1
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLoS Genet 2023; 19:e1010845. [PMID: 37440598 PMCID: PMC10368294 DOI: 10.1371/journal.pgen.1010845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities similar to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far particular to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
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2
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Wang X, Cao C, Tan X, Liao X, Du X, Wang X, Liu T, Gong D, Hu Z, Tian X. SETD8, a frequently mutated gene in cervical cancer, enhances cisplatin sensitivity by impairing DNA repair. Cell Biosci 2023; 13:107. [PMID: 37308924 DOI: 10.1186/s13578-023-01054-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Cisplatin is commonly used to treat cervical cancer while drug resistance limits its effectiveness. There is an urgent need to identify strategies that increase cisplatin sensitivity and improve the outcomes of chemotherapy. RESULTS We performed whole exome sequencing (WES) of 156 cervical cancer tissues to assess genomic features related to platinum-based chemoresistance. By using WES, we identified a frequently mutated locus SETD8 (7%), which was associated with drug sensitivity. Cell functional assays, in vivo xenografts tumor growth experiments, and survival analysis were used to investigate the functional significance and mechanism of chemosensitization after SETD8 downregulation. Knockdown of SETD8 increased the responsiveness of cervical cancer cells to cisplatin treatment. The mechanism is exerted by reduced binding of 53BP1 to DNA breaks and inhibition of the non-homologous end joining (NHEJ) repair pathway. In addition, SETD8 expression was positively correlated with resistance to cisplatin and negatively associated with the prognosis of cervical cancer patients. Further, UNC0379 as a small molecule inhibitor of SETD8 was found to enhance cisplatin sensitivity both in vitro and in vivo. CONCLUSIONS SETD8 was a promising therapeutic target to ameliorate cisplatin resistance and improve the efficacy of chemotherapy.
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Affiliation(s)
- Xin Wang
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Chen Cao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Xiangyu Tan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Xueyao Liao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Xiaofang Du
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Xueqian Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Ting Liu
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Danni Gong
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Zheng Hu
- Department of Gynecologic Oncology, Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
- Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China.
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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3
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540083. [PMID: 37214839 PMCID: PMC10197650 DOI: 10.1101/2023.05.09.540083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus . Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities analogous to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far unique to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261 U.S.A
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
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4
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Crain AT, Klusza S, Armstrong RL, Santa Rosa P, Temple BRS, Strahl BD, McKay DJ, Matera AG, Duronio RJ. Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. Genetics 2022; 221:iyac054. [PMID: 35404465 PMCID: PMC9157153 DOI: 10.1093/genetics/iyac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Mono-methylation of histone H4 lysine 20 (H4K20me1) is catalyzed by Set8/KMT5A and regulates numerous aspects of genome organization and function. Loss-of-function mutations in Drosophila melanogaster Set8 or mammalian KMT5A prevent H4K20me1 and disrupt development. Set8/KMT5A also has non-histone substrates, making it difficult to determine which developmental functions of Set8/KMT5A are attributable to H4K20me1 and which to other substrates or to non-catalytic roles. Here, we show that human KMT5A can functionally substitute for Set8 during Drosophila development and that the catalytic SET domains of the two enzymes are fully interchangeable. We also uncovered a role in eye development for the N-terminal domain of Set8 that cannot be complemented by human KMT5A. Whereas Set820/20 null mutants are inviable, we found that an R634G mutation in Set8 predicted from in vitro experiments to ablate catalytic activity resulted in viable adults. Additionally, Set8(R634G) mutants retain significant, albeit reduced, H4K20me1, indicating that the R634G mutation does not eliminate catalytic activity in vivo and is functionally hypomorphic rather than null. Flies engineered to express only unmodifiable H4 histones (H4K20A) can also complete development, but are phenotypically distinct from H4K20R, Set820/20 null, and Set8R634G mutants. Taken together, our results demonstrate functional conservation of KMT5A and Set8 enzymes, as well as distinct roles for Set8 and H4K20me1 in Drosophila development.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Stephen Klusza
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | | | - Brenda R S Temple
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
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5
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Shi L, Huang L, Long H, Song A, Zhou Z. Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8. FASEB J 2022; 36:e22338. [PMID: 35532550 DOI: 10.1096/fj.202101821r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/26/2022] [Accepted: 04/21/2022] [Indexed: 11/11/2022]
Abstract
Histone H4 lysine 20 monomethylation (H4K20me1) plays a crucial role in multiple processes including DNA damage repair, DNA replication, and cell cycle control. Histone methyltransferase SET8 (previously named PR-Set7/KMT5A) mediates the chromatin deposition of H4K20me1, but how SET8 recognizes and modifies H4 in the context of the nucleosome is not fully understood. Here, we developed a simple chemical modification approach for H4K20 substitution by using the lysine analog S-ethyl-L-cysteine (Ecx). Substitution of H4K20 with H4Ecx20 improves the stability of the SET8-nucleosome complex, allowing us to determine the cryo-EM structure at 3.2 Å resolution. Structural analyses show that SET8 directly interacts with the H4 tail and the H2A-H2B acidic patch to ensure nucleosome binding. SET8 residues R339, K341, K351 make contact with nucleosomal DNA at the super helical location 2 (SHL2). Substitution of SET8 DNA-binding residues with alanines decreases the SET8-nucleosome interaction and impairs the methyltransferase activity. Disrupting the binding between SET8 R192 and H2A-H2B acidic patch decreases the cellular level of H4K20me1. Together, these results reveal a near-atomic resolution structure of SET8-bound nucleosome and provide insights into the SET8-mediated H4K20 recognition and modification. The lysine-to-Ecx substitution approach can be applied to the study of other methyltransferases.
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Affiliation(s)
- Liuxin Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haizhen Long
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Aoqun Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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6
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Xu L, Zhang L, Sun J, Hu X, Kalvakolanu DV, Ren H, Guo B. Roles for the methyltransferase SETD8 in DNA damage repair. Clin Epigenetics 2022; 14:34. [PMID: 35246238 PMCID: PMC8897848 DOI: 10.1186/s13148-022-01251-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/20/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetic posttranslational modifications are critical for fine-tuning gene expression in various biological processes. SETD8 is so far the only known lysyl methyltransferase in mammalian cells to produce mono-methylation of histone H4 at lysine 20 (H4K20me1), a prerequisite for di- and tri-methylation. Importantly, SETD8 is related to a number of cellular activities, impinging upon tissue development, senescence and tumorigenesis. The double-strand breaks (DSBs) are cytotoxic DNA damages with deleterious consequences, such as genomic instability and cancer origin, if unrepaired. The homology-directed repair and canonical nonhomologous end-joining are two most prominent DSB repair pathways evolved to eliminate such aberrations. Emerging evidence implies that SETD8 and its corresponding H4K20 methylation are relevant to establishment of DSB repair pathway choice. Understanding how SETD8 functions in DSB repair pathway choice will shed light on the molecular basis of SETD8-deficiency related disorders and will be valuable for the development of new treatments. In this review, we discuss the progress made to date in roles for the lysine mono-methyltransferase SETD8 in DNA damage repair and its therapeutic relevance, in particular illuminating its involvement in establishment of DSB repair pathway choice, which is crucial for the timely elimination of DSBs.
