51
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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52
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Abstract
The MuvB transcriptional regulatory complex, which controls cell-cycle-dependent gene expression, cooperates with B-Myb to activate genes required for the G2 and M phases of the cell cycle. We have identified the domain in B-Myb that is essential for the assembly of the Myb-MuvB (MMB) complex. We determined a crystal structure that reveals how this B-Myb domain binds MuvB through the adaptor protein LIN52 and the scaffold protein LIN9. The structure and biochemical analysis provide an understanding of how oncogenic B-Myb is recruited to regulate genes required for cell-cycle progression, and the MMB interface presents a potential therapeutic target to inhibit cancer cell proliferation.
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53
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Iness AN, Litovchick L. MuvB: A Key to Cell Cycle Control in Ovarian Cancer. Front Oncol 2018; 8:223. [PMID: 29942794 PMCID: PMC6004728 DOI: 10.3389/fonc.2018.00223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/30/2018] [Indexed: 02/05/2023] Open
Abstract
Cancer cells are characterized by uncontrolled proliferation, whereas the ability to enter quiescence or dormancy is important for cancer cell survival and disease recurrence. Therefore, understanding the mechanisms regulating cell cycle progression and exit is essential for improving patient outcomes. The MuvB complex of five proteins (LIN9, LIN37, LIN52, RBBP4, and LIN54), also known as LINC (LIN complex), is important for coordinated cell cycle gene expression. By participating in the formation of three distinct transcriptional regulatory complexes, including DREAM (DP, RB-like, E2F, and MuvB), MMB (Myb-MuvB), and FoxM1–MuvB, MuvB represents a unique regulator mediating either transcriptional activation (during S–G2 phases) or repression (during quiescence). With no known enzymatic activities in any of the MuvB-associated complexes, studies have focused on the therapeutic potential of protein kinases responsible for initiating DREAM assembly or downstream enzymatic targets of MMB. Furthermore, the mechanisms governing the formation and activity of each complex (DREAM, MMB, or FoxM1–MuvB) may have important consequences for therapeutic response. The MMB complex is associated with prognostic markers of aggressiveness in several cancers, whereas the DREAM complex is tied to disease recurrence through its role in maintaining quiescence. Here, we review recent developments in our understanding of MuvB function in the context of cancer. We specifically highlight the rationale for additional investigation of MuvB in high-grade serous ovarian cancer and the need for further translational research.
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Affiliation(s)
- Audra N Iness
- Division of Hematology, Oncology and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Larisa Litovchick
- Division of Hematology, Oncology and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
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54
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Shi C, Huang D, Lu N, Chen D, Zhang M, Yan Y, Deng L, Lu Q, Lu H, Luo S. Aberrantly activated Gli2-KIF20A axis is crucial for growth of hepatocellular carcinoma and predicts poor prognosis. Oncotarget 2018; 7:26206-19. [PMID: 27036048 PMCID: PMC5041975 DOI: 10.18632/oncotarget.8441] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/14/2016] [Indexed: 01/16/2023] Open
Abstract
Glioma-associated oncogene 2 (Gli2), a primary transcriptional regulator of Hedgehog (Hh) signaling, is essential for hepatocellular carcinoma (HCC) growth and survival. However, the underlying molecular mechanism and crucial downstream targets of Gli2 in human HCC are not fully understood. Here, we report the identification of kinesin family member 20A (KIF20A) as a novel downstream target of Gli2, which is important for HCC proliferation and tumor growth. Inhibition of Hh signaling leads to a remarkable decrease of KIF20A expression in HCC cells, whereas overexpression of Gli2 elevates KIF20A expression by activating Forkhead Box M1 (FoxM1)-MMB complex-mediated transcription of this kinesin gene. Gli2-induced HCC cell growth requires enhanced expression of KIF20A, and knockdown of Gli2 or KIF20A represses the proliferation of HCC cells in vitro and in vivo. Correlated with these results, analyses of clinical HCC samples show that Gli2, FoxM1 and KIF20A are highly elevated in primary HCC samples and represent significant risk factors for HCC recurrence and survival. Conclusion: KIF20A is an important downstream target gene of Hh signaling. And, the Gli2-KIF20A axis is essential for the proliferation and growth of human HCC cells. Our study also suggests Gli2-KIF20A axis as a potential target for future therapeutic intervention and as an independent prognostic biomarker for HCC.
