1
|
Li L, Wu Y, Dai K, Wang Q, Ye S, Shi Q, Chen Z, Huang YC, Zhao W, Li L. The CHCHD2/Sirt1 corepressors involve in G9a-mediated regulation of RNase H1 expression to control R-loop. CELL INSIGHT 2023; 2:100112. [PMID: 37388553 PMCID: PMC10300302 DOI: 10.1016/j.cellin.2023.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 07/01/2023]
Abstract
R-loops are regulators of many cellular processes and are threats to genome integrity. Therefore, understanding the mechanisms underlying the regulation of R-loops is important. Inspired by the findings on RNase H1-mediated R-loop degradation or accumulation, we focused our interest on the regulation of RNase H1 expression. In the present study, we report that G9a positively regulates RNase H1 expression to boost R-loop degradation. CHCHD2 acts as a repressive transcription factor that inhibits the expression of RNase H1 to promote R-loop accumulation. Sirt1 interacts with CHCHD2 and deacetylates it, which functions as a corepressor that suppresses the expression of downstream target gene RNase H1. We also found that G9a methylated the promoter of RNase H1, inhibiting the binding of CHCHD2 and Sirt1. In contrast, when G9a was knocked down, recruitment of CHCHD2 and Sirt1 to the RNase H1 promoter increased, which co-inhibited RNase H1 transcription. Furthermore, knockdown of Sirt1 led to binding of G9a to the RNase H1 promoter. In summary, we demonstrated that G9a regulates RNase H1 expression to maintain the steady-state balance of R-loops by suppressing the recruitment of CHCHD2/Sirt1 corepressors to the target gene promoter.
Collapse
|
2
|
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: 30] [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.
Collapse
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.)
| |
Collapse
|
3
|
Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription. Genes (Basel) 2021; 12:genes12070961. [PMID: 34202617 PMCID: PMC8303148 DOI: 10.3390/genes12070961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 12/29/2022] Open
Abstract
Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.
Collapse
|
4
|
Wang T, Zou Y, Huang N, Teng J, Chen J. CCDC84 Acetylation Oscillation Regulates Centrosome Duplication by Modulating HsSAS-6 Degradation. Cell Rep 2020; 29:2078-2091.e5. [PMID: 31722219 DOI: 10.1016/j.celrep.2019.10.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/16/2019] [Accepted: 10/07/2019] [Indexed: 01/14/2023] Open
Abstract
In animal cells, centriole number is strictly controlled in order to guarantee faithful cell division and genetic stability, but the mechanism by which the accuracy of centrosome duplication is maintained is not fully understood. Here, we show that CCDC84 constrains centriole number by modulating APC/CCdh1-mediated HsSAS-6 degradation. More importantly, CCDC84 acetylation oscillates throughout the cell cycle, and the acetylation state of CCDC84 at lysine 31 is regulated by the deacetylase SIRT1 and the acetyltransferase NAT10. Deacetylated CCDC84 is responsible for its centrosome targeting, and acetylated CCDC84 promotes HsSAS-6 ubiquitination by enhancing the binding affinity of HsSAS-6 for Cdh1. Our findings shed new light on the function of (de)acetylation in centriole number regulation as well as refine the established centrosome duplication model.
Collapse
Affiliation(s)
- Tianning Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yuhong Zou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China.
| |
Collapse
|
5
|
Awasthi S, Verma M, Mahesh A, K Khan MI, Govindaraju G, Rajavelu A, Chavali PL, Chavali S, Dhayalan A. DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA. Nucleic Acids Res 2019; 46:6304-6317. [PMID: 29618122 PMCID: PMC6158705 DOI: 10.1093/nar/gky231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 12/19/2022] Open
Abstract
Among the proteins predicted to be a part of the DExD box RNA helicase family, the functions of DDX49 are unknown. Here, we characterize the enzymatic activities and functions of DDX49 by comparing its properties with the well-studied RNA helicase, DDX39B. We find that DDX49 exhibits a robust ATPase and RNA helicase activity, significantly higher than that of DDX39B. DDX49 is required for the efficient export of poly (A)+ RNA from nucleus in a splicing-independent manner. Furthermore, DDX49 is a resident protein of nucleolus and regulates the steady state levels of pre-ribosomal RNA by regulating its transcription and stability. These dual functions of regulating mRNA export and pre-ribosomal RNA levels enable DDX49 to modulate global translation. Phenotypically, DDX49 promotes proliferation and colony forming potential of cells. Strikingly, DDX49 is significantly elevated in diverse cancer types suggesting that the increased abundance of DDX49 has a role in oncogenic transformation of cells. Taken together, this study shows the physiological role of DDX49 in regulating distinct steps of mRNA and pre-ribosomal RNA metabolism and hence translation and potential pathological role of its dysregulation, especially in cancers.
