regulated by a set of cyclin-dependent kinases (CDKs). Cdk7, associated with the transcription initiation factor TFIIH, is both an effector CDK that phosphorylates Pol II and other targets within the transcriptional machinery, and a CDK-activating kinase (CAK) for at least one other essential CDK involved in transcription. Recent studies have illuminated Cdk7 functions that are executed throughout the Pol II transcription cycle, from promoter clearance and promoter-proximal pausing, to co-transcriptional chromatin modification in gene bodies, to mRNA 3´-end formation and termination. Cdk7 has also emerged as a target of small-molecule inhibitors that show promise in the treatment of cancer and inflammation. The challenges now are to identify the relevant targets of Cdk7 at each step of the transcription cycle, and to understand how heightened dependence on an essential CDK emerges in cancer, and might be exploited therapeutically.
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Affiliation(s)
- Robert P. Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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20
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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21
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Kecman T, Kuś K, Heo DH, Duckett K, Birot A, Liberatori S, Mohammed S, Geis-Asteggiante L, Robinson CV, Vasiljeva L. Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination. Cell Rep 2018; 25:259-269.e5. [PMID: 30282034 PMCID: PMC6180485 DOI: 10.1016/j.celrep.2018.09.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/27/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Termination of RNA polymerase II (Pol II) transcription is a key step that is important for 3' end formation of functional mRNA, mRNA release, and Pol II recycling. Even so, the underlying termination mechanism is not yet understood. Here, we demonstrate that the conserved and essential termination factor Seb1 is found on Pol II near the end of the RNA exit channel and the Rpb4/7 stalk. Furthermore, the Seb1 interaction surface with Pol II largely overlaps with that of the elongation factor Spt5. Notably, Seb1 co-transcriptional recruitment is dependent on Spt5 dephosphorylation by the conserved PP1 phosphatase Dis2, which also dephosphorylates threonine 4 within the Pol II heptad repeated C-terminal domain. We propose that Dis2 orchestrates the transition from elongation to termination phase during the transcription cycle by mediating elongation to termination factor exchange and dephosphorylation of Pol II C-terminal domain.
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Affiliation(s)
- Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Krzysztof Kuś
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Katie Duckett
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Department of Chemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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22
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Kalan S, Amat R, Schachter MM, Kwiatkowski N, Abraham BJ, Liang Y, Zhang T, Olson CM, Larochelle S, Young RA, Gray NS, Fisher RP. Activation of the p53 Transcriptional Program Sensitizes Cancer Cells to Cdk7 Inhibitors. Cell Rep 2018; 21:467-481. [PMID: 29020632 DOI: 10.1016/j.celrep.2017.09.056] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/21/2017] [Accepted: 09/17/2017] [Indexed: 12/23/2022] Open
Abstract
Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors that kill cancer cells by exploiting tumor-specific transcriptional dependencies. However, whereas selective inhibition of analog-sensitive (AS) Cdk7 in colon cancer-derived cells arrests division and disrupts transcription, it does not by itself trigger apoptosis efficiently. Here, we show that p53 activation by 5-fluorouracil or nutlin-3 synergizes with a reversible Cdk7as inhibitor to induce cell death. Synthetic lethality was recapitulated with covalent inhibitors of wild-type Cdk7, THZ1, or the more selective YKL-1-116. The effects were allele specific; a CDK7as mutation conferred both sensitivity to bulky adenine analogs and resistance to covalent inhibitors. Non-transformed colon epithelial cells were resistant to these combinations, as were cancer-derived cells with p53-inactivating mutations. Apoptosis was dependent on death receptor DR5, a p53 transcriptional target whose expression was refractory to Cdk7 inhibition. Therefore, p53 activation induces transcriptional dependency to sensitize cancer cells to Cdk7 inhibition.
