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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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2
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Contreras A, Perea-Resa C. Transcriptional repression across mitosis: mechanisms and functions. Biochem Soc Trans 2024; 52:455-464. [PMID: 38372373 PMCID: PMC10903446 DOI: 10.1042/bst20231071] [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: 12/07/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Transcription represents a central aspect of gene expression with RNA polymerase machineries (RNA Pol) driving the synthesis of RNA from DNA template molecules. In eukaryotes, a total of three RNA Pol enzymes generate the plethora of RNA species and RNA Pol II is the one transcribing all protein-coding genes. A high number of cis- and trans-acting factors orchestrates RNA Pol II-mediated transcription by influencing the chromatin recruitment, activation, elongation, and/or termination steps. The levels of DNA accessibility, defining open-euchromatin versus close-heterochromatin, delimits RNA Pol II activity as well as the encounter with other factors acting on chromatin such as the DNA replication or DNA repair machineries. The stage of the cell cycle highly influences RNA Pol II activity with mitosis representing the major challenge. In fact, there is a massive inhibition of transcription during the mitotic entry coupled with chromatin dissociation of most of the components of the transcriptional machinery. Mitosis, as a consequence, highly compromises the transcriptional memory and the perpetuation of cellular identity. Once mitosis ends, transcription levels immediately recover to define the cell fate and to safeguard the proper progression of daughter cells through the cell cycle. In this review, we evaluate our current understanding of the transcriptional repression associated with mitosis with a special focus on the molecular mechanisms involved, on the potential function behind the general repression, and on the transmission of the transcriptional machinery into the daughter cells. We finally discuss the contribution that errors in the inheritance of the transcriptional machinery across mitosis might play in stem cell aging.
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Affiliation(s)
- A. Contreras
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
| | - C. Perea-Resa
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
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3
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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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Carmo C, Coelho J, Silva RD, Tavares A, Boavida A, Gaetani P, Guilgur LG, Martinho RG, Oliveira RA. A dual-function SNF2 protein drives chromatid resolution and nascent transcripts removal in mitosis. EMBO Rep 2023; 24:e56463. [PMID: 37462213 PMCID: PMC10481674 DOI: 10.15252/embr.202256463] [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: 11/18/2022] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
Mitotic chromatin is largely assumed incompatible with transcription due to changes in the transcription machinery and chromosome architecture. However, the mechanisms of mitotic transcriptional inactivation and their interplay with chromosome assembly remain largely unknown. By monitoring ongoing transcription in Drosophila early embryos, we reveal that eviction of nascent mRNAs from mitotic chromatin occurs after substantial chromosome compaction and is not promoted by condensin I. Instead, we show that the timely removal of transcripts from mitotic chromatin is driven by the SNF2 helicase-like protein Lodestar (Lds), identified here as a modulator of sister chromatid cohesion defects. In addition to the eviction of nascent transcripts, we uncover that Lds cooperates with Topoisomerase 2 to ensure efficient sister chromatid resolution and mitotic fidelity. We conclude that the removal of nascent transcripts upon mitotic entry is not a passive consequence of cell cycle progression and/or chromosome compaction but occurs via dedicated mechanisms with functional parallelisms to sister chromatid resolution.
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Affiliation(s)
| | - João Coelho
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | - Rui D Silva
- Algarve Biomedical Center Research Institute (ABC‐RI) and Faculty of Medicine and Biomedical Sciences (FMCB)Universidade do AlgarveFaroPortugal
| | | | - Ana Boavida
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Present address:
Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle RicercheNaplesItaly
| | | | | | - Rui Gonçalo Martinho
- Algarve Biomedical Center Research Institute (ABC‐RI) and Faculty of Medicine and Biomedical Sciences (FMCB)Universidade do AlgarveFaroPortugal
- Department of Medical Sciences (DCM) and Institute for Biomedicine (iBiMED)Universidade de AveiroAveiroPortugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Católica Biomedical Research Centre, Católica Medical SchoolUniversidade Católica PortuguesaLisbonPortugal
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5
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Sun X, Wang D, Li W, Gao Q, Tao J, Liu H. Comprehensive analysis of nonsurrounded nucleolus and surrounded nucleolus oocytes on chromatin accessibility using ATAC-seq. Mol Reprod Dev 2023; 90:87-97. [PMID: 36598871 DOI: 10.1002/mrd.23668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/13/2022] [Accepted: 12/25/2022] [Indexed: 01/05/2023]
Abstract
Mouse germinal vesicle (GV) oocytes are divided into surrounded nucleolus (SN) and nonsurrounded nucleolus (NSN) oocytes based on chromatin morphology. NSN oocytes spontaneously transform into SN oocytes after accumulating enough maternal transcripts. SN oocytes show transcriptional silencing. When oocyte maturation is abnormal or takes place in vitro, NSN oocytes do not go through SN stage before proceeding to MII. Nontransitive oocytes show developmental retardation, a low fertilization rate, and arrest at the two-cell embryo stage in mice. Here, chromatin-binding ribonucleic acid polymerase II (RNAP II) activity, newly synthesized RNA, and chromatin accessibility in GV oocytes were examined. In SN oocytes, RNAP II did not bind to DNA, neo-RNA was not generated in nuclei, and the phosphorylation state of RNAP II did not affect the chromatin-binding activity. The number of accessible genes in SN oocytes was remarkably lower than that in NSN oocytes. The accessibility of different functional genes was also different between the two types of oocytes. Thus, low chromatin accessibility leads to transcriptional silencing in SN oocytes.
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Affiliation(s)
- Xiaofan Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dayu Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weijian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qian Gao
- Laboratory Animal Center, College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, China
| | - Jingli Tao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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Enserink JM, Chymkowitch P. Cell Cycle-Dependent Transcription: The Cyclin Dependent Kinase Cdk1 Is a Direct Regulator of Basal Transcription Machineries. Int J Mol Sci 2022; 23:ijms23031293. [PMID: 35163213 PMCID: PMC8835803 DOI: 10.3390/ijms23031293] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 12/21/2022] Open
Abstract
The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed that Cdk1 also directly regulates the basal transcription machinery, most notably RNA polymerase II. More recent studies in the budding yeast Saccharomyces cerevisiae have revisited this function of Cdk1 and also revealed that Cdk1 directly controls RNA polymerase III activity. These studies have also provided novel insight into the physiological relevance of this process. For instance, cell cycle-stage-dependent activity of these complexes may be important for meeting the increased demand for various proteins involved in housekeeping, metabolism, and protein synthesis. Recent work also indicates that direct regulation of the RNA polymerase II machinery promotes cell cycle entry. Here, we provide an overview of the regulation of basal transcription by Cdk1, and we hypothesize that the original function of the primordial cell-cycle CDK was to regulate RNAPII and that it later evolved into specialized kinases that govern various aspects of the transcription machinery and the cell cycle.
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Affiliation(s)
- Jorrit M. Enserink
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence: (J.M.E.); (P.C.)
| | - Pierre Chymkowitch
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
- Correspondence: (J.M.E.); (P.C.)
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Zakarya R, Chan YL, Rutting S, Reddy K, Bozier J, Woldhuis RR, Xenaki D, Van Ly D, Chen H, Brandsma CA, Adcock IM, Oliver BG. BET proteins are associated with the induction of small airway fibrosis in COPD. Thorax 2021; 76:647-655. [PMID: 33504568 DOI: 10.1136/thoraxjnl-2020-215092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/03/2022]
Abstract
RATIONALE In COPD, small airway fibrosis occurs due to increased extracellular matrix (ECM) deposition in and around the airway smooth muscle (ASM) layer. Studies of immune cells and peripheral lung tissue have shown that epigenetic changes occur in COPD but it is unknown whether airway mesenchymal cells are reprogrammed. OBJECTIVES Determine if COPD ASM cells have a unique epigenetic response to profibrotic cytokine transforming growth factor β1 (TGF-β1). METHODS Primary human ASM cells from COPD and non-COPD smoking patients were stimulated with TGF-β1. Gene array analysis performed to identify differences in ECM expression. Airway accumulation of collagen 15α1 and tenascin-C proteins was assessed. Aforementioned ASM cells were stimulated with TGF-β1 ± epigenetic inhibitors with qPCR quantification of COL15A1 and TNC. Global histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity were assessed. chromatin immunoprecipitation (ChIP)-qPCR for histone H3 and H4 acetylation at COL15A1 and TNC promoters was carried out. Effects of bromoterminal and extraterminal domain (BET) inhibitor JQ1(+) on expression and acetylation of ECM target genes were assessed. MEASUREMENTS AND MAIN RESULTS COPD ASM show significantly higher COL15A1 and TNC expression in vitro and the same trend for higher levels of collagen 15α1 and tenascin-c deposited in COPD airways in vivo. Epigenetic screening indicated differential response to HDAC inhibition. ChIP-qPCR revealed histone H4 acetylation at COL15A1 and TNC promoters in COPD ASM only. ChIP-qPCR found JQ1(+) pretreatment significantly abrogated TGF-β1 induced histone H4 acetylation at COL15A1 and TNC. CONCLUSIONS BET protein binding to acetylated histones is important in TGF-β1 induced expression of COL15A1 and TNC and maintenance of TGF-β1 induced histone H4 acetylation in cell progeny.