Collapse
Affiliation(s)
- Sharad Awasthi
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Mamta Verma
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arun Mahesh
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Gayathri Govindaraju
- Bacterial and Parasite Disease Biology, Rajiv Gandhi Center for Biotechnology, Trivandrum 695 014, India
| | - Arumugam Rajavelu
- Bacterial and Parasite Disease Biology, Rajiv Gandhi Center for Biotechnology, Trivandrum 695 014, India
| | - Pavithra L Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| |
Collapse
|
6
|
Iyer-Bierhoff A, Grummt I. Stop-and-Go: Dynamics of Nucleolar Transcription During the Cell Cycle. Epigenet Insights 2019; 12:2516865719849090. [PMID: 31206100 PMCID: PMC6537492 DOI: 10.1177/2516865719849090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 12/25/2022] Open
Abstract
Entry into mitosis correlates with nucleolar disassembly and shutdown of ribosomal RNA (rRNA) gene (rDNA) transcription. In telophase, nucleoli reform and transcription is reactivated. The molecular mechanisms underlying the dynamics of nucleolar transcription during the cell cycle are manifold. Although mitotic inactivation of the RNA polymerase I (Pol I) transcription machinery by posttranslational modifications has been extensively studied, little is known about the structure of rDNA chromatin during progression through mitosis. Methylation of histone H2A at glutamine 104 (H2AQ104me), a dedicated nucleolar histone modification, is lost in prometaphase, leading to chromatin compaction, which enforces mitotic repression of rRNA genes. At telophase, restoration of H2AQ104me is required for the activation of transcription. H2AQ104 methylation and chromatin dynamics are regulated by fibrillarin (FBL) and the NAD+-dependent nucleolar deacetylase sirtuin 7 (SIRT7). Deacetylation of FBL is required for the methylation of H2AQ104 and high levels of rDNA transcription during interphase. At the entry into mitosis, nucleoli disassemble and FBL is hyperacetylated, leading to loss of H2AQ104me, chromatin compaction, and shutdown of Pol I transcription. These results reveal that reversible acetylation of FBL regulates methylation of nucleolar H2AQ104, thereby reinforcing oscillation of Pol I transcription during the cell cycle.
Collapse
Affiliation(s)
| | - Ingrid Grummt
- German Cancer Research Centre, DKFZ-ZMBH Alliance, Heidelberg, Germany
| |
Collapse
|
7
|
Bi X, Ye Q, Li D, Peng Q, Wang Z, Wu X, Zhang Y, Zhang Q, Jiang F. Inhibition of nucleolar stress response by Sirt1: A potential mechanism of acetylation-independent regulation of p53 accumulation. Aging Cell 2019; 18:e12900. [PMID: 30623565 PMCID: PMC6413664 DOI: 10.1111/acel.12900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 11/28/2018] [Accepted: 12/08/2018] [Indexed: 02/04/2023] Open
Abstract
The mammalian Sirt1 deacetylase is generally thought to be a nuclear protein, but some pilot studies have suggested that Sirt1 may also be involved in orchestrating nucleolar functions. Here, we show that nucleolar stress response is a ubiquitous cellular reaction that can be induced by different types of stress conditions, and Sirt1 is an endogenous suppressor of nucleolar stress response. Using stable isotope labeling by amino acids in cell culture approach, we have identified a physical interaction of between Sirt1 and the nucleolar protein nucleophosmin, and this protein-protein interaction appears to be necessary for Sirt1 inhibition on nucleolar stress, whereas the deacetylase activity of Sirt1 is not strictly required. Based on the reported prerequisite role of nucleolar stress response in stress-induced p53 protein accumulation, we have also provided evidence suggesting that Sirt1-mediated inhibition on nucleolar stress response may represent a novel mechanism by which Sirt1 can modulate intracellular p53 accumulation independent of lysine deacetylation. This process may represent an alternative mechanism by which Sirt1 regulates functions of the p53 pathway.