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Affiliation(s)
- Sampada Kalan
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ramon Amat
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merzel Schachter
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yanke Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Calla M Olson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stéphane Larochelle
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, MA 02142, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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23
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Parua PK, Booth GT, Sansó M, Benjamin B, Tanny JC, Lis JT, Fisher RP. A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II. Nature 2018; 558:460-464. [PMID: 29899453 PMCID: PMC6021199 DOI: 10.1038/s41586-018-0214-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 04/17/2018] [Indexed: 11/09/2022]
Abstract
The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to prevent interference between neighbouring genes and to safeguard transcriptome integrity 1 . The accumulation of Pol II downstream of the cleavage and polyadenylation signal can facilitate the recruitment of factors involved in mRNA 3'-end formation and termination 2 , but how this sequence is initiated remains unclear. In a chemical-genetic screen, human protein phosphatase 1 (PP1) isoforms were identified as substrates of positive transcription elongation factor b (P-TEFb), also known as the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 (CycT1) complex 3 . Here we show that Cdk9 and PP1 govern phosphorylation of the conserved elongation factor Spt5 in the fission yeast Schizosaccharomyces pombe. Cdk9 phosphorylates both Spt5 and a negative regulatory site on the PP1 isoform Dis2 4 . Sites targeted by Cdk9 in the Spt5 carboxy-terminal domain can be dephosphorylated by Dis2 in vitro, and dis2 mutations retard Spt5 dephosphorylation after inhibition of Cdk9 in vivo. Chromatin immunoprecipitation and sequencing analysis indicates that Spt5 is dephosphorylated as transcription complexes traverse the cleavage and polyadenylation signal, concomitant with the accumulation of Pol II phosphorylated at residue Ser2 of the carboxy-terminal domain consensus heptad repeat 5 . A conditionally lethal Dis2-inactivating mutation attenuates the drop in Spt5 phosphorylation on chromatin, promotes transcription beyond the normal termination zone (as detected by precision run-on transcription and sequencing 6 ) and is genetically suppressed by the ablation of Cdk9 target sites in Spt5. These results suggest that the transition of Pol II from elongation to termination coincides with a Dis2-dependent reversal of Cdk9 signalling-a switch that is analogous to a Cdk1-PP1 circuit that controls mitotic progression 4 .
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Affiliation(s)
- Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Bradley Benjamin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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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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25
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Ebmeier CC, Erickson B, Allen BL, Allen MA, Kim H, Fong N, Jacobsen JR, Liang K, Shilatifard A, Dowell RD, Old WM, Bentley DL, Taatjes DJ. Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications. Cell Rep 2018; 20:1173-1186. [PMID: 28768201 DOI: 10.1016/j.celrep.2017.07.021] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 01/24/2023] Open
Abstract
CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3' ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5' ends and H3K36me3 was displaced toward gene 3' ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent "CTD code" that regulates chromatin marks in addition to RNA processing and pol II pausing.
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Affiliation(s)
- Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA; Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Benjamin Erickson
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Benjamin L Allen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hyunmin Kim
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Nova Fong
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jeremy R Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Kaiwei Liang
- Department of Biochemistry & Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry & Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Robin D Dowell
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - William M Old
- Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David L Bentley
- Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
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26
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Booth GT, Parua PK, Sansó M, Fisher RP, Lis JT. Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast. Nat Commun 2018; 9:543. [PMID: 29416031 PMCID: PMC5803247 DOI: 10.1038/s41467-018-03006-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/12/2018] [Indexed: 12/25/2022] Open
Abstract
Post-translational modifications of the transcription elongation complex provide mechanisms to fine-tune gene expression, yet their specific impacts on RNA polymerase II regulation remain difficult to ascertain. Here, in Schizosaccharomyces pombe, we examine the role of Cdk9, and related Mcs6/Cdk7 and Lsk1/Cdk12 kinases, on transcription at base-pair resolution with Precision Run-On sequencing (PRO-seq). Within a minute of Cdk9 inhibition, phosphorylation of Pol II-associated factor, Spt5 is undetectable. The effects of Cdk9 inhibition are more severe than inhibition of Cdk7 and Cdk12, resulting in a shift of Pol II toward the transcription start site (TSS). A time course of Cdk9 inhibition reveals that early transcribing Pol II can escape promoter-proximal regions, but with a severely reduced elongation rate of only ~400 bp/min. Our results in fission yeast suggest the existence of a conserved global regulatory checkpoint that requires Cdk9 kinase activity.
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Affiliation(s)
- Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, 107 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853-2703, USA
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, 107 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853-2703, USA.
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27
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Abstract
Over the past two decades there has been a great deal of interest in the development of inhibitors of the cyclin-dependent kinases (CDKs). This attention initially stemmed from observations that different CDK isoforms have key roles in cancer cell proliferation through loss of regulation of the cell cycle, a hallmark feature of cancer. CDKs have now been shown to regulate other processes, particularly various aspects of transcription. The early non-selective CDK inhibitors exhibited considerable toxicity and proved to be insufficiently active in most cancers. The lack of patient selection biomarkers and an absence of understanding of the inhibitory profile required for efficacy hampered the development of these inhibitors. However, the advent of potent isoform-selective inhibitors with accompanying biomarkers has re-ignited interest. Palbociclib, a selective CDK4/6 inhibitor, is now approved for the treatment of ER+/HER2- advanced breast cancer. Current developments in the field include the identification of potent and selective inhibitors of the transcriptional CDKs; these include tool compounds that have allowed exploration of individual CDKs as cancer targets and the determination of their potential therapeutic windows. Biomarkers that allow the selection of patients likely to respond are now being discovered. Drug resistance has emerged as a major hurdle in the clinic for most protein kinase inhibitors and resistance mechanism are beginning to be identified for CDK inhibitors. This suggests that the selective inhibitors may be best used combined with standard of care or other molecularly targeted agents now in development rather than in isolation as monotherapies.