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Affiliation(s)
- Chao Shi
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Dengliang Huang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Nonghua Lu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Dan Chen
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Minhong Zhang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yehong Yan
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Libin Deng
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Quqin Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanchang University, Nanchang, Jiangxi, China
| | - Hua Lu
- Department of Biochemistry and Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Shiwen Luo
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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55
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Wang P, Han W, Ma D. Virtual Sorting Has a Distinctive Advantage in Identification of Anticorrelated Genes and Further Negative Regulators of Immune Cell Subpopulations. THE JOURNAL OF IMMUNOLOGY 2017; 199:4155-4164. [PMID: 29093063 DOI: 10.4049/jimmunol.1700946] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022]
Abstract
Immune cells are highly plastic in both gene expression and cell phenotype. We have established a method of gene expressional plasticity and virtual sorting to evaluate immune cell subpopulations and their characteristic genes in human CD4+ T cells. In this study, we continued to investigate the informatics mechanism on the effectiveness of virtual sorting. We found that virtual sorting had an overall positive correlation to the Pearson correlation in the identification of positively correlated genes. However, owing to nonlinear biological anticorrelation, virtual sorting showed a distinctive advantage for anticorrelated genes, suggesting an important role in the identification of negative regulators. In addition, based on virtual sorting results, we identified two basic gene sets among highly plastic genes, i.e., highly plastic cell cycle-associated molecules and highly plastic immune and defense response-associated molecules. Genes within each set tended to be positively connected, but genes between two sets were often anticorrelated. Further analysis revealed preferential transcription factor binding motifs existed between highly plastic cell cycle-associated molecules and highly plastic immune and defense response-associated molecules. Our results strongly suggested predetermined regulation, which was called an immune cell internal phenotype, should exist and could be mined by virtual sorting analysis. This provided efficient functional clues to study immune cell phenotypes and their regulation. Moreover, the current substantial virtual sorting results in both CD4+ T cells and B cells provide a useful resource for big-data-driven experimental studies and knowledge discoveries.
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Affiliation(s)
- Pingzhang Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; .,Peking University Center for Human Disease Genomics, Beijing 100191, China; and .,Key Laboratory of Medical Immunology, Ministry of Health, Beijing 100191, China
| | - Wenling Han
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Peking University Center for Human Disease Genomics, Beijing 100191, China; and.,Key Laboratory of Medical Immunology, Ministry of Health, Beijing 100191, China
| | - Dalong Ma
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Peking University Center for Human Disease Genomics, Beijing 100191, China; and.,Key Laboratory of Medical Immunology, Ministry of Health, Beijing 100191, China
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56
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Cell cycle arrest through indirect transcriptional repression by p53: I have a DREAM. Cell Death Differ 2017; 25:114-132. [PMID: 29125603 PMCID: PMC5729532 DOI: 10.1038/cdd.2017.172] [Citation(s) in RCA: 411] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Activation of the p53 tumor suppressor can lead to cell cycle arrest. The key mechanism of p53-mediated arrest is transcriptional downregulation of many cell cycle genes. In recent years it has become evident that p53-dependent repression is controlled by the p53–p21–DREAM–E2F/CHR pathway (p53–DREAM pathway). DREAM is a transcriptional repressor that binds to E2F or CHR promoter sites. Gene regulation and deregulation by DREAM shares many mechanistic characteristics with the retinoblastoma pRB tumor suppressor that acts through E2F elements. However, because of its binding to E2F and CHR elements, DREAM regulates a larger set of target genes leading to regulatory functions distinct from pRB/E2F. The p53–DREAM pathway controls more than 250 mostly cell cycle-associated genes. The functional spectrum of these pathway targets spans from the G1 phase to the end of mitosis. Consequently, through downregulating the expression of gene products which are essential for progression through the cell cycle, the p53–DREAM pathway participates in the control of all checkpoints from DNA synthesis to cytokinesis including G1/S, G2/M and spindle assembly checkpoints. Therefore, defects in the p53–DREAM pathway contribute to a general loss of checkpoint control. Furthermore, deregulation of DREAM target genes promotes chromosomal instability and aneuploidy of cancer cells. Also, DREAM regulation is abrogated by the human papilloma virus HPV E7 protein linking the p53–DREAM pathway to carcinogenesis by HPV. Another feature of the pathway is that it downregulates many genes involved in DNA repair and telomere maintenance as well as Fanconi anemia. Importantly, when DREAM function is lost, CDK inhibitor drugs employed in cancer treatment such as Palbociclib, Abemaciclib and Ribociclib can compensate for defects in early steps in the pathway upstream from cyclin/CDK complexes. In summary, the p53–p21–DREAM–E2F/CHR pathway controls a plethora of cell cycle genes, can contribute to cell cycle arrest and is a target for cancer therapy.
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57
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Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R, Leach DA, Navaratnam N, Pálinkás HL, Vértessy BG, Fenton TR, Doorbar J, Fuller-Pace F, Meek DW, Coombes RC, Buluwela L, Ali S. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res 2017; 45:11056-11069. [PMID: 28977491 PMCID: PMC5737468 DOI: 10.1093/nar/gkx721] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/30/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022] Open
Abstract
Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression. This occurs through the induction of p21 (CDKN1A) and the recruitment of the repressive DREAM complex to the A3B gene promoter, such that loss of p53 through mutation, or human papilloma virus-mediated inhibition, prevents recruitment of the complex, thereby causing elevated A3B expression and cytosine deaminase activity in cancer cells. As p53 is frequently mutated in cancer, our findings provide a mechanism by which p53 loss can promote cancer mutagenesis.