Collapse
Affiliation(s)
- Xiaolei Bi
- School of Basic MedicineShandong UniversityJinanShandong ProvinceChina
- Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical SciencesJinanChina
- The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
- Present address:
Department of CardiologyQingdao Municipal HospitalQingdaoShandong ProvinceChina
| | - Qing Ye
- School of Basic MedicineShandong UniversityJinanShandong ProvinceChina
- Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical SciencesJinanChina
- The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
| | - Daoyuan Li
- National Glycoengineering Research CenterShandong UniversityJinanChina
| | - Qisheng Peng
- Key Laboratory of Zoonosis ResearchJilin UniversityChangchunJilin ProvinceChina
| | - Zhe Wang
- Division of Endocrinology and MetabolismShandong Provincial Hospital affiliated to Shandong UniversityJinanChina
| | - Xiao Wu
- Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical SciencesJinanChina
- The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
| | - Yun Zhang
- Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical SciencesJinanChina
- The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
| | - Qunye Zhang
- Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical SciencesJinanChina
- The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
| | - Fan Jiang
- School of Basic MedicineShandong UniversityJinanShandong ProvinceChina
- Key Laboratory of Cardiovascular Remodeling and Function ResearchChinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical SciencesJinanChina
- The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
| |
Collapse
|
8
|
Hannig K, Babl V, Hergert K, Maier A, Pilsl M, Schächner C, Stöckl U, Milkereit P, Tschochner H, Seufert W, Griesenbeck J. The C-terminal region of Net1 is an activator of RNA polymerase I transcription with conserved features from yeast to human. PLoS Genet 2019; 15:e1008006. [PMID: 30802237 PMCID: PMC6415870 DOI: 10.1371/journal.pgen.1008006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/13/2019] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
RNA polymerase I (Pol I) synthesizes ribosomal RNA (rRNA) in all eukaryotes, accounting for the major part of transcriptional activity in proliferating cells. Although basal Pol I transcription factors have been characterized in diverse organisms, the molecular basis of the robust rRNA production in vivo remains largely unknown. In S. cerevisiae, the multifunctional Net1 protein was reported to stimulate Pol I transcription. We found that the Pol I-stimulating function can be attributed to the very C-terminal region (CTR) of Net1. The CTR was required for normal cell growth and Pol I recruitment to rRNA genes in vivo and sufficient to promote Pol I transcription in vitro. Similarity with the acidic tail region of mammalian Pol I transcription factor UBF, which could partly functionally substitute for the CTR, suggests conserved roles for CTR-like domains in Pol I transcription from yeast to human. The production of ribosomes, cellular factories of protein synthesis, is an essential process driving proliferation and cell growth. Ribosome biogenesis is controlled at the level of synthesis of its components, ribosomal proteins and ribosomal RNA. In eukaryotes, RNA polymerase I is dedicated to transcribe the ribosomal RNA. RNA polymerase I has been identified as a potential target for cell proliferation inhibition. Here we describe the C-terminal region of Net1 as an activator of RNA polymerase I transcription in baker’s yeast. In the absence of this activator RNA polymerase I transcription is downregulated and cell proliferation is strongly impaired. Strikingly, this activator might be conserved in human cells, which points to a general mechanism. Our discovery will help to gain a better understanding of the molecular basis of ribosomal RNA synthesis and may have implications in developing strategies to control cellular growth.