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Affiliation(s)
- Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Aurélie Mallinger
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul A Clarke
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, United Kingdom; Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SW7 3RP, United Kingdom.
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28
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Shetty A, Kallgren SP, Demel C, Maier KC, Spatt D, Alver BH, Cramer P, Park PJ, Winston F. Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Mol Cell 2017; 66:77-88.e5. [PMID: 28366642 DOI: 10.1016/j.molcel.2017.02.023] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/12/2017] [Accepted: 02/22/2017] [Indexed: 12/11/2022]
Abstract
Spt5 is an essential and conserved factor that functions in transcription and co-transcriptional processes. However, many aspects of the requirement for Spt5 in transcription are poorly understood. We have analyzed the consequences of Spt5 depletion in Schizosaccharomyces pombe using four genome-wide approaches. Our results demonstrate that Spt5 is crucial for a normal rate of RNA synthesis and distribution of RNAPII over transcription units. In the absence of Spt5, RNAPII localization changes dramatically, with reduced levels and a relative accumulation over the first ∼500 bp, suggesting that Spt5 is required for transcription past a barrier. Spt5 depletion also results in widespread antisense transcription initiating within this barrier region. Deletions of this region alter the distribution of RNAPII on the sense strand, suggesting that the barrier observed after Spt5 depletion is normally a site at which Spt5 stimulates elongation. Our results reveal a global requirement for Spt5 in transcription elongation.
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Affiliation(s)
- Ameet Shetty
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Scott P Kallgren
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Carina Demel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Dan Spatt
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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29
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Abstract
Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the "torpedo" exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle.
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Affiliation(s)
- Robert P Fisher
- a Department of Oncological Sciences , Icahn School of Medicine at Mount Sinai , New York , NY , USA
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30
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Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization. Mol Cell 2016; 63:433-44. [PMID: 27477907 DOI: 10.1016/j.molcel.2016.06.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/09/2016] [Accepted: 06/23/2016] [Indexed: 12/25/2022]
Abstract
During transcription initiation, the TFIIH-kinase Kin28/Cdk7 marks RNA polymerase II (Pol II) by phosphorylating the C-terminal domain (CTD) of its largest subunit. Here we describe a structure-guided chemical approach to covalently and specifically inactivate Kin28 kinase activity in vivo. This method of irreversible inactivation recapitulates both the lethal phenotype and the key molecular signatures that result from genetically disrupting Kin28 function in vivo. Inactivating Kin28 impacts promoter release to differing degrees and reveals a "checkpoint" during the transition to productive elongation. While promoter-proximal pausing is not observed in budding yeast, inhibition of Kin28 attenuates elongation-licensing signals, resulting in Pol II accumulation at the +2 nucleosome and reduced transition to productive elongation. Furthermore, upon inhibition, global stabilization of mRNA masks different degrees of reduction in nascent transcription. This study resolves long-standing controversies on the role of Kin28 in transcription and provides a rational approach to irreversibly inhibit other kinases in vivo.
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31
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Booth GT, Wang IX, Cheung VG, Lis JT. Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast. Genome Res 2016; 26:799-811. [PMID: 27197211 PMCID: PMC4889974 DOI: 10.1101/gr.204578.116] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/19/2016] [Indexed: 12/29/2022]
Abstract
Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.
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Affiliation(s)
- Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
| | - Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
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32
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Schwer B, Sanchez AM, Shuman S. RNA polymerase II CTD phospho-sites Ser5 and Ser7 govern phosphate homeostasis in fission yeast. RNA (NEW YORK, N.Y.) 2015; 21:1770-80. [PMID: 26264592 PMCID: PMC4574753 DOI: 10.1261/rna.052555.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/08/2015] [Indexed: 05/08/2023]
Abstract
Phosphorylation of the tandem YSPTSPS repeats of the RNA polymerase II CTD inscribes an informational code that orchestrates eukaryal mRNA synthesis. Here we interrogate the role of the CTD in phosphate homeostasis in fission yeast. Expression of Pho1 acid phosphatase, which is repressed during growth in phosphate-rich medium and induced by phosphate starvation, is governed strongly by CTD phosphorylation status, but not by CTD repeat length. Inability to place a Ser7-PO4 mark (as in S7A) results in constitutive derepression of Pho1 expression in phosphate-replete medium. In contrast, indelible installation of a Ser7-PO4 mimetic (as in S7E) hyper-represses Pho1 in phosphate-replete cells and inhibits Pho1 induction during starvation. Pho1 phosphatase is derepressed by ablation of the CTD Ser5-PO4 mark, achieved either by mutating Ser5 in all consensus heptads to alanine, or replacing all Pro6 residues with alanine. We find that Ser5 status is a tunable determinant of Pho1 regulation, i.e., serial decrements in the number of consensus Ser5 heptads from seven to two elicits a progressive increase in Pho1 expression in phosphate-replete medium. Pho1 is also derepressed by hypomorphic mutations of the CTD kinase Cdk9. Inactivation of the CTD phosphatase Ssu72 attenuates Pho1 induction in wild-type cells and blocks Pho1 derepression in S7A cells. These experiments implicate Ser5, Pro6, and Ser7 as component letters of a CTD coding "word" that transduces a repressive transcriptional signal via serine phosphorylation.