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Affiliation(s)
- Manikandan Periyasamy
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Anup K. Singh
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Carolina Gemma
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Christian Kranjec
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Raed Farzan
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Damien A. Leach
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Naveenan Navaratnam
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Hajnalka L. Pálinkás
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Beata G. Vértessy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Tim R. Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - John Doorbar
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Frances Fuller-Pace
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - David W. Meek
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - R. Charles Coombes
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Laki Buluwela
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
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58
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Goetsch PD, Garrigues JM, Strome S. Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB's innate function as the repressor of DREAM target genes. PLoS Genet 2017; 13:e1007088. [PMID: 29091720 PMCID: PMC5683655 DOI: 10.1371/journal.pgen.1007088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 11/13/2017] [Accepted: 10/24/2017] [Indexed: 12/27/2022] Open
Abstract
The DREAM (Dp/Retinoblastoma(Rb)-like/E2F/MuvB) transcriptional repressor complex acts as a gatekeeper of the mammalian cell cycle by establishing and maintaining cellular quiescence. How DREAM’s three functional components, the E2F-DP heterodimer, the Rb-like pocket protein, and the MuvB subcomplex, form and function at target gene promoters remains unknown. The current model invokes that the pocket protein links E2F-DP and MuvB and is essential for gene repression. We tested this model by assessing how the conserved yet less redundant DREAM system in Caenorhabditis elegans is affected by absence of the sole C. elegans pocket protein LIN-35. Using a LIN-35 protein null mutant, we analyzed the assembly of E2F-DP and MuvB at promoters that are bound by DREAM and the level of expression of those "DREAM target genes" in embryos. We report that LIN-35 indeed mediates the association of E2F-DP and MuvB, a function that stabilizes DREAM subunit occupancy at target genes. In the absence of LIN-35, the occupancy of E2F-DP and MuvB at most DREAM target genes decreases dramatically and many of those genes become upregulated. The retention of E2F-DP and MuvB at some target gene promoters in lin-35 null embryos allowed us to test their contribution to DREAM target gene repression. Depletion of MuvB, but not E2F-DP, in the sensitized lin-35 null background caused further upregulation of DREAM target genes. We conclude that the pocket protein functions primarily to support MuvB-mediated repression of DREAM targets and that transcriptional repression is the innate function of the evolutionarily conserved MuvB complex. Our findings provide important insights into how mammalian DREAM assembly and disassembly may regulate gene expression and the cell cycle. The 8-subunit DREAM transcriptional repressor complex contains 3 functional components that together control expression of cell cycle and developmental genes. How the E2F-DP transcription factor heterodimer, the pocket protein, and the highly conserved MuvB complex coalesce on chromatin and repress DREAM target genes has yet to be determined. We directly tested the prevailing model that the DREAM pocket protein links E2F-DP to MuvB and is required for gene repression. Using a protein null mutant of the sole C. elegans pocket protein LIN-35, we demonstrate that the pocket protein indeed links E2F-DP and MuvB, which aids in the stable occupancy of DREAM components near target genes. Depletion of additional DREAM components in lin-35 null worms revealed that the remaining chromatin-bound MuvB represses target genes. We conclude that the MuvB subcomplex mediates DREAM’s critical repressive function. Our functional genomics approach in the simplified C. elegans system reveals that the ancestral function of the pocket protein is to stabilize the innate repressive activity of MuvB, ensuring proper regulation of DREAM target genes through development.
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Affiliation(s)
- Paul D. Goetsch
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jacob M. Garrigues
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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59
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Mages CF, Wintsche A, Bernhart SH, Müller GA. The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence. eLife 2017; 6. [PMID: 28920576 PMCID: PMC5602299 DOI: 10.7554/elife.26876] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022] Open
Abstract
The retinoblastoma Rb protein is an important factor controlling the cell cycle. Yet, mammalian cells carrying Rb deletions are still able to arrest under growth-limiting conditions. The Rb-related proteins p107 and p130, which are components of the DREAM complex, had been suggested to be responsible for a continued ability to arrest by inhibiting E2f activity and by recruiting chromatin-modifying enzymes. Here, we show that p130 and p107 are not sufficient for DREAM-dependent repression. We identify the MuvB protein Lin37 as an essential factor for DREAM function. Cells not expressing Lin37 proliferate normally, but DREAM completely loses its ability to repress genes in G0/G1 while all remaining subunits, including p130/p107, still bind to target gene promoters. Furthermore, cells lacking both Rb and Lin37 are incapable of exiting the cell cycle. Thus, Lin37 is an essential component of DREAM that cooperates with Rb to induce quiescence.
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Affiliation(s)
- Christina Fs Mages
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Axel Wintsche
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany.,Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Gerd A Müller
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
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60
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Fischer M, Müller GA. Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes. Crit Rev Biochem Mol Biol 2017; 52:638-662. [PMID: 28799433 DOI: 10.1080/10409238.2017.1360836] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The precise timing of cell cycle gene expression is critical for the control of cell proliferation; de-regulation of this timing promotes the formation of cancer and leads to defects during differentiation and development. Entry into and progression through S phase requires expression of genes coding for proteins that function in DNA replication. Expression of a distinct set of genes is essential to pass through mitosis and cytokinesis. Expression of these groups of cell cycle-dependent genes is regulated by the RB pocket protein family, the E2F transcription factor family, and MuvB complexes together with B-MYB and FOXM1. Distinct combinations of these transcription factors promote the transcription of the two major groups of cell cycle genes that are maximally expressed either in S phase (G1/S) or in mitosis (G2/M). In this review, we discuss recent work that has started to uncover the molecular mechanisms controlling the precisely timed expression of these genes at specific cell cycle phases, as well as the repression of the genes when a cell exits the cell cycle.