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Affiliation(s)
- Razia Zakarya
- Respiratory Cell and Molecular Biology, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia .,School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Yik L Chan
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Sandra Rutting
- Airway Physiology and Imaging Group, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
| | - Karosham Reddy
- Respiratory Cell and Molecular Biology, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia.,School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Jack Bozier
- Respiratory Cell and Molecular Biology, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia.,School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Roy R Woldhuis
- Respiratory Cell and Molecular Biology, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia.,School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia.,Pathology and Medical Biology, University Medical Centre Groningen, Groningen, Groningen, The Netherlands
| | - Dikaia Xenaki
- Respiratory Cell and Molecular Biology, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
| | - David Van Ly
- Genome Integrity Unit, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia
| | - Hui Chen
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Corry-Anke Brandsma
- Pathology and Medical Biology, University Medical Centre Groningen, Groningen, Groningen, The Netherlands
| | - Ian M Adcock
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Brian G Oliver
- Respiratory Cell and Molecular Biology, Woolcock Institute of Medical Research, Glebe, New South Wales, Australia.,School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
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9
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Diab S, Yu M, Wang S. CDK7 Inhibitors in Cancer Therapy: The Sweet Smell of Success? J Med Chem 2020; 63:7458-7474. [DOI: 10.1021/acs.jmedchem.9b01985] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah Diab
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Mingfeng Yu
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
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Cell Cycle Arrest in G 2/M Phase Enhances Replication of Interferon-Sensitive Cytoplasmic RNA Viruses via Inhibition of Antiviral Gene Expression. J Virol 2019; 93:JVI.01885-18. [PMID: 30487274 PMCID: PMC6364032 DOI: 10.1128/jvi.01885-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 10/28/2018] [Indexed: 02/06/2023] Open
Abstract
Vesicular stomatitis virus (VSV) (a rhabdovirus) and its variant VSV-ΔM51 are widely used model systems to study mechanisms of virus-host interactions. Here, we investigated how the cell cycle affects replication of these viruses using an array of cell lines with different levels of impairment of antiviral signaling and a panel of chemical compounds arresting the cell cycle at different phases. We observed that all compounds inducing cell cycle arrest in G2/M phase strongly enhanced the replication of VSV-ΔM51 in cells with functional antiviral signaling. G2/M arrest strongly inhibited type I and type III interferon (IFN) production as well as expression of IFN-stimulated genes in response to exogenously added IFN. Moreover, G2/M arrest enhanced the replication of Sendai virus (a paramyxovirus), which is also highly sensitive to the type I IFN response but did not stimulate the replication of a wild-type VSV that is more effective at evading antiviral responses. In contrast, the positive effect of G2/M arrest on virus replication was not observed in cells defective in IFN signaling. Altogether, our data show that replication of IFN-sensitive cytoplasmic viruses can be strongly stimulated during G2/M phase as a result of inhibition of antiviral gene expression, likely due to mitotic inhibition of transcription, a global repression of cellular transcription during G2/M phase. The G2/M phase thus could represent an "Achilles' heel" of the infected cell, a phase when the cell is inadequately protected. This model could explain at least one of the reasons why many viruses have been shown to induce G2/M arrest.IMPORTANCE Vesicular stomatitis virus (VSV) (a rhabdovirus) and its variant VSV-ΔM51 are widely used model systems to study mechanisms of virus-host interactions. Here, we investigated how the cell cycle affects replication of VSV and VSV-ΔM51. We show that G2/M cell cycle arrest strongly enhances the replication of VSV-ΔM51 (but not of wild-type VSV) and Sendai virus (a paramyxovirus) via inhibition of antiviral gene expression, likely due to mitotic inhibition of transcription, a global repression of cellular transcription during G2/M phase. Our data suggest that the G2/M phase could represent an "Achilles' heel" of the infected cell, a phase when the cell is inadequately protected. This model could explain at least one of the reasons why many viruses have been shown to induce G2/M arrest, and it has important implications for oncolytic virotherapy, suggesting that frequent cell cycle progression in cancer cells could make them more permissive to viruses.
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Schaeffer E, Vigneron M, Sibler AP, Oulad-Abdelghani M, Chatton B, Donzeau M. ATF7 is stabilized during mitosis in a CDK1-dependent manner and contributes to cyclin D1 expression. Cell Cycle 2016; 14:2655-66. [PMID: 26101806 DOI: 10.1080/15384101.2015.1064568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The transcription factor ATF7 undergoes multiple post-translational modifications, each of which has distinct effects upon ATF7 function. Here, we show that ATF7 phosphorylation on residue Thr112 exclusively occurs during mitosis, and that ATF7 is excluded from the condensed chromatin. Both processes are CDK1/cyclin B dependent. Using a transduced neutralizing monoclonal antibody directed against the Thr112 epitope in living cells, we could demonstrate that Thr112 phosphorylation protects endogenous ATF7 protein from degradation, while it has no effect on the displacement of ATF7 from the condensed chromatin. The crucial role of Thr112 phosphorylation in stabilizing ATF7 protein during mitosis was confirmed using phospho-mimetic and phospho-deficient mutants. Finally, silencing ATF7 by CRISPR/Cas9 technology leads to a decrease of cyclin D1 protein expression levels. We propose that mitotic stabilized ATF7 protein re-localizes onto chromatin at the end of telophase and contributes to induce the cyclin D1 gene expression.
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Affiliation(s)
- Etienne Schaeffer
- a Université de Strasbourg; UMR7242 Biotechnologie et Signalisation Cellulaire; Ecole Supérieure de Biotechnologie de Strasbourg ; Illkirch Cedex , France
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12
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Liang K, Woodfin AR, Slaughter BD, Unruh JR, Box AC, Rickels RA, Gao X, Haug JS, Jaspersen SL, Shilatifard A. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis. Mol Cell 2016; 60:435-45. [PMID: 26527278 DOI: 10.1016/j.molcel.2015.09.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/04/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division.
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Affiliation(s)
- Kaiwei Liang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Andrew C Box
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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13
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Tajedin L, Tarique M, Tuteja R. Plasmodium falciparum XPD translocates in 5' to 3' direction, is expressed throughout the blood stages, and interacts with p44. PROTOPLASMA 2015; 252:1487-1504. [PMID: 25708921 DOI: 10.1007/s00709-015-0779-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
XPD helicase, a TFIIH subunit, is essential for several processes including transcription, NER, cell cycle regulation, and apoptosis in eukaryotes. Another component of TFIIH, namely p44, is among the well-known interacting partners of XPD and is vital in regulating the helicase activities of latter. However, none of the above mentioned proteins have been functionally characterized in Plasmodium falciparum. Consequently, in this study, we performed detailed studies on XPD and its interacting partner, p44, from P. falciparum 3D7 strain. Accordingly, we expressed and purified recombinant PfXPD and its fragments and Pfp44 proteins and characterized the enzymatic activities of PfXPD and its fragments. The in vivo stage-specific expression and subcellular localizations of PfXPD and Pfp44 proteins were studied using the specific antibodies in the intraerythrocytic developmental stages of P. falciparum 3D7 strain. Our results suggest that PfXPD displays the characteristic ssDNA-dependent ATPase and 5'-3' DNA helicase activities. We also report the existence of two high molecular weight forms of p44 in P. falciparum 3D7 strain. Both PfXPD and Pfp44 colocalize in the nucleus and interact with each other, which suggest that they are most likely components of the same complex apparently, TFIIH. Furthermore, during trophozoite and schizont stages, both proteins exhibit a distinct cytoplasmic distribution pattern which implies that PfXPD and Pfp44 might also be involved in other functions. These studies will aid in understanding the basic biology of malaria parasite.
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Affiliation(s)
- Leila Tajedin
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Mohammed Tarique
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India.