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Affiliation(s)
- Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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33
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Mühlbacher W, Mayer A, Sun M, Remmert M, Cheung ACM, Niesser J, Soeding J, Cramer P. Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold. Proteins 2015. [PMID: 26219431 DOI: 10.1002/prot.24869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CTDK-I is a yeast kinase complex that phosphorylates the C-terminal repeat domain (CTD) of RNA polymerase II (Pol II) to promote transcription elongation. CTDK-I contains the cyclin-dependent kinase Ctk1 (homologous to human CDK9/CDK12), the cyclin Ctk2 (human cyclin K), and the yeast-specific subunit Ctk3, which is required for CTDK-I stability and activity. Here we predict that Ctk3 consists of a N-terminal CTD-interacting domain (CID) and a C-terminal three-helix bundle domain. We determine the X-ray crystal structure of the N-terminal domain of the Ctk3 homologue Lsg1 from the fission yeast Schizosaccharomyces pombe at 2.0 Å resolution. The structure reveals eight helices arranged into a right-handed superhelical fold that resembles the CID domain present in transcription termination factors Pcf11, Nrd1, and Rtt103. Ctk3 however shows different surface properties and no binding to CTD peptides. Together with the known structure of Ctk1 and Ctk2 homologues, our results lead to a molecular framework for analyzing the structure and function of the CTDK-I complex.
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Affiliation(s)
- Wolfgang Mühlbacher
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Andreas Mayer
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Mai Sun
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Michael Remmert
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Alan C M Cheung
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Jürgen Niesser
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Johannes Soeding
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
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34
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Mbogning J, Pagé V, Burston J, Schwenger E, Fisher RP, Schwer B, Shuman S, Tanny JC. Functional interaction of Rpb1 and Spt5 C-terminal domains in co-transcriptional histone modification. Nucleic Acids Res 2015; 43:9766-75. [PMID: 26275777 PMCID: PMC4787787 DOI: 10.1093/nar/gkv837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/09/2015] [Indexed: 12/11/2022] Open
Abstract
Transcription by RNA polymerase II (RNAPII) is accompanied by a conserved pattern of histone modifications that plays important roles in regulating gene expression. The establishment of this pattern requires phosphorylation of both Rpb1 (the largest RNAPII subunit) and the elongation factor Spt5 on their respective C-terminal domains (CTDs). Here we interrogated the roles of individual Rpb1 and Spt5 CTD phospho-sites in directing co-transcriptional histone modifications in the fission yeast Schizosaccharomyces pombe. Steady-state levels of methylation at histone H3 lysines 4 (H3K4me) and 36 (H3K36me) were sensitive to multiple mutations of the Rpb1 CTD repeat motif (Y1S2P3T4S5P6S7). Ablation of the Spt5 CTD phospho-site Thr1 reduced H3K4me levels but had minimal effects on H3K36me. Nonetheless, Spt5 CTD mutations potentiated the effects of Rpb1 CTD mutations on H3K36me, suggesting overlapping functions. Phosphorylation of Rpb1 Ser2 by the Cdk12 orthologue Lsk1 positively regulated H3K36me but negatively regulated H3K4me. H3K36me and histone H2B monoubiquitylation required Rpb1 Ser5 but were maintained upon inactivation of Mcs6/Cdk7, the major kinase for Rpb1 Ser5 in vivo, implicating another Ser5 kinase in these regulatory pathways. Our results elaborate the CTD ‘code’ for co-transcriptional histone modifications.
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Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Jillian Burston
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Emily Schwenger
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
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35
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Srivastava R, Ahn SH. Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function. Biotechnol Adv 2015; 33:856-72. [PMID: 26241863 DOI: 10.1016/j.biotechadv.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/08/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022]
Abstract
At the onset of transcription, many protein machineries interpret the cellular signals that regulate gene expression. These complex signals are mostly transmitted to the indispensable primary proteins involved in transcription, RNA polymerase II (RNAPII) and histones. RNAPII and histones are so well coordinated in this cellular function that each cellular signal is precisely allocated to specific machinery depending on the stage of transcription. The carboxy-terminal domain (CTD) of RNAPII in eukaryotes undergoes extensive posttranslational modification, called the 'CTD code', that is indispensable for coupling transcription with many cellular processes, including mRNA processing. The posttranslational modification of histones, known as the 'histone code', is also critical for gene transcription through the reversible and dynamic remodeling of chromatin structure. Notably, the histone code is closely linked with the CTD code, and their combinatorial effects enable the delicate regulation of gene transcription. This review elucidates recent findings regarding the CTD modifications of RNAPII and their coordination with the histone code, providing integrative pathways for the fine-tuned regulation of gene expression and cellular function.