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Affiliation(s)
- Martin Fischer
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany.,b Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA.,c Department of Medicine, Brigham and Women's Hospital , Harvard Medical School , Boston , MA , USA
| | - Gerd A Müller
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany
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61
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Park JE, Yi H, Kim Y, Chang H, Kim VN. Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. Mol Cell 2017; 62:462-471. [PMID: 27153541 DOI: 10.1016/j.molcel.2016.04.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/07/2016] [Accepted: 04/04/2016] [Indexed: 12/15/2022]
Abstract
Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we investigate poly(A) tail dynamics and translational control in the somatic cell cycle. We find dramatic changes in poly(A) tail lengths of cell-cycle regulatory genes like CDK1, TOP2A, and FBXO5, explaining their translational repression in M phase. We also find that poly(A) tail length is coupled to translation when the poly(A) tail is <20 nucleotides. However, as most genes have >20 nucleotide poly(A) tails, their translation is regulated mainly via poly(A) tail length-independent mechanisms during the cell cycle. Specifically, we find that terminal oligopyrimidine (TOP) tract-containing transcripts escape global translational suppression in M phase and are actively translated. Our quantitative and comprehensive data provide a revised view of translational control in the somatic cell cycle.
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Affiliation(s)
- Jong-Eun Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyerim Yi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yoosik Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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62
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Wolter P, Hanselmann S, Pattschull G, Schruf E, Gaubatz S. Central spindle proteins and mitotic kinesins are direct transcriptional targets of MuvB, B-MYB and FOXM1 in breast cancer cell lines and are potential targets for therapy. Oncotarget 2017; 8:11160-11172. [PMID: 28061449 PMCID: PMC5355254 DOI: 10.18632/oncotarget.14466] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/26/2016] [Indexed: 12/17/2022] Open
Abstract
The MuvB multiprotein complex, together with B-MYB and FOXM1 (MMB-FOXM1), plays an essential role in cell cycle progression by regulating the transcription of genes required for mitosis and cytokinesis. In many tumors, B-MYB and FOXM1 are overexpressed as part of the proliferation signature. However, the transcriptional targets that are important for oncogenesis have not been identified. Given that mitotic kinesins are highly expressed in cancer cells and that selected kinesins have been reported as target genes of MMB-FOXM1, we sought to determine which mitotic kinesins are directly regulated by MMB-FOXM1. We demonstrate that six mitotic kinesins and two microtubule-associated non-motor proteins (MAPs) CEP55 and PRC1 are direct transcriptional targets of MuvB, B-MYB and FOXM1 in breast cancer cells. Suppression of KIF23 and PRC1 strongly suppressed proliferation of MDA-MB-231 cells. The set of MMB-FOXM1 regulated kinesins genes and 4 additional kinesins which we referred to as the mitotic kinesin signature (MKS) is linked to poor outcome in breast cancer patients. Thus, mitotic kinesins could be used as prognostic biomarker and could be potential therapeutic targets for the treatment of breast cancer.
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Affiliation(s)
- Patrick Wolter
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, University of Wuerzburg, Wuerzburg, Germany
| | - Steffen Hanselmann
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, University of Wuerzburg, Wuerzburg, Germany
| | - Grit Pattschull
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, University of Wuerzburg, Wuerzburg, Germany
| | - Eva Schruf
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, University of Wuerzburg, Wuerzburg, Germany
| | - Stefan Gaubatz
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, University of Wuerzburg, Wuerzburg, Germany
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63
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Fischer M, Uxa S, Stanko C, Magin TM, Engeland K. Human papilloma virus E7 oncoprotein abrogates the p53-p21-DREAM pathway. Sci Rep 2017; 7:2603. [PMID: 28572607 PMCID: PMC5453983 DOI: 10.1038/s41598-017-02831-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/18/2017] [Indexed: 12/12/2022] Open
Abstract
High risk human papilloma viruses cause several types of cancer. The HPV oncoproteins E6 and E7 are essential for oncogenic cell transformation. E6 mediates the degradation of the tumor suppressor p53, and E7 can form complexes with the retinoblastoma pRB tumor suppressor. Recently, it has been shown that HPV E7 can also interfere with the function of the DREAM transcriptional repressor complex. Disruption of DREAM-dependent transcriptional repression leads to untimely early expression of central cell cycle regulators. The p53-p21-DREAM pathway represents one important means of cell cycle checkpoint activation by p53. By activating this pathway, p53 can downregulate transcription of genes controlled by DREAM. Here, we present a genome-wide ranked list of genes deregulated by HPV E7 expression and relate it to datasets of cell cycle genes and DREAM targets. We find that DREAM targets are generally deregulated after E7 expression. Furthermore, our analysis shows that p53-dependent downregulation of DREAM targets is abrogated when HPV E7 is expressed. Thus, p53 checkpoint control is impaired by HPV E7 independently of E6. In summary, our analysis reveals that disruption of DREAM through the HPV E7 oncoprotein upregulates most, if not all, cell cycle genes and impairs p53's control of cell cycle checkpoints.
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Affiliation(s)
- Martin Fischer
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany.
| | - Sigrid Uxa
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Clara Stanko
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Thomas M Magin
- Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany
| | - Kurt Engeland
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany.
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64
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Wilson KA, Wetmore SD. Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature. Struct Chem 2017. [DOI: 10.1007/s11224-017-0954-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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65
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Paci P, Colombo T, Fiscon G, Gurtner A, Pavesi G, Farina L. SWIM: a computational tool to unveiling crucial nodes in complex biological networks. Sci Rep 2017; 7:44797. [PMID: 28317894 PMCID: PMC5357943 DOI: 10.1038/srep44797] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/14/2017] [Indexed: 12/14/2022] Open
Abstract
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called “fight-club hubs”, characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called “switch genes”, appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer.