Collapse
Affiliation(s)
- Katharina Hannig
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Virginia Babl
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Kristin Hergert
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Andreas Maier
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Christopher Schächner
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Ulrike Stöckl
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| | - Herbert Tschochner
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| | - Wolfgang Seufert
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| | - Joachim Griesenbeck
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| |
Collapse
|
9
|
Liao W, Zheng Y, Fang W, Liao S, Xiong Y, Li Y, Xiao S, Zhang X, Liu J. Dual Specificity Phosphatase 6 Protects Neural Stem Cells from β-Amyloid-Induced Cytotoxicity through ERK1/2 Inactivation. Biomolecules 2018; 8:E181. [PMID: 30572643 PMCID: PMC6315916 DOI: 10.3390/biom8040181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease with limited treatment options and no cure. Beta-amyloid (Aβ) is a hallmark of AD that has potent neurotoxicity in neural stem cells (NSCs). Dual specificity phosphatase 6 (DUSP6) is a member of the mitogen-activated protein kinases (MAPKs), which is involved in regulating various physiological and pathological processes. Whether DUSP6 has a protective effect on Aβ-induced NSC injury remains to be explored. C17.2 neural stem cells were transfected with DUSP6-overexpressed plasmid. NSCs with or without DUSP6 overexpression were administrated with Aβ25⁻35 at various concentrations (i.e., 0, 2.5, 5 μM). DUSP6 expression after Aβ treatment was detected by Real-Time Polymerase Chain Reaction (RT-PCR) and Western blot and cell vitality was examined by the CCK8 assay. The oxidative stress (intracellular reactive oxygen species (ROS) and malondialdehyde (MDA)), endoplasmic reticulum stress (ER calcium level) and mitochondrial dysfunction (cytochrome c homeostasis) were tested. The expression of p-ERK1/2 and ERK1/2 were assayed by Western blot. Our results showed that Aβ decreased the expression of DUSP6 in a dose-dependent manner. The overexpression of DUSP6 increased the cell vitality of NSCs after Aβ treatment. Oxidative stress, ER stress, and mitochondrial dysfunction induced by Aβ could be restored by DUSP6 overexpression. Additionally, the Aβ-induced ERK1/2 activation was reversed. In summary, DUSP6 might have a neuroprotective effect on Aβ-induced cytotoxicity, probably via ERK1/2 activation.
Collapse
Affiliation(s)
- Wang Liao
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA 02478, USA.
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Yuqiu Zheng
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenli Fang
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Shaowei Liao
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Ying Xiong
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Yi Li
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Songhua Xiao
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| | - Xingcai Zhang
- John A Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA.
| | - Jun Liu
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China.
| |
Collapse
|
10
|
Vadivel Gnanasundram S, Fåhraeus R. Translation Stress Regulates Ribosome Synthesis and Cell Proliferation. Int J Mol Sci 2018; 19:ijms19123757. [PMID: 30486342 PMCID: PMC6321632 DOI: 10.3390/ijms19123757] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 12/11/2022] Open
Abstract
Ribosome and protein synthesis are major metabolic events that control cellular growth and proliferation. Impairment in ribosome biogenesis pathways and mRNA translation is associated with pathologies such as cancer and developmental disorders. Processes that control global protein synthesis are tightly regulated at different levels by numerous factors and linked with multiple cellular signaling pathways. Several of these merge on the growth promoting factor c-Myc, which induces ribosome biogenesis by stimulating Pol I, Pol II, and Pol III transcription. However, how cells sense and respond to mRNA translation stress is not well understood. It was more recently shown that mRNA translation stress activates c-Myc, through a specific induction of E2F1 synthesis via a PI3Kδ-dependent pathway. This review focuses on how this novel feedback pathway stimulates cellular growth and proliferation pathways to synchronize protein synthesis with ribosome biogenesis. It also describes for the first time the oncogenic activity of the mRNA, and not the encoded protein.
Collapse
Affiliation(s)
| | - Robin Fåhraeus
- Inserm UMRS1162, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France.
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic.
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden.
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| |
Collapse
|
11
|
Awasthi S, Chakrapani B, Mahesh A, Chavali PL, Chavali S, Dhayalan A. DDX39B promotes translation through regulation of pre-ribosomal RNA levels. RNA Biol 2018; 15:1157-1166. [PMID: 30176153 DOI: 10.1080/15476286.2018.1517011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
DDX39B, a DExD RNA helicase, is known to be involved in various cellular processes such as mRNA export, splicing and translation. Previous studies showed that the overexpression of DDX39B promotes the global translation but inhibits the mRNA export in a dominant negative manner. This presents a conundrum as to how DDX39B overexpression would increase the global translation if it inhibits the nuclear export of mRNAs. We resolve this by showing that DDX39B affects the levels of pre-ribosomal RNA by regulating its stability as well as synthesis. Furthermore, DDX39B promotes proliferation and colony forming potential of cells and its levels are significantly elevated in diverse cancer types. Thus, increase in DDX39B enhances global translation and cell proliferation through upregulation of pre-ribosomal RNA. This highlights a possible mechanism by which dysregulation of DDX39B expression could lead to oncogenesis.