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Affiliation(s)
- Rakesh Srivastava
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seong Hoon Ahn
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea.
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36
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Schwer B, Ghosh A, Sanchez AM, Lima CD, Shuman S. Genetic and structural analysis of the essential fission yeast RNA polymerase II CTD phosphatase Fcp1. RNA (NEW YORK, N.Y.) 2015; 21:1135-1146. [PMID: 25883047 PMCID: PMC4436666 DOI: 10.1261/rna.050286.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
Protein phosphatases regulate mRNA synthesis and processing by remodeling the carboxy-terminal domain (CTD) of RNA polymerase II (Pol2) to dynamically inscribe a Pol2 CTD code. Fission yeast Fcp1 (SpFcp1) is an essential 723-amino acid CTD phosphatase that preferentially hydrolyzes Ser2-PO4 of the YS(2)PTSPS repeat. The SpFcp1 catalytic domain (aa 140-580) is composed of a DxDxT acyl-phosphatase module (FCPH) and a BRCT module. Here we conducted a genetic analysis of SpFcp1, which shows that (i) phosphatase catalytic activity is required for vegetative growth of fission yeast; (ii) the flanking amino-terminal domain (aa 1-139) and its putative metal-binding motif C(99)H(101)Cys(109)C(112) are essential; (iii) the carboxy-terminal domain (aa 581-723) is dispensable; (iv) a structurally disordered internal segment of the FCPH domain (aa 330-393) is dispensable; (v) lethal SpFcp1 mutations R271A and R299A are rescued by shortening the Pol2 CTD repeat array; and (vi) CTD Ser2-PO4 is not the only essential target of SpFcp1 in vivo. Recent studies highlight a second CTD code involving threonine phosphorylation of a repeat motif in transcription elongation factor Spt5. We find that Fcp1 can dephosphorylate Thr1-PO4 of the fission yeast Spt5 CTD nonamer repeat T(1)PAWNSGSK. We identify Arg271 as a governor of Pol2 versus Spt5 CTD substrate preference. Our findings implicate Fcp1 as a versatile sculptor of both the Pol2 and Spt5 CTD codes. Finally, we report a new 1.45 Å crystal structure of SpFcp1 with Mg(2+) and AlF3 that mimics an associative phosphorane transition state of the enzyme-aspartyl-phosphate hydrolysis reaction.
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Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Agnidipta Ghosh
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Ana M Sanchez
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA Howard Hughes Medical Institute, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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Rzymski T, Mikula M, Wiklik K, Brzózka K. CDK8 kinase--An emerging target in targeted cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1617-29. [PMID: 26006748 DOI: 10.1016/j.bbapap.2015.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase (CDK) inhibitors have been developed as potential anticancer therapeutics and several nonselective compounds are currently in advanced clinical trials. This review is focused on the key biological roles of CDK8 kinase, which provide a proof-of-principle for continued efforts toward effective cancer treatment, targeting activity of this CDK family member. Among currently identified kinase inhibitors, several displayed significant selectivity for CDK8 and notably the effectiveness in targeting cancer specific gene expression programs. Structural features of CDK8 and available ligands were discussed from a perspective of the rational drug design process. Current state of the art confirms that further development of CDK8 inhibitors will translate into targeted therapies in oncology. This article is part of a Special Issue entitled:Inhibitors of Protein Kinases.