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Affiliation(s)
- Libo Xu
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.,Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, People's Republic of China
| | - Ling Zhang
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.,Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, People's Republic of China
| | - Jicheng Sun
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Xindan Hu
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Dhan V Kalvakolanu
- Greenebaum NCI Comprehensive Cancer Center, Department of Microbiology and Immunology, University of Maryland School Medicine, Baltimore, MD, USA
| | - Hui Ren
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.
| | - Baofeng Guo
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.
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7
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Herviou L, Ovejero S, Izard F, Karmous-Gadacha O, Gourzones C, Bellanger C, De Smedt E, Ma A, Vincent L, Cartron G, Jin J, De Bruyne E, Grimaud C, Julien E, Moreaux J. Targeting the methyltransferase SETD8 impairs tumor cell survival and overcomes drug resistance independently of p53 status in multiple myeloma. Clin Epigenetics 2021; 13:174. [PMID: 34530900 PMCID: PMC8447659 DOI: 10.1186/s13148-021-01160-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/27/2021] [Indexed: 01/04/2023] Open
Abstract
Background Multiple myeloma (MM) is a malignancy of plasma cells that largely remains incurable. The search for new therapeutic targets is therefore essential. In addition to a wide panel of genetic mutations, epigenetic alterations also appear as important players in the development of this cancer, thereby offering the possibility to reveal novel approaches and targets for effective therapeutic intervention. Results Here, we show that a higher expression of the lysine methyltransferase SETD8, which is responsible for the mono-methylation of histone H4 at lysine 20, is an adverse prognosis factor associated with a poor outcome in two cohorts of newly diagnosed patients. Primary malignant plasma cells are particularly addicted to the activity of this epigenetic enzyme. Indeed, the inhibition of SETD8 by the chemical compound UNC-0379 and the subsequent decrease in histone H4 methylation at lysine 20 are highly toxic in MM cells compared to normal cells from the bone marrow microenvironment. At the molecular level, RNA sequencing and functional studies revealed that SETD8 inhibition induces a mature non-proliferating plasma cell signature and, as observed in other cancers, triggers an activation of the tumor suppressor p53, which together cause an impairment of myeloma cell proliferation and survival. However, a deadly level of replicative stress was also observed in p53-deficient myeloma cells treated with UNC-0379, indicating that the cytotoxicity associated with SETD8 inhibition is not necessarily dependent on p53 activation. Consistent with this, UNC-0379 triggers a p53-independent nucleolar stress characterized by nucleolin delocalization and reduction of nucleolar RNA synthesis. Finally, we showed that SETD8 inhibition is strongly synergistic with melphalan and may overcome resistance to this alkylating agent widely used in MM treatment. Conclusions Altogether, our data indicate that the up-regulation of the epigenetic enzyme SETD8 is associated with a poor outcome and the deregulation of major signaling pathways in MM. Moreover, we provide evidences that myeloma cells are dependent on SETD8 activity and its pharmacological inhibition synergizes with melphalan, which could be beneficial to improve MM treatment in high-risk patients whatever their status for p53. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01160-z.
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Affiliation(s)
- Laurie Herviou
- IGH, CNRS, Univ Montpellier, Montpellier, France.,Laboratory for Monitoring Innovative Therapies, Department of Biological Hematology, CHU Montpellier, Montpellier, France.,University of Montpellier, 34090, Montpellier, France
| | - Sara Ovejero
- IGH, CNRS, Univ Montpellier, Montpellier, France.,Laboratory for Monitoring Innovative Therapies, Department of Biological Hematology, CHU Montpellier, Montpellier, France.,University of Montpellier, 34090, Montpellier, France
| | - Fanny Izard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), 34298, Montpellier, France.,University of Montpellier, 34090, Montpellier, France
| | - Ouissem Karmous-Gadacha
- Laboratory for Monitoring Innovative Therapies, Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | | | | | - Eva De Smedt
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anqi Ma
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Laure Vincent
- Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Guillaume Cartron
- University of Montpellier, 34090, Montpellier, France.,Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elke De Bruyne
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Charlotte Grimaud
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), 34298, Montpellier, France.,University of Montpellier, 34090, Montpellier, France.,Centre National de La Recherche Scientifique (CNRS), 34293, Montpellier, France
| | - Eric Julien
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), 34298, Montpellier, France. .,University of Montpellier, 34090, Montpellier, France. .,Centre National de La Recherche Scientifique (CNRS), 34293, Montpellier, France.
| | - Jérôme Moreaux
- IGH, CNRS, Univ Montpellier, Montpellier, France. .,Laboratory for Monitoring Innovative Therapies, Department of Biological Hematology, CHU Montpellier, Montpellier, France. .,University of Montpellier, 34090, Montpellier, France. .,Institut Universitaire de France (IUF), Paris, France.
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8
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Huang J, Gujar MR, Deng Q, Y Chia S, Li S, Tan P, Sung W, Wang H. Histone lysine methyltransferase Pr-set7/SETD8 promotes neural stem cell reactivation. EMBO Rep 2021; 22:e50994. [PMID: 33565211 PMCID: PMC8024890 DOI: 10.15252/embr.202050994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 01/07/2023] Open
Abstract
The ability of neural stem cells (NSCs) to switch between quiescence and proliferation is crucial for brain development and homeostasis. Increasing evidence suggests that variants of histone lysine methyltransferases including KMT5A are associated with neurodevelopmental disorders. However, the function of KMT5A/Pr-set7/SETD8 in the central nervous system is not well established. Here, we show that Drosophila Pr-Set7 is a novel regulator of NSC reactivation. Loss of function of pr-set7 causes a delay in NSC reactivation and loss of H4K20 monomethylation in the brain. Through NSC-specific in vivo profiling, we demonstrate that Pr-set7 binds to the promoter region of cyclin-dependent kinase 1 (cdk1) and Wnt pathway transcriptional co-activator earthbound1/jerky (ebd1). Further validation indicates that Pr-set7 is required for the expression of cdk1 and ebd1 in the brain. Similar to Pr-set7, Cdk1 and Ebd1 promote NSC reactivation. Finally, overexpression of Cdk1 and Ebd1 significantly suppressed NSC reactivation defects observed in pr-set7-depleted brains. Therefore, Pr-set7 promotes NSC reactivation by regulating Wnt signaling and cell cycle progression. Our findings may contribute to the understanding of mammalian KMT5A/PR-SET7/SETD8 during brain development.
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Affiliation(s)
- Jiawen Huang
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Mahekta R Gujar
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Qiannan Deng
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Sook Y Chia
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
- Present address:
National Neuroscience InstituteSingaporeSingapore
| | - Song Li
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Patrick Tan
- Genome Institute of SingaporeSingaporeSingapore
- Cancer & Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingaporeSingapore
- Cellular and Molecular ResearchNational Cancer CentreSingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
| | - Wing‐Kin Sung
- Genome Institute of SingaporeSingaporeSingapore
- Department of Computer ScienceNational University of SingaporeSingaporeSingapore
| | - Hongyan Wang
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
- Department of PhysiologyYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Integrative Sciences and Engineering ProgrammeNational University of SingaporeSingaporeSingapore
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9
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Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H. Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase. Life Sci Alliance 2021; 4:4/4/e202000919. [PMID: 33574035 PMCID: PMC7893823 DOI: 10.26508/lsa.202000919] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 11/26/2022] Open
Abstract
Cryo-EM structures of the human SET8–nucleosome complexes reveal the mechanism by which the SET8 methyltransferase binds the nucleosome and specifically recognizes the histone H4 lysine-20 residue. SET8 is solely responsible for histone H4 lysine-20 (H4K20) monomethylation, which preferentially occurs in nucleosomal H4. However, the underlying mechanism by which SET8 specifically promotes the H4K20 monomethylation in the nucleosome has not been elucidated. Here, we report the cryo-EM structures of the human SET8–nucleosome complexes with histone H3 and the centromeric H3 variant, CENP-A. Surprisingly, we found that the overall cryo-EM structures of the SET8–nucleosome complexes are substantially different from the previous crystal structure models. In the complexes with H3 and CENP-A nucleosomes, SET8 specifically binds the nucleosomal acidic patch via an arginine anchor, composed of the Arg188 and Arg192 residues. Mutational analyses revealed that the interaction between the SET8 arginine anchor and the nucleosomal acidic patch plays an essential role in the H4K20 monomethylation activity. These results provide the groundwork for understanding the mechanism by which SET8 specifically accomplishes the H4K20 monomethylation in the nucleosome.