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Voit R, Seiler J, Grummt I. Cooperative Action of Cdk1/cyclin B and SIRT1 Is Required for Mitotic Repression of rRNA Synthesis. PLoS Genet 2015; 11:e1005246. [PMID: 26023773 PMCID: PMC4449194 DOI: 10.1371/journal.pgen.1005246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 04/27/2015] [Indexed: 12/29/2022] Open
Abstract
Mitotic repression of rRNA synthesis requires inactivation of the RNA polymerase I (Pol I)-specific transcription factor SL1 by Cdk1/cyclin B-dependent phosphorylation of TAFI110 (TBP-associated factor 110) at a single threonine residue (T852). Upon exit from mitosis, T852 is dephosphorylated by Cdc14B, which is sequestered in nucleoli during interphase and is activated upon release from nucleoli at prometaphase. Mitotic repression of Pol I transcription correlates with transient nucleolar enrichment of the NAD+-dependent deacetylase SIRT1, which deacetylates another subunit of SL1, TAFI68. Hypoacetylation of TAFI68 destabilizes SL1 binding to the rDNA promoter, thereby impairing transcription complex assembly. Inhibition of SIRT1 activity alleviates mitotic repression of Pol I transcription if phosphorylation of TAFI110 is prevented. The results demonstrate that reversible phosphorylation of TAFI110 and acetylation of TAFI68 are key modifications that regulate SL1 activity and mediate fluctuations of pre-rRNA synthesis during cell cycle progression. In metazoans, transcription is arrested during mitosis. Previous studies have established that mitotic repression of cellular transcription is mediated by Cdk1/cyclin B-dependent phosphorylation of basal transcription factors that nucleate transcription complex formation. Repression of rDNA transcription at the onset of mitosis is brought about by inactivation of the TBP-containing transcription factor SL1 by Cdk1/cyclin B-dependent phosphorylation of the TAFI110 subunit, which impairs the interaction with UBF and the assembly of pre-initiation complexes. Here we show that hCdc14B, the phosphatase that regulates Cdk1/cyclin B activity and progression through mitosis, promotes reactivation of rDNA transcription by dephosphorylating TAFI110. In addition, the NAD+-dependent deacetylase SIRT1 becomes transiently enriched in nucleoli at the onset of mitosis. SIRT1 deacetylates TAFI68, another subunit of SL1, hypoacetylation of TAFI68 destabilizing SL1 binding to the rDNA promoter and impairing transcription complex assembly. The results reveal that modulation of SL1 activity by reversible acetylation of TAFI68 and phosphorylation of TAFI110 are key modifications that mediate oscillation of rDNA transcription during cell cycle progression.
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Affiliation(s)
- Renate Voit
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
| | - Jeanette Seiler
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
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15
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Martinho RG, Guilgur LG, Prudêncio P. How gene expression in fast-proliferating cells keeps pace. Bioessays 2015; 37:514-24. [PMID: 25823409 DOI: 10.1002/bies.201400195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of living organisms requires a precise coordination of all basic cellular processes, in space and time. Early embryogenesis of most species with externally deposited eggs starts with a series of extremely fast cleavage cycles. These divisions have a strong influence on gene expression as mitosis represses transcription and pre-mRNA processing. In this review, we will describe the distinct adaptations for efficient gene expression and discuss the emerging role of the multifunctional NineTeen Complex (NTC) in gene expression and genomic stability during fast proliferation.
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Affiliation(s)
- Rui G Martinho
- Departamento de Ciências Biomédicas e Medicina, Regenerative Medicine Program, Universidade do Algarve, Campus de Gambelas, Faro, Portugal; Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, Faro, Portugal; Instituto Gulbenkian de Ciência, Oeiras, Portugal
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16
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Abstract
The final stage of cell division (mitosis), involves the compaction of the duplicated genome into chromatid pairs. Each pair is captured by microtubules emanating from opposite spindle poles, aligned at the metaphase plate, and then faithfully segregated to form two identical daughter cells. Chromatids that are not correctly attached to the spindle are detected by the constitutively active spindle assembly checkpoint (SAC). Any stress that prevents correct bipolar spindle attachment, blocks the satisfaction of the SAC, and induces a prolonged mitotic arrest, providing the cell time to obtain attachment and complete segregation correctly. Unfortunately, during mitosis repairing damage is not generally possible due to the compaction of DNA into chromosomes, and subsequent suppression of gene transcription and translation. Therefore, in the presence of significant damage cell death is instigated to ensure that genomic stability is maintained. While most stresses lead to an arrest in mitosis, some promote premature mitotic exit, allowing cells to bypass mitotic cell death. This mini-review will focus on the effects and outcomes that common stresses have on mitosis, and how this impacts on the efficacy of mitotic chemotherapies.
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Affiliation(s)
- Andrew Burgess
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research , Sydney, NSW , Australia ; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia , Sydney, NSW , Australia
| | - Mina Rasouli
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research , Sydney, NSW , Australia
| | - Samuel Rogers
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research , Sydney, NSW , Australia
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17
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Rizkallah R, Alexander KE, Hurt MM. Global mitotic phosphorylation of C2H2 zinc finger protein linker peptides. Cell Cycle 2011; 10:3327-36. [PMID: 21941085 DOI: 10.4161/cc.10.19.17619] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cessation of transcriptional activity is a hallmark of cell division. Many biochemical pathways have been shown and proposed over the past few decades to explain the silence of this phase. In particular, many individual transcription factors have been shown to be inactivated by phosphorylation. In this report, we show the simultaneous phosphorylation and mitotic redistribution of a whole class of modified transcription factors. C(2)H(2) zinc finger proteins (ZFPs) represent the largest group of gene expression regulators in the human genome. Despite their diversity, C(2)H(2) ZFPs display striking conservation of small linker peptides joining their adjacent zinc finger modules. These linkers are critical for DNA binding activity. It has been proposed that conserved phosphorylation of these linker peptides could be a common mechanism for the inactivation of the DNA binding activity of C(2)H(2) ZFPs, during mitosis. Using a novel antibody, raised against the phosphorylated form of the most conserved linker peptide sequence, we are able to visualize the massive and simultaneous mitotic phosphorylation of hundreds of these proteins. We show that this wave of phosphorylation is tightly synchronized, starting in mid-prophase right after DNA condensation and before the breakdown of the nuclear envelope. This global phosphorylation is completely reversed in telophase. In addition, the exclusion of the phospho-linker signal from condensed DNA clearly demonstrates a common mechanism for the mitotic inactivation of C(2)H(2) ZFPs.
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Affiliation(s)
- Raed Rizkallah
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
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18
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Ambegaokar SS, Jackson GR. Functional genomic screen and network analysis reveal novel modifiers of tauopathy dissociated from tau phosphorylation. Hum Mol Genet 2011; 20:4947-77. [PMID: 21949350 PMCID: PMC3221533 DOI: 10.1093/hmg/ddr432] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A functional genetic screen using loss-of-function and gain-of-function alleles was performed to identify modifiers of tau-induced neurotoxicity using the 2N/4R (full-length) isoform of wild-type human tau expressed in the fly retina. We previously reported eye pigment mutations, which create dysfunctional lysosomes, as potent modifiers; here, we report 37 additional genes identified from ∼1900 genes screened, including the kinases shaggy/GSK-3beta, par-1/MARK, CamKI and Mekk1. Tau acts synergistically with Mekk1 and p38 to down-regulate extracellular regulated kinase activity, with a corresponding decrease in AT8 immunoreactivity (pS202/T205), suggesting that tau can participate in signaling pathways to regulate its own kinases. Modifiers showed poor correlation with tau phosphorylation (using the AT8, 12E8 and AT270 epitopes); moreover, tested suppressors of wild-type tau were equally effective in suppressing toxicity of a phosphorylation-resistant S11A tau construct, demonstrating that changes in tau phosphorylation state are not required to suppress or enhance its toxicity. Genes related to autophagy, the cell cycle, RNA-associated proteins and chromatin-binding proteins constitute a large percentage of identified modifiers. Other functional categories identified include mitochondrial proteins, lipid trafficking, Golgi proteins, kinesins and dynein and the Hsp70/Hsp90-organizing protein (Hop). Network analysis uncovered several other genes highly associated with the functional modifiers, including genes related to the PI3K, Notch, BMP/TGF-β and Hedgehog pathways, and nuclear trafficking. Activity of GSK-3β is strongly upregulated due to TDP-43 expression, and reduced GSK-3β dosage is also a common suppressor of Aβ42 and TDP-43 toxicity. These findings suggest therapeutic targets other than mitigation of tau phosphorylation.