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Affiliation(s)
- Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.,SysBio Centre for Systems Biology, Rome, 00185, Italy
| | - Teresa Colombo
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Aymone Gurtner
- Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, Regina Elena National Cancer Institute, Rome, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, "Sapienza" University, Rome, Italy
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66
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Sato Y, Katoh Y, Matsumoto M, Sato M, Ebina M, Itoh-Nakadai A, Funayama R, Nakayama K, Unno M, Igarashi K. Regulatory signatures of liver regeneration distilled by integrative analysis of mRNA, histone methylation, and proteomics. J Biol Chem 2017; 292:8019-8037. [PMID: 28302717 DOI: 10.1074/jbc.m116.774547] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/28/2017] [Indexed: 12/30/2022] Open
Abstract
The capacity of the liver to regenerate is likely to be encoded as a plasticity of molecular networks within the liver. By applying a combination of comprehensive analyses of the epigenome, transcriptome, and proteome, we herein depict the molecular landscape of liver regeneration. We demonstrated that histone H3 Lys-4 was trimethylated at the promoter regions of many loci, among which only a fraction, including cell-cycle-related genes, were transcriptionally up-regulated. A cistrome analysis guided by the histone methylation patterns and the transcriptome identified FOXM1 as the key transcription factor promoting liver regeneration, which was confirmed in vitro using a hepatocarcinoma cell line. The promoter regions of cell-cycle-related genes and Foxm1 acquired higher levels of trimethylated histone H3 Lys-4, suggesting that epigenetic regulations of these key regulatory genes define quiescence and regeneration of the liver cells. A quantitative proteome analysis of the regenerating liver revealed that conditional protein degradation also mediated regeneration-specific protein expression. These sets of informational resources should be useful for further investigations of liver regeneration.
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Affiliation(s)
- Yoshihiro Sato
- From the Department of Biochemistry.,Department of Gastroenterological Surgery
| | - Yasutake Katoh
- From the Department of Biochemistry.,Center for Regulatory Epigenome and Diseases, and
| | | | - Masaki Sato
- From the Department of Biochemistry.,Department of Gastroenterological Surgery
| | - Masayuki Ebina
- From the Department of Biochemistry.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
| | | | - Ryo Funayama
- Center for Regulatory Epigenome and Diseases, and.,Department of Cell Proliferation, Tohoku University Graduate School of Medicine, 2-1 Seiryo, Sendai 980-8575, Japan and
| | - Keiko Nakayama
- Center for Regulatory Epigenome and Diseases, and.,Department of Cell Proliferation, Tohoku University Graduate School of Medicine, 2-1 Seiryo, Sendai 980-8575, Japan and
| | | | - Kazuhiko Igarashi
- From the Department of Biochemistry, .,Center for Regulatory Epigenome and Diseases, and.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
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67
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Puig-Butille JA, Vinyals A, Ferreres JR, Aguilera P, Cabré E, Tell-Martí G, Marcoval J, Mateo F, Palomero L, Badenas C, Piulats JM, Malvehy J, Pujana MA, Puig S, Fabra À. AURKA Overexpression Is Driven by FOXM1 and MAPK/ERK Activation in Melanoma Cells Harboring BRAF or NRAS Mutations: Impact on Melanoma Prognosis and Therapy. J Invest Dermatol 2017; 137:1297-1310. [PMID: 28188776 DOI: 10.1016/j.jid.2017.01.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/31/2022]
Abstract
The cell cycle-related genes AURKA and FOXM1 are overexpressed in melanoma. We show here that AURKA overexpression is associated with poor prognosis in three independent cohorts of melanoma patients and correlates with the presence of genomic amplification of AURKA locus and BRAFV600E mutation. AURKA overexpression may also be driven by increased promoter activation through elements such as ETS and FOXM1 found within the 5' proximal promoter region. Activated MAPK/ERK signaling pathway mediates robust AURKA promoter activation, thereby knockdown of BRAFV600E and ERK inhibition results in reduced AURKA transcription and expression. We show a positive correlation between FOXM1 and AURKA expression in three independent cohorts of melanoma patients. FOXM1 silencing decreases expression of AURKA and late cell cycle genes in melanoma cells. We further found that FOXM1 expression levels are significantly higher in tumors carrying the BRAFV600E mutation compared with the wild-type BRAF (BRAFwt). Accordingly, the knockdown of BRAFV600E also reduces the expression of FOXM1 in BRAFV600E cells. Moreover, Aurora kinase A and FOXM1 inhibition by either genetic knockdown or pharmacologic inhibitors impair melanoma growth and survival both in culture and in vivo, underscoring their therapeutic value for melanoma patients who fail to benefit from BRAF/MEK signaling inhibition.