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Affiliation(s)
- Cheng-Han Ho
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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10
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Li M, Wang H, Liao H, Shen J, Wu Y, Wu Y, Weng Q, Zhu C, Geng X, Lan F, Xia Y, Zhang B, Zou H, Zhang N, Zhou Y, Chen Z, Shen H, Ying S, Li W. SETD8C302R Mutation Revealed from Myofibroblastoma-Discordant Monozygotic Twins Leads to p53/p21 Deficit and WEE1 Inhibitor Sensitivity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001041. [PMID: 33042742 PMCID: PMC7539211 DOI: 10.1002/advs.202001041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/21/2020] [Indexed: 06/11/2023]
Abstract
High-throughput gene sequencing has identified various genetic variants as the culprits for some common hereditary cancers. However, the heritability of a substantial proportion of cancers remains unexplained, which may result from rare deleterious mutations hidden in a myriad of nonsense genetic variations. This poses a great challenge to the understanding of the pathology and thus the rational design of effective treatments for affected patients. Here, whole genome sequencing is employed in a representative case in which one monozygotic twin is discordant for lung inflammatory myofibroblastoma to disclose rare tumor-related mutations. A missense single nucleotide variation rs61955126 T>C in the lysine methyltransferase SETD8 (accession: NM_020382, SETD8C302R ) is exposed. It is shown that SETD8 is vital for genomic integrity by promoting faithful DNA replication, and its C302R mutation downregulates the p53/p21 pathway. Importantly, the SETD8C302R mutation significantly increases the sensitivity of cancer cells to WEE1 inhibition. Given that WEE1 inhibitors have shown great promise for clinical approval, these results impart a potential therapeutic approach using WEE1 inhibitor for cancer patients carrying the same mutation, and indicate that genome sequencing and genetic functional studies can be integrated into individualized therapies.
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Affiliation(s)
- Miao Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Hongwu Wang
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Hongwei Liao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Jiaxin Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Yinfang Wu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Yanping Wu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Qingyu Weng
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Chen Zhu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Xinwei Geng
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Fen Lan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Yang Xia
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Bin Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Hang Zou
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Nan Zhang
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Yunzhi Zhou
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Zhihua Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Songmin Ying
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
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11
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Zhou Y, Pozo PN, Oh S, Stone HM, Cook JG. Distinct and sequential re-replication barriers ensure precise genome duplication. PLoS Genet 2020; 16:e1008988. [PMID: 32841231 PMCID: PMC7473519 DOI: 10.1371/journal.pgen.1008988] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/04/2020] [Accepted: 07/12/2020] [Indexed: 01/19/2023] Open
Abstract
Achieving complete and precise genome duplication requires that each genomic segment be replicated only once per cell division cycle. Protecting large eukaryotic genomes from re-replication requires an overlapping set of molecular mechanisms that prevent the first DNA replication step, the DNA loading of MCM helicase complexes to license replication origins, after S phase begins. Previous reports have defined many such origin licensing inhibition mechanisms, but the temporal relationships among them are not clear, particularly with respect to preventing re-replication in G2 and M phases. Using a combination of mutagenesis, biochemistry, and single cell analyses in human cells, we define a new mechanism that prevents re-replication through hyperphosphorylation of the essential MCM loading protein, Cdt1. We demonstrate that Cyclin A/CDK1 can hyperphosphorylate Cdt1 to inhibit MCM re-loading in G2 phase. The mechanism of inhibition is to block Cdt1 binding to MCM independently of other known Cdt1 inactivation mechanisms such as Cdt1 degradation during S phase or Geminin binding. Moreover, our findings suggest that Cdt1 dephosphorylation at the mitosis-to-G1 phase transition re-activates Cdt1. We propose that multiple distinct, non-redundant licensing inhibition mechanisms act in a series of sequential relays through each cell cycle phase to ensure precise genome duplication. The initial step of DNA replication is loading the DNA helicase, MCM, onto DNA during the first phase of the cell division cycle. If MCM loading occurs inappropriately onto DNA that has already been replicated, then cells risk DNA re-replication, a source of endogenous DNA damage and genome instability. How mammalian cells prevent any sections of their very large genomes from re-replicating is still not fully understood. We found that the Cdt1 protein, one of the critical MCM loading factors, is inhibited specifically in late cell cycle stages through a mechanism involving protein phosphorylation. This phosphorylation prevents Cdt1 from binding MCM; when Cdt1 cannot be phosphorylated MCM is inappropriately re-loaded onto DNA and cells are prone to re-replication. When cells divide and transition into G1 phase, Cdt1 is then dephosphorylated to re-activate it for MCM loading. Based on these findings we assert that the different mechanisms that cooperate to avoid re-replication are not redundant. Instead, different cell cycle phases are dominated by different re-replication control mechanisms. These findings have implications for understanding how genomes are duplicated precisely once per cell cycle and shed light on how that process is perturbed by changes in Cdt1 levels or phosphorylation activity.
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Affiliation(s)
- Yizhuo Zhou
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
| | - Pedro N. Pozo
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
| | - Seeun Oh
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute and the Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United State of America
| | - Haley M. Stone
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
- Lineberger Comprehensive Cancer, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
- * E-mail:
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12
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Zouaz A, Fernando C, Perez Y, Sardet C, Julien E, Grimaud C. Cell-cycle regulation of non-enzymatic functions of the Drosophila methyltransferase PR-Set7. Nucleic Acids Res 2019; 46:2834-2849. [PMID: 29373730 PMCID: PMC5888314 DOI: 10.1093/nar/gky034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/16/2018] [Indexed: 12/27/2022] Open
Abstract
Tight cell-cycle regulation of the histone H4-K20 methyltransferase PR-Set7 is essential for the maintenance of genome integrity. In mammals, this mainly involves the interaction of PR-Set7 with the replication factor PCNA, which triggers the degradation of the enzyme by the CRL4CDT2 E3 ubiquitin ligase. PR-Set7 is also targeted by the SCFβ-TRCP ligase, but the role of this additional regulatory pathway remains unclear. Here, we show that Drosophila PR-Set7 undergoes a cell-cycle proteolytic regulation, independently of its interaction with PCNA. Instead, Slimb, the ortholog of β-TRCP, is specifically required for the degradation of the nuclear pool of PR-Set7 prior to S phase. Consequently, inactivation of Slimb leads to nuclear accumulation of PR-Set7, which triggers aberrant chromatin compaction and G1/S arrest. Strikingly, these phenotypes result from non-enzymatic PR-Set7 functions that prevent proper histone H4 acetylation independently of H4K20 methylation. Altogether, these results identify the Slimb-mediated PR-Set7 proteolysis as a new critical regulatory mechanism required for proper interphase chromatin organization at G1/S transition.