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Affiliation(s)
| | - Michał Mikula
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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38
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Dunn S, Cowling VH. Myc and mRNA capping. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1849:501-5. [PMID: 24681440 PMCID: PMC6414814 DOI: 10.1016/j.bbagrm.2014.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/12/2014] [Accepted: 03/18/2014] [Indexed: 01/05/2023]
Abstract
c-Myc is upregulated in response to growth factors and transmits the signal to proliferate by altering the gene expression landscape. When genetic alterations result in growth factor-independent c-Myc expression, it can become an oncogene. The majority of human tumour types exhibit a degree of c-Myc deregulation, resulting in unrestrained cell proliferation. c-Myc binds proximal to the promoter region of genes and recruits co-factors including histone acetyltransferases and RNA pol II kinases, which promote transcription. c-Myc also promotes formation of the cap structure at the 5' end of mRNA. The cap is 7-methylguanosine linked to the first transcribed nucleotide of RNA pol II transcripts via a 5' to 5' triphosphate bridge. The cap is added to the first transcribed nucleotide by the capping enzymes, RNGTT and RNMT-RAM. During the early stages of transcription, the capping enzymes are recruited to RNA pol II phosphorylated on Serine-5 of the C-terminal domain. The mRNA cap protects transcripts from degradation during transcription and recruits factors which promote RNA processing including, splicing, export and translation initiation. The proportion of transcripts with a cap structure is increased by elevating c-Myc expression, resulting in increased rates of translation. c-Myc promotes capping by promoting RNA pol II phosphorylation and by upregulating the enzyme SAHH which neutralises the inhibitory bi-product of methylation reactions, SAH. c-Myc-induced capping is required for c-Myc-dependent gene expression and cell proliferation. Targeting capping may represent a new therapeutic opportunity to inhibit c-Myc function in tumours. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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Affiliation(s)
- Sianadh Dunn
- MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Fission yeast Cdk7 controls gene expression through both its CAK and C-terminal domain kinase activities. Mol Cell Biol 2015; 35:1480-90. [PMID: 25691663 DOI: 10.1128/mcb.00024-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/03/2015] [Indexed: 11/20/2022] Open
Abstract
Cyclin-dependent kinase (Cdk) activation and RNA polymerase II transcription are linked by the Cdk7 kinase, which phosphorylates Cdks as a trimeric Cdk-activating kinase (CAK) complex, and serine 5 within the polymerase II (Pol II) C-terminal domain (CTD) as transcription factor TFIIH-bound CAK. However, the physiological importance of integrating these processes is not understood. Besides the Cdk7 ortholog Mcs6, fission yeast possesses a second CAK, Csk1. The two enzymes have been proposed to act redundantly to activate Cdc2. Using an improved analogue-sensitive Mcs6-as kinase, we show that Csk1 is not a relevant CAK for Cdc2. Further analyses revealed that Csk1 lacks a 20-amino-acid sequence required for its budding yeast counterpart, Cak1, to bind Cdc2. Transcriptome profiling of the Mcs6-as mutant in the presence or absence of the budding yeast Cak1 kinase, in order to uncouple the CTD kinase and CAK activities of Mcs6, revealed an unanticipated role of the CAK branch in the transcriptional control of the cluster of genes implicated in ribosome biogenesis and cell growth. The analysis of a Cdc2 CAK site mutant confirmed these data. Our data show that the Cdk7 kinase modulates transcription through its well-described RNA Pol II CTD kinase activity and also through the Cdc2-activating kinase activity.
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40
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Abstract
Transcription elongation by RNA polymerase II (RNAP II) involves the coordinated action of numerous regulatory factors. Among these are chromatin-modifying enzymes, which generate a stereotypic and conserved pattern of histone modifications along transcribed genes. This pattern implies a precise coordination between regulators of histone modification and the RNAP II elongation complex. Here I review the pathways and molecular events that regulate co-transcriptional histone modifications. Insight into these events will illuminate the assembly of functional RNAP II elongation complexes and how the chromatin landscape influences their composition and function.
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Affiliation(s)
- Jason C Tanny
- a Department of Pharmacology and Therapeutics ; McGill University ; Montreal , Canada
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41
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Doamekpor SK, Schwer B, Sanchez AM, Shuman S, Lima CD. Fission yeast RNA triphosphatase reads an Spt5 CTD code. RNA (NEW YORK, N.Y.) 2015; 21:113-123. [PMID: 25414009 PMCID: PMC4274631 DOI: 10.1261/rna.048181.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/24/2014] [Indexed: 06/04/2023]
Abstract
mRNA capping enzymes are directed to nascent RNA polymerase II (Pol2) transcripts via interactions with the carboxy-terminal domains (CTDs) of Pol2 and transcription elongation factor Spt5. Fission yeast RNA triphosphatase binds to the Spt5 CTD, comprising a tandem repeat of nonapeptide motif TPAWNSGSK. Here we report the crystal structure of a Pct1·Spt5-CTD complex, which revealed two CTD docking sites on the Pct1 homodimer that engage TPAWN segments of the motif. Each Spt5 CTD interface, composed of elements from both subunits of the homodimer, is dominated by van der Waals contacts from Pct1 to the tryptophan of the CTD. The bound CTD adopts a distinctive conformation in which the peptide backbone makes a tight U-turn so that the proline stacks over the tryptophan. We show that Pct1 binding to Spt5 CTD is antagonized by threonine phosphorylation. Our results fortify an emerging concept of an "Spt5 CTD code" in which (i) the Spt5 CTD is structurally plastic and can adopt different conformations that are templated by particular cellular Spt5 CTD receptor proteins; and (ii) threonine phosphorylation of the Spt5 CTD repeat inscribes a binary on-off switch that is read by diverse CTD receptors, each in its own distinctive manner.