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Affiliation(s)
- Joan Anton Puig-Butille
- Biochemistry and Molecular Genetics Service, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Antònia Vinyals
- IDIBELL (Bellvitge Biomedical Research Institute), Centre d' Oncologia Molecular, Barcelona, Spain
| | - Josep R Ferreres
- Dermatology Service, IDIBELL-Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Paula Aguilera
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Eduard Cabré
- IDIBELL (Bellvitge Biomedical Research Institute), Centre d' Oncologia Molecular, Barcelona, Spain
| | - Gemma Tell-Martí
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Joaquim Marcoval
- Dermatology Service, IDIBELL-Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Luís Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Celia Badenas
- Biochemistry and Molecular Genetics Service, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Josep M Piulats
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Josep Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Miquel A Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Àngels Fabra
- IDIBELL (Bellvitge Biomedical Research Institute), Centre d' Oncologia Molecular, Barcelona, Spain.
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68
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Timing of transcription during the cell cycle: Protein complexes binding to E2F, E2F/CLE, CDE/CHR, or CHR promoter elements define early and late cell cycle gene expression. Oncotarget 2016; 8:97736-97748. [PMID: 29228647 PMCID: PMC5716687 DOI: 10.18632/oncotarget.10888] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
A central question in cell cycle control is how differential gene expression is regulated. Timing of expression is important for correct progression through the cell cycle. E2F, CDE, and CHR promoter sites have been linked to transcriptional repression in resting cells and activation during the cell cycle. Further, the DREAM complex binds CHR or CDE/CHR elements of G2/M genes resulting in repression during G0/G1. Here, we show that DREAM also binds to E2F sites of S phase genes in quiescence and upon p53 activation. Furthermore, we describe a novel class of promoter sites, the CHR-like elements (CLE), which can support binding of DREAM to E2F elements. Activation of such S phase genes is achieved through binding of E2F1-3/DP complexes to E2F sites. In contrast, the activating MuvB complexes MMB and FOXM1-MuvB bind to CHR elements and mediate peak expression in G2/M. In conclusion, data presented here in combination with earlier results leads us to propose a model that explains how DREAM can repress early cell cycle genes through E2F or E2F/CLE sites and late genes through CHR or CDE/CHR elements. Also p53-dependent indirect transcriptional repression through the p53-p21-Cyclin/CDK-DREAM-E2F/CLE/CDE/CHR pathway requires DREAM binding to E2F or E2F/CLE sites in early cell cycle genes and binding of DREAM to CHR or CDE/CHR elements of late cell cycle genes. Specific timing of activation is achieved through binding of E2F1-3/DP to E2F sites and MMB or FOXM1-MuvB complexes to CHR elements.
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69
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Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. Nat Commun 2016; 7:12301. [PMID: 27465258 PMCID: PMC4974476 DOI: 10.1038/ncomms12301] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 06/20/2016] [Indexed: 12/13/2022] Open
Abstract
The MuvB complex recruits transcription factors to activate or repress genes with cell cycle-dependent expression patterns. MuvB contains the DNA-binding protein LIN54, which directs the complex to promoter cell cycle genes homology region (CHR) elements. Here we characterize the DNA-binding properties of LIN54 and describe the structural basis for recognition of a CHR sequence. We biochemically define the CHR consensus as TTYRAA and determine that two tandem cysteine rich regions are required for high-affinity DNA association. A crystal structure of the LIN54 DNA-binding domain in complex with a CHR sequence reveals that sequence specificity is conferred by two tyrosine residues, which insert into the minor groove of the DNA duplex. We demonstrate that this unique tyrosine-mediated DNA binding is necessary for MuvB recruitment to target promoters. Our results suggest a model in which MuvB binds near transcription start sites and plays a role in positioning downstream nucleosomes.
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70
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Fischer M, Grossmann P, Padi M, DeCaprio JA. Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks. Nucleic Acids Res 2016; 44:6070-86. [PMID: 27280975 PMCID: PMC4994865 DOI: 10.1093/nar/gkw523] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/26/2016] [Accepted: 05/28/2016] [Indexed: 12/11/2022] Open
Abstract
Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest.
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Affiliation(s)
- Martin Fischer
- Molecular Oncology, Medical School, University of Leipzig, Leipzig 04103, Germany Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Patrick Grossmann
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Megha Padi
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
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71
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Nicolas E, Golemis EA, Arora S. POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies. Gene 2016; 590:128-41. [PMID: 27320729 PMCID: PMC4969162 DOI: 10.1016/j.gene.2016.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
The evolutionarily conserved human polymerase delta (POLD1) gene encodes the large p125 subunit which provides the essential catalytic activities of polymerase δ (Polδ), mediated by 5′–3′ DNA polymerase and 3′–5′ exonuclease moieties. POLD1 associates with three smaller subunits (POLD2, POLD3, POLD4), which together with Replication Factor C and Proliferating Nuclear Cell Antigen constitute the polymerase holoenzyme. Polδ function is essential for replication, with a primary role as the replicase for the lagging strand. Polδ also has an important proofreading ability conferred by the exonuclease activity, which is critical for ensuring replicative fidelity, but also serves to repair DNA lesions arising as a result of exposure to mutagens. Polδ has been shown to be important for multiple forms of DNA repair, including nucleotide excision repair, double strand break repair, base excision repair, and mismatch repair. A growing number of studies in the past decade have linked germline and sporadic mutations in POLD1 and the other subunits of Polδ with human pathologies. Mutations in Polδ in mice and humans lead to genomic instability, mutator phenotype and tumorigenesis. The advent of genome sequencing techniques has identified damaging mutations in the proofreading domain of POLD1 as the underlying cause of some inherited cancers, and suggested that mutations in POLD1 may influence therapeutic management. In addition, mutations in POLD1 have been identified in the developmental disorders of mandibular hypoplasia, deafness, progeroid features and lipodystrophy and atypical Werner syndrome, while changes in expression or activity of POLD1 have been linked to senescence and aging. Intriguingly, some recent evidence suggests that POLD1 function may also be altered in diabetes. We provide an overview of critical Polδ activities in the context of these pathologic conditions.