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Affiliation(s)
- Amel Zouaz
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier F-34298, France.,University of Montpellier, Montpellier F-34090, France
| | - Céline Fernando
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier F-34298, France.,University of Montpellier, Montpellier F-34090, France
| | - Yannick Perez
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier F-34298, France.,University of Montpellier, Montpellier F-34090, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier F-34298, France.,University of Montpellier, Montpellier F-34090, France
| | - Eric Julien
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier F-34298, France.,University of Montpellier, Montpellier F-34090, France
| | - Charlotte Grimaud
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier F-34298, France.,University of Montpellier, Montpellier F-34090, France
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13
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Paroni G, Bolis M, Zanetti A, Ubezio P, Helin K, Staller P, Gerlach LO, Fratelli M, Neve RM, Terao M, Garattini E. HER2-positive breast-cancer cell lines are sensitive to KDM5 inhibition: definition of a gene-expression model for the selection of sensitive cases. Oncogene 2018; 38:2675-2689. [DOI: 10.1038/s41388-018-0620-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022]
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14
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Li Z, Liu H, Niu Z, Zhong W, Xue M, Wang J, Yang F, Zhou Y, Zhou Y, Xu T, Hou J. Temporal Proteomic Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity. Mol Cell Proteomics 2018; 17:2119-2131. [PMID: 30082485 DOI: 10.1074/mcp.ra118.000698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/03/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic hyperlipidemia causes the dysfunction of pancreatic β-cells, such as apoptosis and impaired insulin secretion, which are aggravated in the presence of hyperglycemia. The underlying mechanisms, such as endoplasmic reticulum (ER) stress, oxidative stress and metabolic disorders, have been reported before; however, the time sequence of these molecular events is not fully understood. Here, using isobaric labeling-based mass spectrometry, we investigated the dynamic proteomes of INS-1 cells exposed to high palmitate in the absence and presence of high glucose. Using bioinformatics analysis of differentially expressed proteins, including the time-course expression pattern, protein-protein interaction, gene set enrichment and KEGG pathway analysis, we analyzed the dynamic features of previously reported and newly identified lipotoxicity- and glucolipotoxicity-related molecular events in more detail. Our temporal data highlight cholesterol metabolism occurring at 4 h, earlier than fatty acid metabolism that started at 8 h and likely acting as an early toxic event highly associated with ER stress induced by palmitate. Interestingly, we found that the proliferation of INS-1 cells was significantly increased at 48 h by combined treatment of palmitate and glucose. Moreover, benefit from the time-course quantitative data, we identified and validated two new molecular targets: Setd8 for cell replication and Rhob for apoptosis, demonstrating that our temporal dataset serves as a valuable resource to identify potential candidates for mechanistic studies of lipotoxicity and glucolipotoxicity in pancreatic β-cells.
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Affiliation(s)
- Zonghong Li
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Hongyang Liu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,‖Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhangjing Niu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,‖Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Zhong
- ***College of Life Science and Technology, HuaZhong University of Science and Technology, Wuhan 430074, China
| | - Miaomiao Xue
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jifeng Wang
- ‡‡Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- ‡‡Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Zhou
- §§ThermoFisher Scientific, Building 6, No. 27, Xin Jinqiao Rd, Pudong, Shanghai, 201206, China
| | - Yifa Zhou
- §Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China;
| | - Tao Xu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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15
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Jiang T, Hoover ME, Holt MV, Freitas MA, Marshall AG, Young NL. Middle-Down Characterization of the Cell Cycle Dependence of Histone H4 Posttranslational Modifications and Proteoforms. Proteomics 2018; 18:e1700442. [PMID: 29667342 PMCID: PMC8087174 DOI: 10.1002/pmic.201700442] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/28/2018] [Indexed: 12/12/2022]
Abstract
Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This procedure provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis. We use ultrahigh mass accuracy and resolution Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer to unambiguously distinguish between acetylation and tri-methylation (∆m = 0.036 Da). In total, we identify and quantify 233 proteoforms of histone H4 in two breast cancer cell lines. We observe significant increases in S1 phosphorylation during mitosis, implicating an important role in mitotic chromatin condensation. A decrease of K20 unmodified proteoforms is observed as the cell cycle progresses, corresponding to an increase of K20 mono- and di-methylation. Acetylation at K5, K8, K12, and K16 declines as cells traverse from S phase to mitosis, suggesting cell cycle-dependence and an important role during chromatin replication and condensation. These new insights into the epigenetics of the cell cycle may provide new diagnostic and prognostic biomarkers.
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Affiliation(s)
- Tingting Jiang
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Michael E Hoover
- Department of Cancer Biology and Genetics, Ohio State University, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Matthew V Holt
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, Ohio State University, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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16
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Brustel J, Kirstein N, Izard F, Grimaud C, Prorok P, Cayrou C, Schotta G, Abdelsamie AF, Déjardin J, Méchali M, Baldacci G, Sardet C, Cadoret JC, Schepers A, Julien E. Histone H4K20 tri-methylation at late-firing origins ensures timely heterochromatin replication. EMBO J 2017; 36:2726-2741. [PMID: 28778956 DOI: 10.15252/embj.201796541] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/19/2017] [Accepted: 07/07/2017] [Indexed: 01/09/2023] Open
Abstract
Among other targets, the protein lysine methyltransferase PR-Set7 induces histone H4 lysine 20 monomethylation (H4K20me1), which is the substrate for further methylation by the Suv4-20h methyltransferase. Although these enzymes have been implicated in control of replication origins, the specific contribution of H4K20 methylation to DNA replication remains unclear. Here, we show that H4K20 mutation in mammalian cells, unlike in Drosophila, partially impairs S-phase progression and protects from DNA re-replication induced by stabilization of PR-Set7. Using Epstein-Barr virus-derived episomes, we further demonstrate that conversion of H4K20me1 to higher H4K20me2/3 states by Suv4-20h is not sufficient to define an efficient origin per se, but rather serves as an enhancer for MCM2-7 helicase loading and replication activation at defined origins. Consistent with this, we find that Suv4-20h-mediated H4K20 tri-methylation (H4K20me3) is required to sustain the licensing and activity of a subset of ORCA/LRWD1-associated origins, which ensure proper replication timing of late-replicating heterochromatin domains. Altogether, these results reveal Suv4-20h-mediated H4K20 tri-methylation as a critical determinant in the selection of active replication initiation sites in heterochromatin regions of mammalian genomes.