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Affiliation(s)
- Surendra S Ambegaokar
- Department of Neurology, University of Texas Medical Branch, 301 University Blvd., MRB 10.138, Galveston, TX 77555, USA
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19
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Biggar KK, Storey KB. Perspectives in cell cycle regulation: lessons from an anoxic vertebrate. Curr Genomics 2011; 10:573-84. [PMID: 20514219 PMCID: PMC2817888 DOI: 10.2174/138920209789503905] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 08/04/2009] [Accepted: 08/06/2009] [Indexed: 01/07/2023] Open
Abstract
The ability of an animal, normally dependent on aerobic respiration, to suspend breathing and enter an anoxic state for long term survival is clearly a fascinating feat, and has been the focus of numerous biochemical studies. When anoxia tolerant turtles are faced with periods of oxygen deprivation, numerous physiological and biochemical alterations take place in order to facilitate vital reductions in ATP consumption. Such strategies include reversible post-translational modifications as well as the implementation of translation and transcription controls facilitating metabolic depression. Although it is clear that anoxic survival relies on the suppression of ATP consuming processes, the state of the cell cycle in anoxia tolerant vertebrates remain elusive. Several anoxia tolerant invertebrate and embryonic vertebrate models display cell cycle arrest when presented with anoxic stress. Despite this, the cell cycle has not yet been characterized for anoxia tolerant turtles. Understanding how vertebrates respond to anoxia can have important clinical implications. Uncontrollable cellular proliferation and hypoxic tumor progression are inescapably linked in vertebrate tissues. Consequentially, the molecular mechanisms controlling these processes have profound clinical consequences. This review article will discuss the theory of cell cycle arrest in anoxic vertebrates and more specifically, the control of the retinoblastoma pathway, the molecular markers of cell cycle arrest, the activation of checkpoint kinases, and the possibility of translational controls implemented by microRNAs.
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Affiliation(s)
- Kyle K Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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20
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Sansregret L, Gallo D, Santaguida M, Leduy L, Harada R, Nepveu A. Hyperphosphorylation by cyclin B/CDK1 in mitosis resets CUX1 DNA binding clock at each cell cycle. J Biol Chem 2010; 285:32834-32843. [PMID: 20729212 DOI: 10.1074/jbc.m110.156406] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The p110 CUX1 homeodomain protein participates in the activation of DNA replication genes in part by increasing the affinity of E2F factors for the promoters of these genes. CUX1 expression is very weak in quiescent cells and increases during G(1). Biochemical activities associated with transcriptional activation by CUX1 are potentiated by post-translational modifications in late G(1), notably a proteolytic processing event that generates p110 CUX1. Constitutive expression of p110 CUX1, as observed in some transformed cells, leads to accelerated entry into the S phase. In this study, we investigated the post-translation regulation of CUX1 during mitosis and the early G(1) phases of proliferating cells. We observed a major electrophoretic mobility shift and a complete inhibition of DNA binding during mitosis. We show that cyclin B/CDK1 interacts with CUX1 and phosphorylates it at multiple sites. Serine to alanine replacement mutations at 10 SP dipeptide sites were required to restore DNA binding in mitosis. Passage into G(1) was associated with the degradation of some p110 CUX1 proteins, and the remaining proteins were gradually dephosphorylated. Indirect immunofluorescence and subfractionation assays using a phospho-specific antibody showed that most of the phosphorylated protein remained in the cytoplasm, whereas the dephosphorylated protein was preferentially located in the nucleus. Globally, our results indicate that the hyperphosphorylation of CUX1 by cyclin B/CDK1 inhibits its DNA binding activity in mitosis and interferes with its nuclear localization following cell division and formation of the nuclear membrane, whereas dephosphorylation and de novo synthesis contribute to gradually restore CUX1 expression and activity in G(1).
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Affiliation(s)
- Laurent Sansregret
- From the McGill University Cancer Pavilion, Montreal, Quebec H3A 1A3, Canada; Departments of Biochemistry, Montreal, Quebec H3A 1A3, Canada
| | - David Gallo
- From the McGill University Cancer Pavilion, Montreal, Quebec H3A 1A3, Canada; Departments of Biochemistry, Montreal, Quebec H3A 1A3, Canada
| | - Marianne Santaguida
- From the McGill University Cancer Pavilion, Montreal, Quebec H3A 1A3, Canada; Departments of Biochemistry, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- From the McGill University Cancer Pavilion, Montreal, Quebec H3A 1A3, Canada
| | - Ryoko Harada
- From the McGill University Cancer Pavilion, Montreal, Quebec H3A 1A3, Canada
| | - Alain Nepveu
- From the McGill University Cancer Pavilion, Montreal, Quebec H3A 1A3, Canada; Departments of Biochemistry, Montreal, Quebec H3A 1A3, Canada; Oncology, Montreal, Quebec H3A 1A3, Canada; Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada.
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21
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Patzlaff JS, Terrenoire E, Turner BM, Earnshaw WC, Paulson JR. Acetylation of core histones in response to HDAC inhibitors is diminished in mitotic HeLa cells. Exp Cell Res 2010; 316:2123-35. [PMID: 20452346 DOI: 10.1016/j.yexcr.2010.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 04/08/2010] [Accepted: 05/03/2010] [Indexed: 01/16/2023]
Abstract
Histone acetylation is a key modification that regulates chromatin accessibility. Here we show that treatment with butyrate or other histone deacetylase (HDAC) inhibitors does not induce histone hyperacetylation in metaphase-arrested HeLa cells. When compared to similarly treated interphase cells, acetylation levels are significantly decreased in all four core histones and at all individual sites examined. However, the extent of the decrease varies, ranging from only slight reduction at H3K23 and H4K12 to no acetylation at H3K27 and barely detectable acetylation at H4K16. Our results show that the bulk effect is not due to increased or butyrate-insensitive HDAC activity, though these factors may play a role with some individual sites. We conclude that the lack of histone acetylation during mitosis is primarily due to changes in histone acetyltransferases (HATs) or changes in chromatin. The effects of protein phosphatase inhibitors on histone acetylation in cell lysates suggest that the reduced ability of histones to become acetylated in mitotic cells depends on protein phosphorylation.
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Affiliation(s)
- Jason S Patzlaff
- Department of Chemistry, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA.
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22
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Boeing S, Rigault C, Heidemann M, Eick D, Meisterernst M. RNA polymerase II C-terminal heptarepeat domain Ser-7 phosphorylation is established in a mediator-dependent fashion. J Biol Chem 2009; 285:188-96. [PMID: 19901026 DOI: 10.1074/jbc.m109.046565] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The largest subunit of RNA polymerase II (RNAPII) C-terminal heptarepeat domain (CTD) is subject to phosphorylation during initiation and elongation of transcription by RNA polymerase II. Here we study the molecular mechanisms leading to phosphorylation of Ser-7 in the human enzyme. Ser-7 becomes phosphorylated before initiation of transcription at promoter regions. We identify cyclin-dependent kinase 7 (CDK7) as one responsible kinase. Phosphorylation of both Ser-5 and Ser-7 is fully dependent on the cofactor complex Mediator. A subform of Mediator associated with an active RNAPII is critical for preinitiation complex formation and CTD phosphorylation. The Mediator-RNAPII complex independently recruits TFIIB and CDK7 to core promoter regions. CDK7 phosphorylates Ser-7 selectively in the context of an intact preinitiation complex. CDK7 is not the only kinase that can modify Ser-7 of the CTD. ChIP experiments with chemical inhibitors provide evidence that other yet to be identified kinases further phosphorylate Ser-7 in coding regions.
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Affiliation(s)
- Stefan Boeing
- Institute of Molecular Tumor Biology, University of Muenster, Robert-Koch-Strasse 43, 48149 Muenster, Germany
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23
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Functional Evolution of Cyclin-Dependent Kinases. Mol Biotechnol 2009; 42:14-29. [DOI: 10.1007/s12033-008-9126-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 11/01/2008] [Indexed: 10/21/2022]
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24
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Xu YX, Manley JL. Pin1 modulates RNA polymerase II activity during the transcription cycle. Genes Dev 2007; 21:2950-62. [PMID: 18006688 DOI: 10.1101/gad.1592807] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The C-terminal domain of the RNA polymerase (RNAP) II largest subunit (CTD) plays a critical role in coordinating multiple events in pre-mRNA transcription and processing. Previously we reported that the peptidyl prolyl isomerase Pin1 modulates RNAP II function during the cell cycle. Here we provide evidence that Pin1 affects multiple aspects of RNAP II function via its regulation of CTD phosphorylation. Using chromatin immunoprecipitation (ChIP) assays with CTD phospho-specific antibodies, we confirm that RNAP II displays a dynamic association with specific genes during the cell cycle, preferentially associating with transcribed genes in S phase, while disassociating in M phase in a matter that correlates with changes in CTD phosphorylation. Using inducible Pin1 cell lines, we show that Pin1 overexpression is sufficient to release RNAP II from chromatin, which then accumulates in a hyperphosphorylated form in nuclear speckle-associated structures. In vitro transcription assays show that Pin1 inhibits transcription in nuclear extract, while an inactive Pin1 mutant in fact stimulates it. Several assays indicate that the inhibition largely reflects Pin1 activity during transcription initiation and not elongation, suggesting that Pin1 modulates CTD phosphorylation, and RNAP II activity, during an early stage of the transcription cycle.