Collapse
Affiliation(s)
- Sharad Awasthi
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| | - Baskar Chakrapani
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| | - Arun Mahesh
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| | - Pavithra L Chavali
- b Structural Studies Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Sreenivas Chavali
- b Structural Studies Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Arunkumar Dhayalan
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| |
Collapse
|
12
|
Chen X, Lu L, Qian S, Scalf M, Smith LM, Zhong X. Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. THE PLANT CELL 2018; 30:134-152. [PMID: 29343504 PMCID: PMC5810568 DOI: 10.1105/tpc.17.00626] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/11/2017] [Accepted: 01/12/2018] [Indexed: 05/13/2023]
Abstract
Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis thaliana histone deacetylase HD2C in pre-rRNA processing via both canonical and noncanonical manners. HD2C interacts with another histone deacetylase HD2B and forms homo- and/or hetero-oligomers in the nucleolus. Depletion of HD2C and HD2B induces a ribosome-biogenesis deficient phenotype and aberrant accumulation of 18S pre-rRNA intermediates. Our genome-wide analysis revealed that HD2C binds and represses the expression of key genes involved in ribosome biogenesis. Using RNA immunoprecipitation and sequencing, we further uncovered a noncanonical mechanism of HD2C directly associating with pre-rRNA and small nucleolar RNAs to regulate rRNA methylation. Together, this study reveals a multifaceted role of HD2C in ribosome biogenesis and provides mechanistic insights into how histone deacetylases modulate rRNA maturation at the transcriptional and posttranscriptional levels.
Collapse
Affiliation(s)
- Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Li Lu
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Shuiming Qian
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
13
|
Sarlós K, Biebricher A, Petermann EJG, Wuite GJL, Hickson ID. Knotty Problems during Mitosis: Mechanistic Insight into the Processing of Ultrafine DNA Bridges in Anaphase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:187-195. [PMID: 29167280 DOI: 10.1101/sqb.2017.82.033647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To survive and proliferate, cells have to faithfully segregate their newly replicated genomic DNA to the two daughter cells. However, the sister chromatids of mitotic chromosomes are frequently interlinked by so-called ultrafine DNA bridges (UFBs) that are visible in the anaphase of mitosis. UFBs can only be detected by the proteins bound to them and not by staining with conventional DNA dyes. These DNA bridges are presumed to represent entangled sister chromatids and hence pose a threat to faithful segregation. A failure to accurately unlink UFB DNA results in chromosome segregation errors and binucleation. This, in turn, compromises genome integrity, which is a hallmark of cancer. UFBs are actively removed during anaphase, and most known UFB-associated proteins are enzymes involved in DNA repair in interphase. However, little is known about the mitotic activities of these enzymes or the exact DNA structures present on UFBs. We focus on the biology of UFBs, with special emphasis on their underlying DNA structure and the decatenation machineries that process UFBs.
Collapse
Affiliation(s)
- Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Biebricher
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Erwin J G Petermann
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| |
Collapse
|
14
|
Gil J, Ramírez-Torres A, Chiappe D, Luna-Peñaloza J, Fernandez-Reyes FC, Arcos-Encarnación B, Contreras S, Encarnación-Guevara S. Lysine acetylation stoichiometry and proteomics analyses reveal pathways regulated by sirtuin 1 in human cells. J Biol Chem 2017; 292:18129-18144. [PMID: 28893905 DOI: 10.1074/jbc.m117.784546] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 09/01/2017] [Indexed: 01/03/2023] Open
Abstract
Lysine acetylation is a widespread posttranslational modification affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make it difficult to confidently assign these numbers, limiting understanding of their biological significance. Here, we tested three common sample preparation methods to determine their suitability for assessing acetylation stoichiometry in three human cell lines, identifying the acetylation occupancy in more than 1,300 proteins from each cell line. The stoichiometric analysis in combination with quantitative proteomics also enabled us to explore their functional roles. We found that higher abundance of the deacetylase sirtuin 1 (SIRT1) correlated with lower acetylation occupancy and lower levels of ribosomal proteins, including those involved in ribosome biogenesis and rRNA processing. Treatment with the SIRT1 inhibitor EX-527 confirmed SIRT1's role in the regulation of pre-rRNA synthesis and processing. Specifically, proteins involved in pre-rRNA transcription, including subunits of the polymerase I and SL1 complexes and the RNA polymerase I-specific transcription initiation factor RRN3, were up-regulated after SIRT1 inhibition. Moreover, many protein effectors and regulators of pre-rRNA processing needed for rRNA maturation were also up-regulated after EX-527 treatment with the outcome that pre-rRNA and 28S rRNA levels also increased. More generally, we found that SIRT1 inhibition down-regulates metabolic pathways, including glycolysis and pyruvate metabolism. Together, these results provide the largest data set thus far of lysine acetylation stoichiometry (available via ProteomeXchange with identifier PXD005903) and set the stage for further biological investigations of this central posttranslational modification.