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Affiliation(s)
- Julien Brustel
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Nina Kirstein
- Research Unit Gene Vectors, Helmholtz Zentrum München, Munich, Germany
| | - Fanny Izard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Charlotte Grimaud
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Paulina Prorok
- Institute of Human Genetics (IGH), CNRS, Montpellier, France
| | | | | | | | - Jérôme Déjardin
- Institute of Human Genetics (IGH), CNRS, Montpellier, France
| | - Marcel Méchali
- Institute of Human Genetics (IGH), CNRS, Montpellier, France
| | - Giuseppe Baldacci
- Institut Jacques Monod, UMR7592, CNRS and University Paris-Diderot, Paris, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Jean-Charles Cadoret
- Institut Jacques Monod, UMR7592, CNRS and University Paris-Diderot, Paris, France
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München, Munich, Germany
| | - Eric Julien
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Montpellier, France .,University of Montpellier, Montpellier, France
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17
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Abstract
![]()
Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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18
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Milite C, Feoli A, Viviano M, Rescigno D, Cianciulli A, Balzano AL, Mai A, Castellano S, Sbardella G. The emerging role of lysine methyltransferase SETD8 in human diseases. Clin Epigenetics 2016; 8:102. [PMID: 27688818 PMCID: PMC5034662 DOI: 10.1186/s13148-016-0268-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/14/2016] [Indexed: 01/07/2023] Open
Abstract
SETD8/SET8/Pr-SET7/KMT5A is the only known lysine methyltransferase (KMT) that monomethylates lysine 20 of histone H4 (H4K20) in vivo. Lysine residues of non-histone proteins including proliferating cell nuclear antigen (PCNA) and p53 are also monomethylated. As a consequence, the methyltransferase activity of the enzyme is implicated in many essential cellular processes including DNA replication, DNA damage response, transcription modulation, and cell cycle regulation. This review aims to provide an overview of the roles of SETD8 in physiological and pathological pathways and to discuss the progress made to date in inhibiting the activity of SETD8 by small molecules, with an emphasis on their discovery, selectivity over other methyltransferases and cellular activity.
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Affiliation(s)
- Ciro Milite
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Alessandra Feoli
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Monica Viviano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Donatella Rescigno
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Agostino Cianciulli
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Amodio Luca Balzano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Antonello Mai
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, I-00185 Rome, Italy
| | - Sabrina Castellano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Dipartimento di Medicina e Chirurgia, Università degli Studi di Salerno, Via Salvador Allende, Baronissi, I-84081 Salerno, Italy
| | - Gianluca Sbardella
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
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Sakano T, Mahamood MI, Yamashita T, Fujitani H. Molecular dynamics analysis to evaluate docking pose prediction. Biophys Physicobiol 2016; 13:181-194. [PMID: 27924273 PMCID: PMC5042163 DOI: 10.2142/biophysico.13.0_181] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/27/2016] [Indexed: 02/06/2023] Open
Abstract
The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position. Here we investigated two proteins that are important potential therapeutic targets: β2 adrenergic receptor (β2AR) and PR-Set7. While β2AR is rigid and its ligands are very similar to the template ligand (carazolol), PR-Set7 is very flexible and its ligands vary greatly from the template ligand (histone H4 tail peptide). On an empirical basis, we usually expect that the docking prediction is accurate when the protein is rigid and its ligands are similar to the template ligand. The MD analyses in this study clearly suggested such a tendency. Furthermore, we discuss the possibility that the MD simulation can predict the binding pose of a ligand.
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Affiliation(s)
- Takako Sakano
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo 153-8904, Japan
| | - Md Iqbal Mahamood
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo 153-8904, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo 153-8904, Japan
| | - Hideaki Fujitani
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo 153-8904, Japan
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20
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Hale CJ, Potok ME, Lopez J, Do T, Liu A, Gallego-Bartolome J, Michaels SD, Jacobsen SE. Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006092. [PMID: 27253878 PMCID: PMC4890748 DOI: 10.1371/journal.pgen.1006092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/10/2016] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes are regulated by epigenetic marks that act to modulate transcriptional control as well as to regulate DNA replication and repair. In Arabidopsis thaliana, mutation of the ATXR5 and ATXR6 histone methyltransferases causes reduction in histone H3 lysine 27 monomethylation, transcriptional upregulation of transposons, and a genome instability defect in which there is an accumulation of excess DNA corresponding to pericentromeric heterochromatin. We designed a forward genetic screen to identify suppressors of the atxr5/6 phenotype that uncovered loss-of-function mutations in two components of the TREX-2 complex (AtTHP1, AtSAC3B), a SUMO-interacting E3 ubiquitin ligase (AtSTUbL2) and a methyl-binding domain protein (AtMBD9). Additionally, using a reverse genetic approach, we show that a mutation in a plant homolog of the tumor suppressor gene BRCA1 enhances the atxr5/6 phenotype. Through characterization of these mutations, our results suggest models for the production atxr5 atxr6-induced extra DNA involving conflicts between the replicative and transcriptional processes in the cell, and suggest that the atxr5 atxr6 transcriptional defects may be the cause of the genome instability defects in the mutants. These findings highlight the critical intersection of transcriptional silencing and DNA replication in the maintenance of genome stability of heterochromatin. In eukaryotic genomes cellular processes such as transcription and replication need to be tightly controlled in order to promote genomic stability and prevent deleterious mutations. In Arabidopsis thaliana, two redundant histone methyltransferases, ATXR5 and ATXR6, are responsible for the deposition of a silencing epigenetic mark, histone H3 lysine 27 monomethylation. Loss of ATXR5/6 results in transcriptional activation of transposable elements (TEs), upregulation of DNA damage response genes and a genomic instability defect characterized as an excess of DNA corresponding to heterochromatin regions. Using a genetic screen, we sought to find suppressors of the atxr5/6 phenotype, and interestingly, we identified multiple genes implicated in general transcriptional activity. Through genomic characterization of the mutants our data suggest a model where transcriptional silencing of heterochromatin during S-phase is required for proper replication and maintenance of genome stability. These findings emphasize the important relationship between chromatin, transcriptional control and replication in the maintenance of genome stability in a eukaryotic system and identify new players involved in these processes.
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Affiliation(s)
- Christopher J. Hale
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Center for Precision Diagnostics, University of Washington, Seattle, Washington, United States of America
| | - Magdalena E. Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Jennifer Lopez
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Truman Do
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Ao Liu
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Scott D. Michaels
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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21
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Li Y, Armstrong RL, Duronio RJ, MacAlpine DM. Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila. Nucleic Acids Res 2016; 44:7204-18. [PMID: 27131378 PMCID: PMC5009726 DOI: 10.1093/nar/gkw333] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/15/2016] [Indexed: 12/16/2022] Open
Abstract
The methylation state of lysine 20 on histone H4 (H4K20) has been linked to chromatin compaction, transcription, DNA repair and DNA replication. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7. PR-Set7 depletion in mammalian cells results in defective S phase progression and the accumulation of DNA damage, which has been partially attributed to defects in origin selection and activation. However, these studies were limited to only a handful of mammalian origins, and it remains unclear how PR-Set7 and H4K20 methylation impact the replication program on a genomic scale. We employed genetic, cytological, and genomic approaches to better understand the role of PR-Set7 and H4K20 methylation in regulating DNA replication and genome stability in Drosophila cells. We find that deregulation of H4K20 methylation had no impact on origin activation throughout the genome. Instead, depletion of PR-Set7 and loss of H4K20me1 results in the accumulation of DNA damage and an ATR-dependent cell cycle arrest. Coincident with the ATR-dependent cell cycle arrest, we find increased DNA damage that is specifically limited to late replicating regions of the Drosophila genome, suggesting that PR-Set7-mediated monomethylation of H4K20 is critical for maintaining the genomic integrity of late replicating domains.
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Affiliation(s)
- Yulong Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, and Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
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22
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Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate. J Mol Biol 2016; 428:1531-43. [PMID: 26953260 DOI: 10.1016/j.jmb.2016.02.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/03/2016] [Accepted: 02/27/2016] [Indexed: 12/19/2022]
Abstract
Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. Our studies indicate that Set8 employs its i-SET and c-SET domains to engage nucleosomal DNA 1 to 1.5 turns from the nucleosomal dyad and in doing so, it positions the SET domain for catalysis with H4 Lys20. Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. We further show that proliferating cell nuclear antigen and the nucleosome compete for binding to Set8 through this basic extension, suggesting a mechanism for how nucleosome binding protects Set8 from proliferating cell nuclear antigen-dependent degradation during the cell cycle.