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Affiliation(s)
- Selom K Doamekpor
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ana M Sanchez
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA Howard Hughes Medical Institute, Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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42
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Bartkowiak B, Greenleaf AL. Phosphorylation of RNAPII: To P-TEFb or not to P-TEFb? Transcription 2014; 2:115-119. [PMID: 21826281 DOI: 10.4161/trns.2.3.15004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 11/19/2022] Open
Abstract
The C-terminal domain of RNA polymerase II undergoes a cycle of phosphorylation which allows it to temporally couple transcription with transcription-associated processes. The characterization of hitherto unrecognized metazoan elongation phase CTD kinase activities expands our understanding of this coupling. We discuss the circumstances that delayed the recognition of these kinase activities.
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Affiliation(s)
- Bartlomiej Bartkowiak
- Department of Biochemistry; Duke Center for RNA Biology; Duke University Medical Center; Durham, NC USA
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43
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Abstract
CDKs (cyclin-dependent kinases) ensure directionality and fidelity of the eukaryotic cell division cycle. In a similar fashion, the transcription cycle is governed by a conserved subfamily of CDKs that phosphorylate Pol II (RNA polymerase II) and other substrates. A genetic model organism, the fission yeast Schizosaccharomyces pombe, has yielded robust models of cell-cycle control, applicable to higher eukaryotes. From a similar approach combining classical and chemical genetics, fundamental principles of transcriptional regulation by CDKs are now emerging. In the present paper, we review the current knowledge of each transcriptional CDK with respect to its substrate specificity, function in transcription and effects on chromatin modifications, highlighting the important roles of CDKs in ensuring quantity and quality control over gene expression in eukaryotes.
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44
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Doamekpor SK, Sanchez AM, Schwer B, Shuman S, Lima CD. How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes. Genes Dev 2014; 28:1323-36. [PMID: 24939935 PMCID: PMC4066402 DOI: 10.1101/gad.242768.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Interactions between RNA guanylyltransferase (GTase) and the C-terminal domain (CTD) repeats of RNA polymerase II (Pol2) and elongation factor Spt5 are thought to orchestrate cotranscriptional capping of nascent mRNAs. The crystal structure of a fission yeast GTase•Pol2 CTD complex reveals a unique docking site on the nucleotidyl transferase domain for an 8-amino-acid Pol2 CTD segment, S5PPSYSPTS5P, bracketed by two Ser5-PO4 marks. Analysis of GTase mutations that disrupt the Pol2 CTD interface shows that at least one of the two Ser5-PO4-binding sites is required for cell viability and that each site is important for cell growth at 37°C. Fission yeast GTase binds the Spt5 CTD at a separate docking site in the OB-fold domain that captures the Trp4 residue of the Spt5 nonapeptide repeat T(1)PAW(4)NSGSK. A disruptive mutation in the Spt5 CTD-binding site of GTase is synthetically lethal with mutations in the Pol2 CTD-binding site, signifying that the Spt5 and Pol2 CTDs cooperate to recruit capping enzyme in vivo. CTD phosphorylation has opposite effects on the interaction of GTase with Pol2 (Ser5-PO4 is required for binding) versus Spt5 (Thr1-PO4 inhibits binding). We propose that the state of Thr1 phosphorylation comprises a binary "Spt5 CTD code" that is read by capping enzyme independent of and parallel to its response to the state of the Pol2 CTD.
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Affiliation(s)
- Selom K Doamekpor
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Ana M Sanchez
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA; Howard Hughes Medical Institute, Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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45
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Bowman EA, Kelly WG. RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. Nucleus 2014; 5:224-36. [PMID: 24879308 DOI: 10.4161/nucl.29347] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transition between initiation and productive elongation during RNA Polymerase II (Pol II) transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. Here, we discuss the roles and regulation of these kinases and their relationship to Pol II elongation control, and focus on recent data from work in C. elegans that point out gaps in our current understand of transcription elongation.