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Affiliation(s)
- Yu-Xin Xu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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25
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Abstract
The PLZF gene is one of five partners fused to the retinoic acid receptor alpha in acute promyelocytic leukemia. PLZF encodes a DNA-binding transcriptional repressor and the PLZF-RARalpha fusion protein like other RARalpha fusions can inhibit the genetic program mediated by the wild tpe retinoic acid receptor. However an increasing body of literature indicates an important role for the PLZF gene in growth control and development. This information suggests that loss of PLZF function might also contribute to leukemogenesis.
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Affiliation(s)
- M J McConnell
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, 303 E Superior St, Chicago, IL 60611, USA
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26
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Aguilar-Fuentes J, Valadez-Graham V, Reynaud E, Zurita M. TFIIH trafficking and its nuclear assembly during early Drosophila embryo development. J Cell Sci 2006; 119:3866-75. [PMID: 16940351 DOI: 10.1242/jcs.03150] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the first analysis of the dynamics of the transcription DNA-repair factor TFIIH at the onset of transcription in early Drosophila development. TFIIH is composed of ten polypeptides that are part of two complexes - the core and the CAK. We found that the TFIIH core is initially located in the cytoplasm of syncytial blastoderm embryos, and that after mitotic division ten and until the cellular blastoderm stage, the core moves from the cytoplasm to the nucleus. By contrast, the CAK complex is mostly cytoplasmic during cellularization and during gastrulation. However, both components are positioned at promoters of genes that are activated at transcription onset. Later in development, the CAK complex becomes mostly nuclear and co-localizes in most chromosomal regions with the TFIIH core, but not in all sites, suggesting that the CAK complex could have a TFIIH-independent role in transcription of some loci. We also demonstrate that even though the CAK and the core coexist in the early embryo cytoplasm, they do not interact until they are in the nucleus and suggest that the complete assembly of the ten subunits of TFIIH occurs in the nucleus at the mid-blastula transition. In addition, we present evidence that suggests that DNA helicase subunits XPB and XPD are assembled in the core when they are transported into the nucleus and are required for the onset of transcription.
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Affiliation(s)
- Javier Aguilar-Fuentes
- Department of Developmental Genetics and Molecular Physiology, Institute of Biotechnology, National Autonomous University of México, Av. Universidad 2001, Cuernavaca Morelos 62250, Mexico
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27
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Souid AK, Gao C, Wang L, Milgrom E, Shen WCW. ELM1 is required for multidrug resistance in Saccharomyces cerevisiae. Genetics 2006; 173:1919-37. [PMID: 16751665 PMCID: PMC1569693 DOI: 10.1534/genetics.106.057596] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 05/30/2006] [Indexed: 02/08/2023] Open
Abstract
In Saccharomyces cerevisiae, transcription of several drug transporter genes, including the major transporter gene PDR5, has been shown to peak during mitosis. The significance of this observation, however, remains unclear. PDR1 encodes the primary transcription activator of multiple drug transporter genes in S. cerevisiae, including PDR5. Here, we show that in synchronized PDR1 and pdr1-3 (multidrug resistant) strains, cellular efflux of a known substrate of ATP-binding-cassette transporters, doxorubicin (a fluorescent anticancer drug), is highest during mitosis when PDR5 transcription peaks. A genetic screen performed to identify regulators of multidrug resistance revealed that a truncation mutation in ELM1 (elm1-300) suppressed the multidrug resistance of pdr1-3. ELM1 encodes a serine/threonine protein kinase required for proper regulation of multiple cellular kinases, including those involved in mitosis, cytokinesis, and cellular morphogenesis. elm1-300 as well as elm1Delta mutations in a pdr1-3 strain also caused elongated bud morphology (indicating a G2/M delay) and reduction of PDR5 transcription under induced and noninduced conditions. Interestingly, mutations in several genes functionally related to ELM1, including cla4Delta, gin4Delta, and cdc28-C127Y, also caused drastic reductions in drug resistance and PDR5 transcription. Collectively, these data show that ELM1, and genes encoding related serine/threonine protein kinases, are required for regulation of multidrug resistance involving, at least in part, control of PDR5 transcription.
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Affiliation(s)
- Abdul-Kader Souid
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA
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28
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Hatfield MD, Reis AMC, Obeso D, Cook JR, Thompson DM, Rao M, Friedberg EC, Queimado L. Identification of MMS19 domains with distinct functions in NER and transcription. DNA Repair (Amst) 2006; 5:914-24. [PMID: 16797255 DOI: 10.1016/j.dnarep.2006.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/08/2006] [Accepted: 05/11/2006] [Indexed: 12/14/2022]
Abstract
Nucleotide excision repair (NER) and RNA polymerase II (Pol II) transcription are essential cellular processes which are intimately intertwined. They share an indispensable multiprotein complex, TFIIH, and impairments in either process can impact the efficiency of the other. Like TFIIH, MMS19 is required for NER and Pol II transcription, but its precise role in each process is unknown. We showed previously that the human MMS19 gene originates multiple splice variants, some of which may encode distinct MMS19 protein isoforms. Here we characterize a novel MMS19 transcript and demonstrate for the first time that MMS19 splice variants are conserved across species and are functionally distinct. Expression of human MMS19 splice variants in mms19-deleted yeast cells produced unique patterns of thermosensitivity and ultraviolet radiation-sensitivity that point to three MMS19 structural domains with distinct in vivo functions. MMS19 polypeptides lacking domain A are able to fulfill the role of full-length MMS19 in NER but not in transcription. MMS19 polypeptides lacking part of domain B are efficient in transcription but not in NER. MMS19 polypeptides lacking domain C (HEAT repeats) are unable to fulfill either function. Our data suggest that the MMS19 HEAT repeat domain is essential for MMS19 function in NER and transcription, while domains A and B, within MMS19 N-terminus, modulate the balance between DNA repair and transcription. Our results highlight the functional significance of MMS19 transcripts and the possible contribution of MMS19 isoforms to regulate the switch between NER and transcription. Furthermore, our work associates for the first time specific protein domains with MMS19's role in NER and transcription.
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Affiliation(s)
- Melissa D Hatfield
- Department of Otorhinolaryngology, University of Oklahoma Health Sciences Center, Oklahoma City, 73104, USA
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29
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Sridhar J, Akula N, Pattabiraman N. Selectivity and potency of cyclin-dependent kinase inhibitors. AAPS JOURNAL 2006; 8:E204-21. [PMID: 16584130 PMCID: PMC2751441 DOI: 10.1208/aapsj080125] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Members of the cyclin-dependent kinase (CDK) family play key roles in various cellular processes. There are 11 members of the CDK family known till now. CDKs are activated by forming noncovalent complexes with cyclins such as A-, B-, C-, D- (D1, D2, and D3), and E-type cyclins. Each isozyme of this family is responsible for particular aspects (cell signaling, transcription, etc) of the cell cycle, and some of the CDK isozymes are specific to certain kinds of tissues. Aberrant expression and overexpression of these kinases are evidenced in many disease conditions. Inhibition of isozymes of CDKs specifically can yield beneficiary treatment modalities with minimum side effects. More than 80 3-dimensional structures of CDK2, CDK5, and CDK6 complexed with inhibitors have been published. This review provides an understanding of the structural aspects of CDK isozymes and binding modes of various known CDK inhibitors so that these kinases can be better targeted for drug discovery and design. The amino acid residues that constitute the cyclin binding region, the substrate binding region, and the area around the adenosine triphosphate (ATP) binding site have been compared for CDK isozymes. Those amino acids at the ATP binding site that could be used to improve the potency and subtype specificity have been described.