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23
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Williams DE, Izard F, Arnould S, Dalisay DS, Tantapakul C, Maneerat W, Matainaho T, Julien E, Andersen RJ. Structures of Nahuoic Acids B-E Produced in Culture by a Streptomyces sp. Isolated from a Marine Sediment and Evidence for the Inhibition of the Histone Methyl Transferase SETD8 in Human Cancer Cells by Nahuoic Acid A. J Org Chem 2016; 81:1324-32. [PMID: 26815947 DOI: 10.1021/acs.joc.5b02569] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Nahuoic acids A-E (1-5) have been isolated from laboratory cultures of a Streptomyces sp. obtained from a tropical marine sediment. The structures of the new polyketides 2-5 were elucidated by analysis of spectroscopic data of the natural products and the chemical derivatives 6 and 7. Nahuoic acids 1-5 are in vitro inhibitors of the histone methyltransferase SETD8, and nahuoic acid A (1) and its pentaacetate derivative 8 inhibit the proliferation of several cancer cells lines in vitro with modest potency. At the IC50 for cancer cell proliferation, nahuoic acid A (1) showed selective inhibition of SETD8 in U2OS osteosarcoma cells that reflect its selectivity against a panel of pure histone methyl transferases. A cell cycle analysis revealed that the cellular toxicity of nahuoic acid A (1) is likely linked to its ability to inhibit SETD8 activity.
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Affiliation(s)
- David E Williams
- Departments of Chemistry and Earth, Ocean and Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Fanny Izard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier (ICM) , Montpellier F-34298, France
| | - Stéphanie Arnould
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier (ICM) , Montpellier F-34298, France
| | - Doralyn S Dalisay
- Departments of Chemistry and Earth, Ocean and Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Cholpisut Tantapakul
- Departments of Chemistry and Earth, Ocean and Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Wisanu Maneerat
- Departments of Chemistry and Earth, Ocean and Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | | | - Eric Julien
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier (ICM) , Montpellier F-34298, France
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean and Atmospheric Sciences, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
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24
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MicroRNA-127-3p inhibits proliferation and invasion by targeting SETD8 in human osteosarcoma cells. Biochem Biophys Res Commun 2015; 469:1006-11. [PMID: 26707641 DOI: 10.1016/j.bbrc.2015.12.067] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/16/2015] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) play an essential role in cancer development. Several studies have indicated that miRNAs mediate tumorigenesis processes, such as, inflammation, proliferation, apoptosis and invasion. In the present study, we focused on the influence of the miR-127-3p on the proliferation, migration and invasion of osteosarcoma (OS). MiR-127-3p was found at reduced levels in OS tissues and cell lines. Overexpression of miR-127-3p in the OS cell lines significantly inhibited the cell proliferation, migration and invasion; however, inhibition of miR-127-3p increased the proliferation, migration and invasion of OS in vitro. SETD8 was identified as a direct target of miR-127-3p, and SETD8 expression decreased post miR-127-3p overexpression, while SETD8 overexpression could reverse the potential influence of miR-127-3p on the migration and invasion of OS cells. MiR-127-3p is suggested to act mainly via the suppression of SETD8 expression. Overall, the results revealed that miR-127-3p acts as a tumor suppressor and that its down-regulation in cancer may contribute to OS progression and metastasis, suggesting that miR-127-3p could be a potential therapeutic target in the treatment of OS.
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25
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Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, Delarue M, Bergounioux C, Benhamed M. Chromatin meets the cell cycle. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2677-89. [PMID: 24497647 DOI: 10.1093/jxb/ert433] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The cell cycle is one of the most comprehensively studied biological processes, due primarily to its significance in growth and development, and its deregulation in many human disorders. Studies using a diverse set of model organisms, including yeast, worms, flies, frogs, mammals, and plants, have greatly expanded our knowledge of the cell cycle and have contributed to the universally accepted view of how the basic cell cycle machinery is regulated. In addition to the oscillating activity of various cyclin-dependent kinase (CDK)-cyclin complexes, a plethora of proteins affecting various aspects of chromatin dynamics has been shown to be essential for cell proliferation during plant development. Furthermore, it was reported recently that core cell cycle regulators control gene expression by modifying histone patterns. This review focuses on the intimate relationship between the cell cycle and chromatin. It describes the dynamics and functions of chromatin structures throughout cell cycle progression and discusses the role of heterochromatin as a barrier against re-replication and endoreduplication. It also proposes that core plant cell cycle regulators control gene expression in a manner similar to that described in mammals. At present, our challenge in plants is to define the complete set of effectors and actors that coordinate cell cycle progression and chromatin structure and to understand better the functional interplay between these two processes.
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Affiliation(s)
- Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Allison C Mallory
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Quentin Bruggeman
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
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26
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Doenecke D. Chromatin dynamics from S-phase to mitosis: contributions of histone modifications. Cell Tissue Res 2014; 356:467-75. [PMID: 24816984 DOI: 10.1007/s00441-014-1873-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/13/2014] [Indexed: 10/25/2022]
Abstract
This review focuses on the major protein moiety of chromosomes, i.e., the histone proteins, on the contribution of their posttranslational modification to structural and functional chromatin dynamics, on the acetylation and methylation of lysine residues, and on the phosphorylation of serine or threonine with respect to various steps during the cell cycle.
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Affiliation(s)
- Detlef Doenecke
- Department for Molecular Biology, Georg August University, Göttingen, Germany,
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27
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Corney DC, Coller HA. On form and function: does chromatin packing regulate the cell cycle? Physiol Genomics 2014; 46:191-4. [PMID: 24474443 PMCID: PMC3949104 DOI: 10.1152/physiolgenomics.00002.2014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/23/2014] [Indexed: 12/26/2022] Open
Abstract
The Systems Biology of Cell State Regulation Section is dedicated to considering how we can define a cellular state and how cells transition between states. One important decision that a cell makes is whether to cycle, that is, replicate DNA and generate daughter cells, or to exit the cell cycle in a reversible manner. The members of the Systems Biology of Cell State Regulation Editorial Board have an interest in the role of epigenetics and the commitment to a dividing or nondividing state. The ability of cells to transition between proliferating and nonproliferating states is essential for the proper formation of tissues. The ability to enter the cell cycle when needed is necessary for complex multicellular processes, such as healing injuries or mounting an immune response. Cells that fail to quiesce properly can contribute to the formation of tumors. In this perspective piece, we focus on research exploring the relationship between epigenetics and the cell cycle.