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Affiliation(s)
- Elizabeth A Bowman
- National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
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46
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Bösken CA, Farnung L, Hintermair C, Merzel Schachter M, Vogel-Bachmayr K, Blazek D, Anand K, Fisher RP, Eick D, Geyer M. The structure and substrate specificity of human Cdk12/Cyclin K. Nat Commun 2014; 5:3505. [PMID: 24662513 PMCID: PMC3973122 DOI: 10.1038/ncomms4505] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/25/2014] [Indexed: 02/06/2023] Open
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain (CTD) by cyclin-dependent kinases is important for productive transcription. Here we determine the crystal structure of Cdk12/CycK and analyse its requirements for substrate recognition. Active Cdk12/CycK is arranged in an open conformation similar to that of Cdk9/CycT but different from those of cell cycle kinases. Cdk12 contains a C-terminal extension that folds onto the N- and C-terminal lobes thereby contacting the ATP ribose. The interaction is mediated by an HE motif followed by a polybasic cluster that is conserved in transcriptional CDKs. Cdk12/CycK showed the highest activity on a CTD substrate prephosphorylated at position Ser7, whereas the common Lys7 substitution was not recognized. Flavopiridol is most potent towards Cdk12 but was still 10-fold more potent towards Cdk9. T-loop phosphorylation of Cdk12 required coexpression with a Cdk-activating kinase. These results suggest the regulation of Pol II elongation by a relay of transcriptionally active CTD kinases. Cyclin-dependent kinase 12 (Cdk12) phosphorylates the C-terminal domain (CTD) of RNA polymerase II to regulate transcription. Here, the authors solve the crystal structure of the Cdk12 kinase domain and show that Cdk12 has its highest activity on a CTD substrate that carries a serine 7 phosphorylation.
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Affiliation(s)
- Christian A Bösken
- 1] Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany [2] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Lucas Farnung
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Corinna Hintermair
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science (CIPSM), Marchioninistrasse 25, München 81377, Germany
| | - Miriam Merzel Schachter
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Karin Vogel-Bachmayr
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Kanchan Anand
- Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany
| | - Robert P Fisher
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science (CIPSM), Marchioninistrasse 25, München 81377, Germany
| | - Matthias Geyer
- 1] Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany [2] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
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47
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Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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48
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Gonatopoulos-Pournatzis T, Cowling VH. Cap-binding complex (CBC). Biochem J 2014. [PMID: 24354960 DOI: 10.1042/bj2013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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Affiliation(s)
| | - Victoria H Cowling
- *MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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49
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Mbogning J, Nagy S, Pagé V, Schwer B, Shuman S, Fisher RP, Tanny JC. The PAF complex and Prf1/Rtf1 delineate distinct Cdk9-dependent pathways regulating transcription elongation in fission yeast. PLoS Genet 2013; 9:e1004029. [PMID: 24385927 PMCID: PMC3873232 DOI: 10.1371/journal.pgen.1004029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/31/2013] [Indexed: 11/19/2022] Open
Abstract
Cyclin-dependent kinase 9 (Cdk9) promotes elongation by RNA polymerase II (RNAPII), mRNA processing, and co-transcriptional histone modification. Cdk9 phosphorylates multiple targets, including the conserved RNAPII elongation factor Spt5 and RNAPII itself, but how these different modifications mediate Cdk9 functions is not known. Here we describe two Cdk9-dependent pathways in the fission yeast Schizosaccharomyces pombe that involve distinct targets and elicit distinct biological outcomes. Phosphorylation of Spt5 by Cdk9 creates a direct binding site for Prf1/Rtf1, a transcription regulator with functional and physical links to the Polymerase Associated Factor (PAF) complex. PAF association with chromatin is also dependent on Cdk9 but involves alternate phosphoacceptor targets. Prf1 and PAF are biochemically separate in cell extracts, and genetic analyses show that Prf1 and PAF are functionally distinct and exert opposing effects on the RNAPII elongation complex. We propose that this opposition constitutes a Cdk9 auto-regulatory mechanism, such that a positive effect on elongation, driven by the PAF pathway, is kept in check by a negative effect of Prf1/Rtf1 and downstream mono-ubiquitylation of histone H2B. Thus, optimal RNAPII elongation may require balanced action of functionally distinct Cdk9 pathways.
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Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Stephen Nagy
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Robert P. Fisher
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
- * E-mail:
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Putting an 'End' to HIV mRNAs: capping and polyadenylation as potential therapeutic targets. AIDS Res Ther 2013; 10:31. [PMID: 24330569 PMCID: PMC3874655 DOI: 10.1186/1742-6405-10-31] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/26/2013] [Indexed: 01/27/2023] Open
Abstract
Like most cellular mRNAs, the 5′ end of HIV mRNAs is capped and the 3′ end matured by the process of polyadenylation. There are, however, several rather unique and interesting aspects of these post-transcriptional processes on HIV transcripts. Capping of the highly structured 5′ end of HIV mRNAs is influenced by the viral TAT protein and a population of HIV mRNAs contains a trimethyl-G cap reminiscent of U snRNAs involved in splicing. HIV polyadenylation involves active repression of a promoter-proximal polyadenylation signal, auxiliary upstream regulatory elements and moonlighting polyadenylation factors that have additional impacts on HIV biology outside of the constraints of classical mRNA 3’ end formation. This review describes these post-transcriptional novelties of HIV gene expression as well as their implications in viral biology and as possible targets for therapeutic intervention.
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