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Affiliation(s)
- Jayalakshmi Sridhar
- />Laboratory for In-silico Biology and Drug Discovery, Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room W417, 3970 Reservoir Rd NW, 20005 Washington, DC
| | - Nagaraju Akula
- />Laboratory for In-silico Biology and Drug Discovery, Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room W417, 3970 Reservoir Rd NW, 20005 Washington, DC
| | - Nagarajan Pattabiraman
- />Laboratory for In-silico Biology and Drug Discovery, Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room W417, 3970 Reservoir Rd NW, 20005 Washington, DC
- />Department of Biochemistry & Molecular Biology, Georgetown University, Washington DC
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30
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Staudt N, Fellert S, Chung HR, Jäckle H, Vorbrüggen G. Mutations of the Drosophila zinc finger-encoding gene vielfältig impair mitotic cell divisions and cause improper chromosome segregation. Mol Biol Cell 2006; 17:2356-65. [PMID: 16525017 PMCID: PMC1446075 DOI: 10.1091/mbc.e05-11-1056] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We describe the molecular characterization and function of vielfältig (vfl), a X-chromosomal gene that encodes a nuclear protein with six Krüppel-like C2H2 zinc finger motifs. vfl transcripts are maternally contributed and ubiquitously distributed in eggs and preblastoderm embryos, excluding the germline precursor cells. Zygotically, vfl is expressed strongly in the developing nervous system, the brain, and in other mitotically active tissues. Vfl protein shows dynamic subcellular patterns during the cell cycle. In interphase nuclei, Vfl is associated with chromatin, whereas during mitosis, Vfl separates from chromatin and becomes distributed in a granular pattern in the nucleoplasm. Functional gain-of-function and lack-of-function studies show that vfl activity is necessary for normal mitotic cell divisions. Loss of vfl activity disrupts the pattern of mitotic waves in preblastoderm embryos, elicits asynchronous DNA replication, and causes improper chromosome segregation during mitosis.
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Affiliation(s)
- Nicole Staudt
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, 37077 Göttingen, Germany
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31
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Fisher RP. Secrets of a double agent: CDK7 in cell-cycle control and transcription. J Cell Sci 2006; 118:5171-80. [PMID: 16280550 DOI: 10.1242/jcs.02718] [Citation(s) in RCA: 245] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In metazoans, cyclin-dependent kinase 7 (CDK7) has essential roles in both the cell-division cycle and transcription, as a CDK-activating kinase (CAK) and as a component of the general transcription factor TFIIH, respectively. Controversy over its double duty has been resolved, but questions remain. First, how does CDK7 achieve the dual substrate specificity necessary to perform both roles? Second, is there a deeper connection implied by the dichotomy of CDK7 function, for example similar mechanisms controlling cell division and gene expression, and/or actual coordination of the two processes? Enzymological studies have revealed solutions to the unusual substrate recognition problem, and there is evidence that the distinct functions of CDK7 can be regulated independently. Finally, despite divergence in their wiring, the CAK-CDK networks of budding yeast, fission yeast and metazoans all link transcriptional regulation with operation of the cell-cycle machinery. This connection might help to ensure that mRNAs encoding effectors of cell division are expressed at the right time in the cycle.
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Affiliation(s)
- Robert P Fisher
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.
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32
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Burke LJ, Zhang R, Bartkuhn M, Tiwari VK, Tavoosidana G, Kurukuti S, Weth C, Leers J, Galjart N, Ohlsson R, Renkawitz R. CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin. EMBO J 2005; 24:3291-300. [PMID: 16107875 PMCID: PMC1224683 DOI: 10.1038/sj.emboj.7600793] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Accepted: 07/29/2005] [Indexed: 11/09/2022] Open
Abstract
Most of the transcription factors, RNA polymerases and enhancer binding factors are absent from condensed mitotic chromosomes. In contrast, epigenetic marks of active and inactive genes somehow survive mitosis, since the activity status from one cell generation to the next is maintained. For the zinc-finger protein CTCF, a role in interpreting and propagating epigenetic states and in separating expression domains has been documented. To test whether such a domain structure is preserved during mitosis, we examined whether CTCF is bound to mitotic chromatin. Here we show that in contrast to other zinc-finger proteins, CTCF indeed is bound to mitotic chromosomes. Mitotic binding is mediated by a portion of the zinc-finger DNA binding domain and involves sequence specific binding to target sites. Furthermore, the chromatin loop organized by the CTCF-bound, differentially methylated region at the Igf2/H19 locus can be detected in mitosis. In contrast, the enhancer/promoter loop of the same locus is lost in mitosis. This may provide a novel form of epigenetic memory during cell division.
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Affiliation(s)
- Les J Burke
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Giessen, Germany
| | - Ru Zhang
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Giessen, Germany
| | - Vijay K Tiwari
- Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Uppsala, Sweden
| | - Gholamreza Tavoosidana
- Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Uppsala, Sweden
| | - Sreenivasulu Kurukuti
- Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Uppsala, Sweden
| | - Christine Weth
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Giessen, Germany
| | - Joerg Leers
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Giessen, Germany
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, DR Rotterdam, Netherlands
| | - Rolf Ohlsson
- Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Uppsala, Sweden
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Giessen, Germany
- Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany. Tel.: +49 641 99 35460; Fax: +49 641 99 35469; E-mail:
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33
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Coin F, Auriol J, Tapias A, Clivio P, Vermeulen W, Egly JM. Phosphorylation of XPB helicase regulates TFIIH nucleotide excision repair activity. EMBO J 2004; 23:4835-46. [PMID: 15549133 PMCID: PMC535092 DOI: 10.1038/sj.emboj.7600480] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 10/20/2004] [Indexed: 11/08/2022] Open
Abstract
Nucleotide excision repair (NER) removes damage from DNA in a tightly regulated multiprotein process. The xeroderma pigmentosum group B (XPB) helicase subunit of TFIIH functions in NER and transcription. The serine 751 (S751) residue of XPB was found to be phosphorylated in vivo. This phosphorylation inhibits NER and the microinjection of a phosphomimicking XPB-S751E mutant is unable to correct the NER defect of XP-B cells. Conversely, XPB-S751 dephosphorylation or its substitution with alanine (S751A) restores NER both in vivo and in vitro. Surprisingly, phospho/dephosphorylation of S751 spares TFIIH-dependent transcription. Finally, the phosphorylation of XPB-S751 does not impair the TFIIH unwinding of the DNA around the lesion, but rather prevents the 5' incision triggered by the ERCC1-XPF endonuclease. These data support an additional role for XPB in promoting the incision of the damaged fragment and reveal a point of NER regulation on TFIIH without interference in its transcription activity.
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Affiliation(s)
- Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
| | - Jérome Auriol
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
| | - Angel Tapias
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
| | - Pascale Clivio
- Institut de Chimie des Substances Naturelles du CNRS, ICSN-CNRS, Gif sur Yvette, France
| | - Wim Vermeulen
- Department of Genetics, Medical Genetic Cluster, Erasmus MC, Rotterdam, The Netherlands
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, CU de Strasbourg, France. Tel.: +33 388 65 34 47; Fax: +33 388 65 32 01; E-mail:
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Abstract
The transcripts of most metazoan protein-coding genes are alternatively spliced, but the mechanisms that are involved in the control of splicing are not well understood. Recent evidence supports the potential of both extra- and intracellular signalling to the splicing machinery as a means of regulating gene expression, and indicates that this form of gene control is widespread and mechanistically complex. However, important questions about these pathways need to be answered before this method of post-transcriptional regulation can be fully appreciated.
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Affiliation(s)
- Chanseok Shin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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35
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Lin HHS, Khosla M, Huang HJ, Hsu DW, Michaelis C, Weeks G, Pears C. A homologue of Cdk8 is required for spore cell differentiation in Dictyostelium. Dev Biol 2004; 271:49-58. [PMID: 15196949 DOI: 10.1016/j.ydbio.2004.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 01/30/2004] [Accepted: 03/04/2004] [Indexed: 11/25/2022]
Abstract
The Cdk8 proteins are kinases which phosphorylate the carboxy terminal domain (CTD) of RNA polymerase II (Pol II) as well as some transcription factors and, therefore, are involved in the regulation of transcription. Here, we report that a Cdk8 homologue from Dictyostelium discoideum is localized in the nucleus where it forms part of a high molecular weight complex that has CTD kinase activity. Insertional mutagenesis was used to abrogate gene function, and analysis of the null strain revealed that the DdCdk8 protein plays an important role in spore formation during late development. As previously reported [Dev. Growth Differ. 44 (2002) 213] Ddcdk8- cells also exhibit impaired aggregation, although we report that the severity of the defect depends upon experimental conditions. When aggregation occurs, Ddcdk8- cells form abnormal terminally differentiated structures within which the Ddcdk8- cells differentiate into stalk cells but fail to form spores, indicating a role for DdCdk8 in cell differentiation. When Ddcdk8 is expressed from its own promoter, the protein is able to rescue both the late developmental defect and the impaired aggregation. However, when expressed from an heterologous promoter, only the impaired aggregation is rescued. This result demonstrates that the defect during late development is not a consequence of impaired aggregation and indicates a direct role for DdCdk8 in spore formation.