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Affiliation(s)
- David C Corney
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California; and Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, California
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28
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Julienne H, Zoufir A, Audit B, Arneodo A. Human genome replication proceeds through four chromatin states. PLoS Comput Biol 2013; 9:e1003233. [PMID: 24130466 PMCID: PMC3794905 DOI: 10.1371/journal.pcbi.1003233] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/06/2013] [Indexed: 12/26/2022] Open
Abstract
Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a framework for further studies in different cell types, in both health and disease. Previous studies revealed spatially coherent and biological-meaningful chromatin mark combinations in human cells. Here, we analyze thirteen epigenetic mark maps in the human cell line K562 at 100 kb resolution of MRT data. The complexity of epigenetic data is reduced to four chromatin states that display remarkable similarities with those reported in fly, worm and plants. These states have different MRT: (C1) is transcriptionally active, early replicating, enriched in CTCF; (C2) is Polycomb repressed, mid-S replicating; (C3) lacks of marks and replicates late and (C4) is a late-replicating gene-poor HP1 repressed heterochromatin state. When mapping these states inside the 876 replication U-domains of K562, the replication fork polarity gradient observed in these U-domains comes along with a remarkable epigenetic organization from C1 at U-domain borders to C2, C3 and ultimately C4 at centers. The remaining genome half displays early replicating, gene rich and high GC domains of intermingled C1 and C2 states segregating from late replicating, gene poor and low GC domains of concatenated C3 and/or C4 states. This constitutes the first evidence of epigenetic compartmentalization of the human genome into replication domains likely corresponding to autonomous units in the 3D chromatin architecture.
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Affiliation(s)
- Hanna Julienne
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Azedine Zoufir
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Benjamin Audit
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
| | - Alain Arneodo
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
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29
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The G2/M regulator histone demethylase PHF8 is targeted for degradation by the anaphase-promoting complex containing CDC20. Mol Cell Biol 2013; 33:4166-80. [PMID: 23979597 DOI: 10.1128/mcb.00689-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monomethylated histone H4 lysine 20 (H4K20me1) is tightly regulated during the cell cycle. The H4K20me1 demethylase PHF8 transcriptionally regulates many cell cycle genes and is therefore predicted to play key roles in the cell cycle. Here, we show that PHF8 protein levels are the highest during G2 phase and mitosis, and we found PHF8 protein stability to be regulated by the ubiquitin-proteasome system. Purification of the PHF8 complex led to the identification of many subunits of the anaphase-promoting complex (APC) associated with PHF8. We showed that PHF8 interacts with the CDC20-containing APC (APC(cdc20)) primarily during mitosis. In addition, we defined a novel, KEN- and D-box-independent, LXPKXLF motif on PHF8 that is required for binding to CDC20. Through various in vivo and in vitro assays, we demonstrate that mutations of the LXPKXLF motif abrogate polyubiquitylation of PHF8 by the APC. APC substrates are typically cell cycle regulators, and consistent with this, the loss of PHF8 leads to prolonged G2 phase and defective mitosis. Furthermore, we provide evidence that PHF8 plays an important role in transcriptional activation of key G2/M genes during G2 phase. Taken together, these findings suggest that PHF8 is regulated by APC(cdc20) and plays an important role in the G2/M transition.
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Hsiao KY, Mizzen CA. Histone H4 deacetylation facilitates 53BP1 DNA damage signaling and double-strand break repair. J Mol Cell Biol 2013; 5:157-65. [PMID: 23329852 DOI: 10.1093/jmcb/mjs066] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
53BP1 and other DNA damage response (DDR) proteins form foci at double-strand breaks (DSBs) which promote their repair by nonhomologous end joining (NHEJ). Focal accumulation of 53BP1 depends on the specific interaction of its tandem Tudor domain with dimethylated lysine 20 in histone H4 (H4K20me2). How 53BP1 foci dynamics are regulated is unclear since H4K20me2 is highly abundant, established largely in the absence of DNA damage, and uncertainty exists about the roles of candidate H4K20 methyltransferases in 53BP1 foci formation. Here, we show that 53BP1 foci assemble primarily on H4K20me2 established prior to DNA damage by the SETD8 and SUV420 methyltransferases rather than de novo H4K20 methylation mediated by MMSET/WHSC1. Moreover, we define a novel role for H4K16 acetylation in regulating 53BP1 foci dynamics. Concurrent acetylation at H4K16 antagonizes 53BP1 binding to extant H4K20me2 until DSBs elicit transient, localized H4 deacetylation that facilitates 53BP1 foci formation and NHEJ, and is associated with global repression of gene transcription. Our findings demonstrate that rapid induction of H4 deacetylation by DSBs affects multiple aspects of the DDR, and also suggest that antagonism of 53BP1 binding to H4K20me2 by H4K16 hyperacetylation may contribute to the efficacy of histone deacetylase inhibitors for cancer therapy.
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Affiliation(s)
- Kuei-Yang Hsiao
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana, IL 61801, USA
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Brants J, Semenchenko K, Wasylyk C, Robert A, Carles A, Zambrano A, Pradeau-Aubreton K, Birck C, Schalken JA, Poch O, de Mey J, Wasylyk B. Tubulin tyrosine ligase like 12, a TTLL family member with SET- and TTL-like domains and roles in histone and tubulin modifications and mitosis. PLoS One 2012; 7:e51258. [PMID: 23251473 PMCID: PMC3520985 DOI: 10.1371/journal.pone.0051258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 01/15/2023] Open
Abstract
hTTLL12 is a member of the tubulin tyrosine ligase (TTL) family that is highly conserved in phylogeny. It has both SET-like and TTL-like domains, suggesting that it could have histone methylation and tubulin tyrosine ligase activities. Altered expression of hTTLL12 in human cells leads to specific changes in H4K20 trimethylation, and tubulin detyrosination, hTTLL12 does not catalyse histone methylation or tubulin tyrosination in vitro, as might be expected from the lack of critical amino acids in its SET-like and TTLL-like domains. hTTLL12 misexpression increases mitotic duration and chromosome numbers. These results suggest that hTTLL12 has non-catalytic functions related to tubulin and histone modification, which could be linked to its effects on mitosis and chromosome number stability.
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Affiliation(s)
- Jan Brants
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Kostyantyn Semenchenko
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Christine Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Aude Robert
- Université de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg C.N.R.S. - U.M.R.7100, Equipe “Microtubules et Morphogenèse”, Parc d'Innovation, Illkirch, France
| | - Annaick Carles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Alberto Zambrano
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Karine Pradeau-Aubreton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Jack A. Schalken
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Olivier Poch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Jan de Mey
- Université de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg C.N.R.S. - U.M.R.7100, Equipe “Microtubules et Morphogenèse”, Parc d'Innovation, Illkirch, France
| | - Bohdan Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
- * E-mail:
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Sakaguchi A, Joyce E, Aoki T, Schedl P, Steward R. The histone H4 lysine 20 monomethyl mark, set by PR-Set7 and stabilized by L(3)mbt, is necessary for proper interphase chromatin organization. PLoS One 2012; 7:e45321. [PMID: 23024815 PMCID: PMC3443217 DOI: 10.1371/journal.pone.0045321] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 08/21/2012] [Indexed: 11/28/2022] Open
Abstract
Drosophila PR-Set7 or SET8 is a histone methyltransferase that specifically monomethylates histone H4 lysine 20 (H4K20). L(3)MBT has been identified as a reader of methylated H4K20. It contains several conserved domains including three MBT repeats binding mono- and dimethylated H4K20 peptides. We find that the depletion of PR-Set7 blocks de novo H4K20me1 resulting in the immediate activation of the DNA damage checkpoint, an increase in the size of interphase nuclei, and drastic reduction of cell viability. L(3)mbt on the other hand stabilizes the monomethyl mark, as L(3)mbt-depleted S2 cells show a reduction of more than 60% of bulk monomethylated H4K20 (H4K20me1) while viability is barely affected. Ploidy and basic chromatin structure show only small changes in PR-Set7-depleted cells, but higher order interphase chromatin organization is significantly affected presumably resulting in the activation of the DNA damage checkpoint. In the absence of any other known functions of PR-Set7, the setting of the de novo monomethyl mark appears essential for cell viability in the presence or absence of the DNA damage checkpoint, but once newly assembled chromatin is established the monomethyl mark, protected by L(3)mbt, is dispensable.