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Affiliation(s)
- Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sanjeevani Arora
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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72
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Clare SE, Gupta A, Choi M, Ranjan M, Lee O, Wang J, Ivancic DZ, Kim JJ, Khan SA. Progesterone receptor blockade in human breast cancer cells decreases cell cycle progression through G2/M by repressing G2/M genes. BMC Cancer 2016; 16:326. [PMID: 27215412 PMCID: PMC4878043 DOI: 10.1186/s12885-016-2355-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/11/2016] [Indexed: 12/15/2022] Open
Abstract
Background The synthesis of specific, potent progesterone antagonists adds potential agents to the breast cancer prevention and treatment armamentarium. The identification of individuals who will benefit from these agents will be a critical factor for their clinical success. Methods We utilized telapristone acetate (TPA; CDB-4124) to understand the effects of progesterone receptor (PR) blockade on proliferation, apoptosis, promoter binding, cell cycle progression, and gene expression. We then identified a set of genes that overlap with human breast luteal-phase expressed genes and signify progesterone activity in both normal breast cells and breast cancer cell lines. Results TPA administration to T47D cells results in a 30 % decrease in cell number at 24 h, which is maintained over 72 h only in the presence of estradiol. Blockade of progesterone signaling by TPA for 24 h results in fewer cells in G2/M, attributable to decreased expression of genes that facilitate the G2/M transition. Gene expression data suggest that TPA affects several mechanisms that progesterone utilizes to control gene expression, including specific post-translational modifications, and nucleosomal organization and higher order chromatin structure, which regulate access of PR to its DNA binding sites. Conclusions By comparing genes induced by the progestin R5020 in T47D cells with those increased in the luteal-phase normal breast, we have identified a set of genes that predict functional progesterone signaling in tissue. These data will facilitate an understanding of the ways in which drugs such as TPA may be utilized for the prevention, and possibly the therapy, of human breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2355-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susan E Clare
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - Akash Gupta
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - MiRan Choi
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - Manish Ranjan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - Oukseub Lee
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - Jun Wang
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - David Z Ivancic
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA
| | - J Julie Kim
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA.
| | - Seema A Khan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Lurie 4-111, Chicago, IL, 60611, USA.
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73
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Fischer M, Quaas M, Nickel A, Engeland K. Indirect p53-dependent transcriptional repression of Survivin, CDC25C, and PLK1 genes requires the cyclin-dependent kinase inhibitor p21/CDKN1A and CDE/CHR promoter sites binding the DREAM complex. Oncotarget 2015; 6:41402-17. [PMID: 26595675 PMCID: PMC4747163 DOI: 10.18632/oncotarget.6356] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/11/2015] [Indexed: 12/15/2022] Open
Abstract
The transcription factor p53 is central to cell cycle control by downregulation of cell cycle-promoting genes upon cell stress such as DNA damage. Survivin (BIRC5), CDC25C, and PLK1 encode important cell cycle regulators that are repressed following p53 activation. Here, we provide evidence that p53-dependent repression of these genes requires activation of p21 (CDKN1A, WAF1, CIP1). Chromatin immunoprecipitation (ChIP) data indicate that promoter binding of B-MYB switches to binding of E2F4 and p130 resulting in a replacement of the MMB (Myb-MuvB) by the DREAM complex. We demonstrate that this replacement depends on p21. Furthermore, transcriptional repression by p53 requires intact DREAM binding sites in the target promoters. The CDE and CHR cell cycle promoter elements are the sites for DREAM binding. These elements as well as the p53 response of Survivin, CDC25C, and PLK1 are evolutionarily conserved. No binding of p53 to these genes is detected by ChIP and mutation of proposed p53 binding sites does not alter the p53 response. Thus, a mechanism for direct p53-dependent transcriptional repression is not supported by the data. In contrast, repression by DREAM is consistent with most previous findings and unifies models based on p21-, E2F4-, p130-, and CDE/CHR-dependent repression by p53. In conclusion, the presented data suggest that the p53-p21-DREAM-CDE/CHR pathway regulates p53-dependent repression of Survivin, CDC25C, and PLK1.