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36
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Jantz D, Berg JM. Reduction in DNA-binding affinity of Cys2His2 zinc finger proteins by linker phosphorylation. Proc Natl Acad Sci U S A 2004; 101:7589-93. [PMID: 15128941 PMCID: PMC419650 DOI: 10.1073/pnas.0402191101] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cys(2)His(2) zinc finger proteins make up the largest class of transcription factors encoded in the genomes of higher eukaryotes. Recent studies of the Ikaros transcription factor demonstrated that this zinc finger protein undergoes cell cycle-dependent changes in association with DNA that seem to be due to phosphorylation of Thr or Ser residues in the linker regions connecting adjacent zinc finger domains. The high degree of conservation of this linker sequence within the Cys(2)His(2) superfamily suggested a common mechanism for the cell cycle-dependent modulation of DNA-binding affinity throughout this large class of transcription factors. The effects of linker phosphorylation on DNA-binding affinity were investigated through a direct comparison of the DNA-binding properties of four synthetic zinc finger proteins produced by native chemical ligation. The four proteins, comprising three zinc finger domains joined by two consensus Thr-Gly-Glu-Lys-Pro linkers, correspond to all four possible combinations of linker Thr phosphorylation states. Fluorescence-based DNA-binding studies of a specific DNA-binding site revealed that phosphorylation of a single linker reduced binding affinity approximately 40-fold, whereas phosphorylation of both linkers reduced binding affinity 130-fold. These results with purified components demonstrate that linker phosphorylation does, indeed, produce a significant reduction in DNA-binding affinity and support a model wherein a single cell cycle-dependent Ser/Thr kinase could simultaneously inactivate a large number of zinc finger transcription factors.
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Affiliation(s)
- Derek Jantz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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37
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Trembley JH, Loyer P, Hu D, Li T, Grenet J, Lahti JM, Kidd VJ. Cyclin Dependent Kinase 11 in RNA Transcription and Splicing. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY VOLUME 77 2004; 77:263-88. [PMID: 15196895 DOI: 10.1016/s0079-6603(04)77007-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Janeen H Trembley
- Department of Genetics and Tumor Cell Biology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
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38
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Fairley JA, Scott PH, White RJ. TFIIIB is phosphorylated, disrupted and selectively released from tRNA promoters during mitosis in vivo. EMBO J 2003; 22:5841-50. [PMID: 14592981 PMCID: PMC275401 DOI: 10.1093/emboj/cdg544] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitosis involves a generalized repression of gene expression. In the case of RNA polymerase III transcription, this is due to phosphorylation-mediated inactivation of TFIIIB, an essential complex comprising the TATA-binding protein TBP and the TAF subunits Brf1 and Bdp1. In HeLa cells, this repression is mediated by a mitotic kinase other than cdc2-cyclin B and is antagonized by protein phosphatase 2A. Brf1 is hyperphosphorylated in metaphase-arrested cells, but remains associated with promoters in condensed chromosomes, along with TBP. In contrast, Bdp1 is selectively released. Repression can be reversed by raising the concentration of Brf1 or Bdp1. The data support a model in which hyperphosphorylation disrupts TFIIIB during mitosis, compromising its ability to support transcription.
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Affiliation(s)
- Jennifer A Fairley
- Institute of Biomedical and Life Sciences, Division of Biochemistry and Molecular Biology, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
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39
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Xu YX, Hirose Y, Zhou XZ, Lu KP, Manley JL. Pin1 modulates the structure and function of human RNA polymerase II. Genes Dev 2003; 17:2765-76. [PMID: 14600023 PMCID: PMC280625 DOI: 10.1101/gad.1135503] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Accepted: 09/17/2003] [Indexed: 01/01/2023]
Abstract
The C-terminal domain of the RNA polymerase (RNAP) II largest subunit (CTD) plays critical roles both in transcription of mRNA precursors and in the processing reactions needed to form mature mRNAs. The CTD undergoes dynamic changes in phosphorylation during the transcription cycle, and this plays a significant role in coordinating its multiple activities. But how these changes themselves are regulated is not well understood. Here we show that the peptidyl-prolyl isomerase Pin1 influences the phosphorylation status of the CTD in vitro by inhibiting the CTD phosphatase FCP1 and stimulating CTD phosphorylation by cdc2/cyclin B. This is reflected in vivo by accumulation of hypophosphorylated RNAP II in pin1-/- cells, and of a novel hyper-hyperphosphorylated form in cells induced to overexpress Pin1. This hyper-hyperphosphorylated form of RNAP II also accumulates in M-phase cells, in a Pin1-dependent manner, and associates specifically with Pin1. Functionally, we find that Pin1 overexpression specifically inhibits ongoing transcription of mRNA precursors in vivo and both transcription and RNAP II-stimulated pre-mRNA splicing in cell extracts. Pin1 thus plays a significant role in regulating RNAP II CTD structure and function.
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Affiliation(s)
- Yu-Xin Xu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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40
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Chen J, Larochelle S, Li X, Suter B. Xpd/Ercc2 regulates CAK activity and mitotic progression. Nature 2003; 424:228-32. [PMID: 12853965 DOI: 10.1038/nature01746] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2003] [Accepted: 05/08/2003] [Indexed: 11/09/2022]
Abstract
General transcription factor IIH (TFIIH) consists of nine subunits: cyclin-dependent kinase 7 (Cdk7), cyclin H and MAT1 (forming the Cdk-activating-kinase or CAK complex), the two helicases Xpb/Hay and Xpd, and p34, p44, p52 and p62 (refs 1-3). As the kinase subunit of TFIIH, Cdk7 participates in basal transcription by phosphorylating the carboxy-terminal domain of the largest subunit of RNA polymerase II. As part of CAK, Cdk7 also phosphorylates other Cdks, an essential step for their activation. Here we show that the Drosophila TFIIH component Xpd negatively regulates the cell cycle function of Cdk7, the CAK activity. Excess Xpd titrates CAK activity, resulting in decreased Cdk T-loop phosphorylation, mitotic defects and lethality, whereas a decrease in Xpd results in increased CAK activity and cell proliferation. Moreover, Xpd is downregulated at the beginning of mitosis when Cdk1, a cell cycle target of Cdk7, is most active. Downregulation of Xpd thus seems to contribute to the upregulation of mitotic CAK activity and to regulate mitotic progression positively. Simultaneously, the downregulation of Xpd might be a major mechanism of mitotic silencing of basal transcription.
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Affiliation(s)
- Jian Chen
- Present address: Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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41
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Abstract
Many genes are repressed during mitosis, and this is known to involve differential phosphorylation of specific factors required for transcription, 3'-end RNA processing and translation. A recent study suggests that splicing is also targeted for mitotic repression, in this case by dephosphorylation of the newly identified splicing factor SRp38.
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Affiliation(s)
- Benjamin J Blencowe
- C.H. Best Institute, University of Toronto, 112 College Street, Room 410, Toronto, Ontario, Canada M5G 1L6.
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42
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Dovat S, Ronni T, Russell D, Ferrini R, Cobb BS, Smale ST. A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains. Genes Dev 2002; 16:2985-90. [PMID: 12464629 PMCID: PMC187490 DOI: 10.1101/gad.1040502] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many nuclear proteins are inactivated during mitotic entry, presumably as a prerequisite to chromatin condensation and cell division. C2H2 zinc fingers define the largest transcription factor family in the human proteome. The linker separating finger motifs is highly conserved and resembles TGEKP in more than 5000 occurrences. However, the reason for this conservation is not fully understood. We demonstrate that all three linkers in the DNA-binding domain of Ikaros are phosphorylated during mitosis. Phosphomimetic substitutions abolished DNA-binding and pericentromeric localization. A linker within Sp1 was also phosphorylated, suggesting that linker phosphorylation provides a global mechanism for inactivation of the C2H2 family.
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Affiliation(s)
- Sinisa Dovat
- Howard Hughes Medical Institute, Department of Microbiology, Immunology, and Molecular Genetics, California 90095, USA
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43
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Abstract
SR proteins constitute a family of pre-mRNA splicing factors that play important roles in both constitutive and regulated splicing. Here, we describe one member of the family, which we call SRp38, with unexpected properties. Unlike other SR proteins, SRp38 cannot activate splicing and is essentially inactive in splicing assays. However, dephosphorylation converts SRp38 to a potent, general repressor that inhibits splicing at an early step. To investigate the cellular function of SRp38, we examined its possible role in cell cycle control. We show first that splicing, like other steps in gene expression, is inhibited in extracts of mitotic cells. Strikingly, SRp38 was found to be dephosphorylated specifically in mitotic cells, and we show that dephosphorylated SRp38 is required for the observed splicing repression.