Collapse
Affiliation(s)
- Jeovanis Gil
- From the Programa de Genómica Funcional de Procariotes and.,Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Avenida Universidad s/n, Colonia Chamilpa, Cuernavaca, Morelos CP 62210, México
| | | | - Diego Chiappe
- Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | | | - Francis C Fernandez-Reyes
- Centro de Investigación en Ciencia-Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos CP 62210, México
| | | | | | | |
Collapse
|
15
|
Brighenti E, Treré D, Derenzini M. Targeted cancer therapy with ribosome biogenesis inhibitors: a real possibility? Oncotarget 2016; 6:38617-27. [PMID: 26415219 PMCID: PMC4770724 DOI: 10.18632/oncotarget.5775] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/04/2015] [Indexed: 12/13/2022] Open
Abstract
The effects of many chemotherapeutic drugs on ribosome biogenesis have been underestimated for a long time. Indeed, many drugs currently used for cancer treatment--and which are known to either damage DNA or hinder DNA synthesis--have been shown to exert their toxic action mainly by inhibiting rRNA synthesis or maturation. Moreover, there are new drugs that have been proposed recently for cancer chemotherapy, which only hinder ribosome biogenesis without any genotoxic activity. Even though ribosome biogenesis occurs in both normal and cancer cells, whether resting or proliferating, there is evidence that the selective inhibition of ribosome biogenesis may, in some instances, result in a selective damage to neoplastic cells. The higher sensitivity of cancer cells to inhibitors of rRNA synthesis appears to be the consequence of either the loss of the mechanisms controlling the cell cycle progression or the acquisition of activating oncogene and inactivating tumor suppressor gene mutations that up-regulate the ribosome biogenesis rate. This article reviews those cancer cell characteristics on which the selective cancer cell cytotoxicity induced by the inhibitors of ribosome biogenesis is based.
Collapse
Affiliation(s)
- Elisa Brighenti
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna, Italy
| | - Davide Treré
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna, Italy
| | - Massimo Derenzini
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna, Italy
| |
Collapse
|
16
|
Nielsen CF, Hickson ID. PICH promotes mitotic chromosome segregation: Identification of a novel role in rDNA disjunction. Cell Cycle 2016; 15:2704-11. [PMID: 27565185 DOI: 10.1080/15384101.2016.1222336] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
PICH is an SNF2-family DNA translocase that appears to play a role specifically in mitosis. Characterization of PICH in human cells led to the initial discovery of "ultra-fine DNA bridges" (UFBs) that connect the 2 segregating DNA masses in the anaphase of mitosis. These bridge structures, which arise from specific regions of the genome, are a normal feature of anaphase but had escaped detection previously because they do not stain with commonly used DNA dyes. Nevertheless, UFBs are important for genome maintenance because defects in UFB resolution can lead to cytokinesis failure. We reported recently that PICH stimulates the unlinking (decatenation) of entangled DNA by Topoisomerase IIα (Topo IIα), and is important for the resolution of UFBs. We also demonstrated that PICH and Topo IIα co-localize at the rDNA (rDNA). In this Extra View article, we discuss the mitotic roles of PICH and explore further the role of PICH in the timely segregation of the rDNA locus.
Collapse
Affiliation(s)
- Christian F Nielsen
- a Center for Chromosome Stability , Department of Cellular and Molecular Medicine , University of Copenhagen , Copenhagen , Denmark.,b Chromosome Research, Murdoch Children's Research Institute, Royal Children's Hospital , Parkville , VIC , Australia
| | - Ian D Hickson
- a Center for Chromosome Stability , Department of Cellular and Molecular Medicine , University of Copenhagen , Copenhagen , Denmark
| |
Collapse
|
17
|
Abstract
Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.
Collapse
|