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Affiliation(s)
- Martin Fischer
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
- Department of Medical Oncology, Dana–Farber Cancer Institute, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marianne Quaas
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Annina Nickel
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Kurt Engeland
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
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74
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Fischer M, Quaas M, Steiner L, Engeland K. The p53-p21-DREAM-CDE/CHR pathway regulates G2/M cell cycle genes. Nucleic Acids Res 2015; 44:164-74. [PMID: 26384566 PMCID: PMC4705690 DOI: 10.1093/nar/gkv927] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/08/2015] [Indexed: 11/13/2022] Open
Abstract
The tumor suppressor p53 functions predominantly as a transcription factor by activating and downregulating gene expression, leading to cell cycle arrest or apoptosis. p53 was shown to indirectly repress transcription of the CCNB2, KIF23 and PLK4 cell cycle genes through the recently discovered p53-p21-DREAM-CDE/CHR pathway. However, it remained unclear whether this pathway is commonly used. Here, we identify genes regulated by p53 through this pathway in a genome-wide computational approach. The bioinformatic analysis is based on genome-wide DREAM complex binding data, p53-depedent mRNA expression data and a genome-wide definition of phylogenetically conserved CHR promoter elements. We find 210 target genes that are expected to be regulated by the p53-p21-DREAM-CDE/CHR pathway. The target gene list was verified by detailed analysis of p53-dependent repression of the cell cycle genes B-MYB (MYBL2), BUB1, CCNA2, CCNB1, CHEK2, MELK, POLD1, RAD18 and RAD54L. Most of the 210 target genes are essential regulators of G2 phase and mitosis. Thus, downregulation of these genes through the p53-p21-DREAM-CDE/CHR pathway appears to be a principal mechanism for G2/M cell cycle arrest by p53.
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Affiliation(s)
- Martin Fischer
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Marianne Quaas
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
| | - Lydia Steiner
- Centre for Complexity & Collective Computation, Wisconsin Institute for Discovery, Madison, WI, USA Computational EvoDevo Group & Bioinformatics Group, Department of Computer Science, and Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Kurt Engeland
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
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75
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Abstract
The predominant function of the tumor suppressor p53 is transcriptional regulation. It is generally accepted that p53-dependent transcriptional activation occurs by binding to a specific recognition site in promoters of target genes. Additionally, several models for p53-dependent transcriptional repression have been postulated. Here, we evaluate these models based on a computational meta-analysis of genome-wide data. Surprisingly, several major models of p53-dependent gene regulation are implausible. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and falsifies models of direct repression. This notion is supported by experimental re-analysis of representative genes reported as directly repressed by p53. Therefore, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors as well as models based on the function of ncRNAs are also not supported by the meta-analysis. As an alternative to models of direct repression, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21-DREAM/RB pathway.
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Key Words
- CDE, cell cycle-dependent element
- CDKN1A
- CHR, cell cycle genes homology region
- ChIP, chromatin immunoprecipitation
- DREAM complex
- DREAM, DP, RB-like, E2F4, and MuvB complex
- E2F/RB complex
- HPV, human papilloma virus
- NF-Y, Nuclear factor Y
- cdk, cyclin-dependent kinase
- genome-wide meta-analysis
- p53
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Affiliation(s)
- Martin Fischer
- a Molecular Oncology; Medical School ; University of Leipzig ; Leipzig , Germany
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76
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Abstract
Strict temporal control of cell cycle gene expression is essential for all eukaryotes including animals and plants. DREAM complexes have been identified in worm, fly, and mammals, linking several distinct transcription factors to coordinate gene expression throughout the cell cycle. In this issue of The EMBO Journal, Kobayashi et al (2015) identify distinct activator and repressor complexes for genes expressed during the G2 and M phases in Arabidopsis that can be temporarily separated during proliferating and post‐mitotic stages of development. The complexes incorporate specific activator and repressor MYB and E2F transcription factors and indicate the possibility of the existence of multiple DREAM complexes in plants.
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Affiliation(s)
- Martin Fischer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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77
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Klein DK, Hoffmann S, Ahlskog JK, O'Hanlon K, Quaas M, Larsen BD, Rolland B, Rösner HI, Walter D, Kousholt AN, Menzel T, Lees M, Johansen JV, Rappsilber J, Engeland K, Sørensen CS. Cyclin F suppresses B-Myb activity to promote cell cycle checkpoint control. Nat Commun 2015; 6:5800. [PMID: 25557911 DOI: 10.1038/ncomms6800] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/07/2014] [Indexed: 01/31/2023] Open
Abstract
Cells respond to DNA damage by activating cell cycle checkpoints to delay proliferation and facilitate DNA repair. Here, to uncover new checkpoint regulators, we perform RNA interference screening targeting genes involved in ubiquitylation processes. We show that the F-box protein cyclin F plays an important role in checkpoint control following ionizing radiation. Cyclin F-depleted cells initiate checkpoint signalling after ionizing radiation, but fail to maintain G2 phase arrest and progress into mitosis prematurely. Importantly, cyclin F suppresses the B-Myb-driven transcriptional programme that promotes accumulation of crucial mitosis-promoting proteins. Cyclin F interacts with B-Myb via the cyclin box domain. This interaction is important to suppress cyclin A-mediated phosphorylation of B-Myb, a key step in B-Myb activation. In summary, we uncover a regulatory mechanism linking the F-box protein cyclin F with suppression of the B-Myb/cyclin A pathway to ensure a DNA damage-induced checkpoint response in G2.
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Affiliation(s)
- Ditte Kjærsgaard Klein
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Saskia Hoffmann
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Johanna K Ahlskog
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Karen O'Hanlon
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Marianne Quaas
- Department of Molecular Oncology, Medical School, University of Leipzig, Semmelweisstr. 14, 04103, Leipzig, Germany
| | - Brian D Larsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Baptiste Rolland
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Heike I Rösner
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - David Walter
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Arne Nedergaard Kousholt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Tobias Menzel
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Michael Lees
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland
| | - Kurt Engeland
- Department of Molecular Oncology, Medical School, University of Leipzig, Semmelweisstr. 14, 04103, Leipzig, Germany
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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