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Affiliation(s)
- Chanseok Shin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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44
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Labbaye C, Quaranta MT, Pagliuca A, Militi S, Licht JD, Testa U, Peschle C. PLZF induces megakaryocytic development, activates Tpo receptor expression and interacts with GATA1 protein. Oncogene 2002; 21:6669-79. [PMID: 12242665 DOI: 10.1038/sj.onc.1205884] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2002] [Revised: 07/16/2002] [Accepted: 07/18/2002] [Indexed: 11/09/2022]
Abstract
We investigated the expression of the PLZF gene in purified human hematopoietic progenitors induced to unilineage erythroid, granulocytic or megakaryocytic differentiation and maturation in serum-free culture. PLZF is expressed in quiescent progenitors: the expression level progressively rises through megakaryocytic development, whereas it gradually declines in erythroid and granulopoietic culture. To investigate the role of PLZF in megakaryopoiesis, we transduced the PLZF gene into the erythro-megakaryocytic TF1 cell line. PLZF overexpression upmodulates the megakaryocytic specific markers (CD42a, CD42b, CD61, PF4) and induces the thrombopoietin receptor (TpoR). The proximal promoter of the TpoR gene is activated in PLZF-expressing TF1 cells: in this promoter region, a PLZF DNA-binding site was identified by deletion constructs studies. Interestingly, PLZF and GATA1 proteins coimmunoprecipitate in PLZF-expressing TF1 cells: enforced expression of both PLZF and GATA1 in TF1 cells results in increased upregulation of megakaryocytic markers, as compared to exogenous PLZF or GATA1 alone, suggesting a functional role for the PLZF/GATA1 complex. Our data indicate that PLZF plays a significant stimulatory role in megakaryocytic development, seemingly mediated in part by induction of TpoR expression at transcriptional level. This stimulatory effect is potentiated by physical interaction of PLZF and GATA1, which are possibly assembled in a multiprotein transcriptional complex.
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Affiliation(s)
- Catherine Labbaye
- Department of Hematology-Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
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45
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Kobor MS, Greenblatt J. Regulation of transcription elongation by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:261-275. [PMID: 12213657 DOI: 10.1016/s0167-4781(02)00457-8] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The synthesis of mRNA by RNA polymerase II (RNAPII) is a multistep process that is regulated by different mechanisms. One important aspect of transcriptional regulation is phosphorylation of components of the transcription apparatus. The phosphorylation state of RNAPII carboxy-terminal domain (CTD) is controlled by a variety of protein kinases and at least one protein phosphatase. We discuss emerging genetic and biochemical evidence that points to a role of these factors not only in transcription initiation but also in elongation and possibly termination. In addition, we review phosphorylation events involving some of the general transcription factors (GTFs) and other regulatory proteins. As an interesting example, we describe the modulation of transcription associated kinases and phosphatase by the HIV Tat protein. We focus on bringing together recent findings and propose a revised model for the RNAPII phosphorylation cycle.
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Affiliation(s)
- Michael S Kobor
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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46
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Ehley JA, Melander C, Herman D, Baird EE, Ferguson HA, Goodrich JA, Dervan PB, Gottesfeld JM. Promoter scanning for transcription inhibition with DNA-binding polyamides. Mol Cell Biol 2002; 22:1723-33. [PMID: 11865052 PMCID: PMC135605 DOI: 10.1128/mcb.22.6.1723-1733.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When targeted to sequences adjacent to a TATA element, pyrrole-imidazole (Py-Im) polyamides inhibit the DNA binding activity of TATA box binding protein (TBP) and basal transcription by RNA polymerase II. In the present study, we scanned the human immunodeficiency virus type 1 promoter for polyamide inhibition of TBP binding and transcription using a series of DNA constructs in which a polyamide binding site was placed at various distances from the TATA box. Polyamide interference with either TBP-DNA or TFIID-TFIIA-DNA contacts both upstream and downstream of the TATA element resulted in inhibition of transcription. Our results define important protein-DNA interactions outside of the TATA element and suggest that transcription inhibition of selected gene promoters can be achieved with polyamides that target unique sequences within these promoters at a distance from the TATA element. Our studies also demonstrate the utility of the Py-Im polyamides for discovery of functionally important protein-DNA contacts involved in transcription.
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Affiliation(s)
- Jennifer A Ehley
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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47
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Oelgeschläger T. Regulation of RNA polymerase II activity by CTD phosphorylation and cell cycle control. J Cell Physiol 2002; 190:160-9. [PMID: 11807820 DOI: 10.1002/jcp.10058] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The carboxyl-terminal domain (CTD) of the largest subunit of mammalian RNA polymerase II (RNAP II) consists of 52 repeats of a consensus heptapeptide and is subject to phosphorylation and dephosphorylation events during each round of transcription. RNAP II activity is regulated during the cell cycle and cell cycle-dependend changes in RNAP II activity correlate well with CTD phosphorylation. In addition, global changes in the CTD phosphorylation status are observed in response to mitogenic or cytostatic signals such as growth factors, mitogens and DNA-damaging agents. Several CTD kinases are members of the cyclin-dependent kinase (CDK) superfamily and associate with transcription initiation complexes. Other CTD kinases implicated in cell cycle regulation include the mitogen-activated protein kinases ERK-1/2 and the c-Abl tyrosine kinase. These observations suggest that reversible RNAP II CTD phosphorylation may play a key role in linking cell cycle regulatory events to coordinated changes in transcription.
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Affiliation(s)
- Thomas Oelgeschläger
- Eukaryotic Gene Regulation Laboratory, Marie Curie Research Institute, The Chart, Oxted, Surrey, United Kingdom.
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48
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Nasiadka A, Dietrich BH, Krause HM. Anterior-posterior patterning in the Drosophila embryo. GENE EXPRESSION AT THE BEGINNING OF ANIMAL DEVELOPMENT 2002. [DOI: 10.1016/s1569-1799(02)12027-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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49
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Christova R, Oelgeschläger T. Association of human TFIID-promoter complexes with silenced mitotic chromatin in vivo. Nat Cell Biol 2002; 4:79-82. [PMID: 11744923 DOI: 10.1038/ncb733] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
When eukaryotic cells enter mitosis, transcription is abruptly silenced. Earlier studies indicated that most transcription factors and RNA polymerase II (RNAP II) are displaced when chromatin is condensed into mitotic chromosomes. A more recent study suggested that hitherto unidentified factors might 'bookmark' previously active genes for rapid reactivation after cell division. Here we used chromatin immunoprecipitation (ChIP) assays to examine the association of TFIID, TFIIB, NC2 and RNAP II with various gene promoters in asynchronous and mitotic human cell populations. We show that TFIID and TFIIB can remain associated with active gene promoters during mitosis whereas RNA polymerase II is displaced, and also that NC2, originally identified as ubiquitous repressor of transcription, is associated with active gene promoters in asynchronous cell populations and is displaced from some, but not all, genes in mitotic cells. Consistent with the remarkable stability of TFIID-promoter complexes observed in vitro, our data suggest that these complexes can withstand condensation of chromatin into transcriptionally silent chromosomes. Stable TFIID-promoter complexes are therefore implicated in the propagation of cell-type-specific gene expression patterns through cell division.
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Affiliation(s)
- Rossitza Christova
- Eukaryotic Gene Regulation Laboratory, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK
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Zhou M, Nekhai S, Bharucha DC, Kumar A, Ge H, Price DH, Egly JM, Brady JN. TFIIH inhibits CDK9 phosphorylation during human immunodeficiency virus type 1 transcription. J Biol Chem 2001; 276:44633-40. [PMID: 11572868 DOI: 10.1074/jbc.m107466200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tat stimulates human immunodeficiency virus, type 1 (HIV-1), transcription elongation by recruitment of the human transcription elongation factor P-TEFb, consisting of CDK9 and cyclin T1, to the TAR RNA structure. It has been demonstrated further that CDK9 phosphorylation is required for high affinity binding of Tat/P-TEFb to the TAR RNA structure and that the state of P-TEFb phosphorylation may regulate Tat transactivation. We now demonstrate that CDK9 phosphorylation is uniquely regulated in the HIV-1 preinitiation and elongation complexes. The presence of TFIIH in the HIV-1 preinitiation complex inhibits CDK9 phosphorylation. As TFIIH is released from the elongation complex between +14 and +36, CDK9 phosphorylation is observed. In contrast to the activity in the "soluble" complex, phosphorylation of CDK9 is increased by the presence of Tat in the transcription complexes. Consistent with these observations, we have demonstrated that purified TFIIH directly inhibits CDK9 autophosphorylation. By using recombinant TFIIH subcomplexes, our results suggest that the XPB subunit of TFIIH is responsible for this inhibition of CDK9 phosphorylation. Interestingly, our results further suggest that the phosphorylated form of CDK9 is the active kinase for RNA polymerase II carboxyl-terminal domain phosphorylation.
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Affiliation(s)
- M Zhou
- Virus Tumor Biology Section, Basic Research Laboratory, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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