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Affiliation(s)
- Ayako Sakaguchi
- Waksman Institute, Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
| | - Eric Joyce
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ruth Steward
- Waksman Institute, Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
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Hossain M, Stillman B. Meier-Gorlin syndrome mutations disrupt an Orc1 CDK inhibitory domain and cause centrosome reduplication. Genes Dev 2012; 26:1797-810. [PMID: 22855792 DOI: 10.1101/gad.197178.112] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Like DNA replication, centrosomes are licensed to duplicate once per cell division cycle to ensure genetic stability. In addition to regulating DNA replication, the Orc1 subunit of the human origin recognition complex controls centriole and centrosome copy number. Here we report that Orc1 harbors a PACT centrosome-targeting domain and a separate domain that differentially inhibits the protein kinase activities of Cyclin E-CDK2 and Cyclin A-CDK2. A cyclin-binding motif (Cy motif) is required for Orc1 to bind Cyclin A and inhibit Cyclin A-CDK2 kinase activity but has no effect on Cyclin E-CDK2 kinase activity. In contrast, Orc1 inhibition of Cyclin E-CDK2 kinase activity occurs by a different mechanism that is affected by Orc1 mutations identified in Meier-Gorlin syndrome patients. The cyclin/CDK2 kinase inhibitory domain of Orc1, when tethered to the PACT domain, localizes to centrosomes and blocks centrosome reduplication. Meier-Gorlin syndrome mutations that disrupt Cyclin E-CDK2 kinase inhibition also allow centrosome reduplication. Thus, Orc1 contains distinct domains that control centrosome copy number and DNA replication. We suggest that the Orc1 mutations present in some Meier-Gorlin syndrome patients contribute to the pronounced microcephaly and dwarfism observed in these individuals by altering centrosome duplication in addition to DNA replication defects.
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Affiliation(s)
- Manzar Hossain
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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A genome-wide screen identifies genes that affect somatic homolog pairing in Drosophila. G3-GENES GENOMES GENETICS 2012; 2:731-40. [PMID: 22870396 PMCID: PMC3385979 DOI: 10.1534/g3.112.002840] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 04/24/2012] [Indexed: 12/03/2022]
Abstract
In Drosophila and other Dipterans, homologous chromosomes are in close contact in virtually all nuclei, a phenomenon known as somatic homolog pairing. Although homolog pairing has been recognized for over a century, relatively little is known about its regulation. We performed a genome-wide RNAi-based screen that monitored the X-specific localization of the male-specific lethal (MSL) complex, and we identified 59 candidate genes whose knockdown via RNAi causes a change in the pattern of MSL staining that is consistent with a disruption of X-chromosomal homolog pairing. Using DNA fluorescent in situ hybridization (FISH), we confirmed that knockdown of 17 of these genes has a dramatic effect on pairing of the 359 bp repeat at the base of the X. Furthermore, dsRNAs targeting Pr-set7, which encodes an H4K20 methyltransferase, cause a modest disruption in somatic homolog pairing. Consistent with our results in cultured cells, a classical mutation in one of the strongest candidate genes, pebble (pbl), causes a decrease in somatic homolog pairing in developing embryos. Interestingly, many of the genes identified by our screen have known roles in diverse cell-cycle events, suggesting an important link between somatic homolog pairing and the choreography of chromosomes during the cell cycle.
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Kuo AJ, Song J, Cheung P, Ishibe-Murakami S, Yamazoe S, Chen JK, Patel DJ, Gozani O. The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature 2012; 484:115-9. [PMID: 22398447 PMCID: PMC3321094 DOI: 10.1038/nature10956] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/17/2012] [Indexed: 12/18/2022]
Abstract
Recognition of distinctly modified histones by specialized “effector” proteins constitutes a key mechanism for transducing molecular events at chromatin to biological outcomes1. Effector proteins influence DNA-templated processes, including transcription, DNA recombination, and DNA repair; however, no effector functions have yet been identified within the mammalian machinery that regulates DNA replication. Here we show that ORC1 – a component of ORC (origin of replication complex), which mediates pre-DNA replication licensing2 – contains a BAH (bromo adjacent homology) domain that specifically recognizes histone H4 dimethylated at lysine 20 (H4K20me2). Recognition of H4K20me2 is a property common to BAH domains present within diverse metazoan ORC1 proteins. Structural studies reveal that the specificity of the BAH domain for H4K20me2 is mediated by a dynamic aromatic dimethyllysine-binding cage and multiple intermolecular contacts involving the bound peptide. H4K20me2 is enriched at replication origins and abrogating ORC1 recognition of H4K20me2 in cells impairs ORC1 occupancy at origins, ORC chromatin loading, and cell-cycle progression. Mutation of the ORC1 BAH domain has been implicated in the etiology of Meier-Gorlin syndrome (MGS)3,4, a form of primordial dwarfism5, and ORC1 depletion in zebrafish results in an MGS-like phenotype4. We find that wild-type human ORC1, but not ORC1 H4K20me2-binding mutants, rescues the growth retardation of orc1 morphants. Moreover, zebrafish depleted of H4K20me2 have diminished body size, mirroring the phenotype of orc1 morphants. Together, our results identify the BAH domain as a novel methyllysine-binding module, thereby establishing the first direct link between histone methylation and the metazoan DNA replication machinery, and defining a pivotal etiologic role for the canonical H4K20me2 mark, via ORC1, in primordial dwarfism.
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Affiliation(s)
- Alex J Kuo
- Department of Biology, Stanford University, Stanford, California 94305, USA
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Giri S, Prasanth SG. Replicating and transcribing on twisted roads of chromatin. Brief Funct Genomics 2012; 11:188-204. [PMID: 22267489 DOI: 10.1093/bfgp/elr047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromatin, a complex of DNA and proteins in the eukaryotic cell nucleus governs various cellular processes including DNA replication, DNA repair and transcription. Chromatin architecture and dynamics dictates the timing of cellular events by regulating proteins' accessibility to DNA as well as by acting as a scaffold for protein-protein interactions. Nucleosome, the basic unit of chromatin consists of a histone octamer comprised of (H3-H4)2 tetramer and two H2A-H2B dimers on which 146 bp of DNA is wrapped around ~1.6 times. Chromatin changes brought about by histone modifications, histone-modifying enzymes, chromatin remodeling factors, histone chaperones, histone variants and chromatin dynamics influence the regulation and timing of gene expression. Similarly, the timing of DNA replication is dependent on the chromatin context that in turn dictates origin selection. Further, during the process of DNA replication, not only does an organism's DNA have to be accurately replicated but also the chromatin structure and the epigenetic marks have to be faithfully transmitted to the daughter cells. Active transcription has been shown to repress replication while at the same time it has been shown that when origins are located at promoters, because of enhanced chromatin accessibility, they fire efficiently. In this review, we focus on how chromatin modulates two fundamental processes, DNA replication and transcription.
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Affiliation(s)
- Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
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Stress-stimulated mitogen-activated protein kinases control the stability and activity of the Cdt1 DNA replication licensing factor. Mol Cell Biol 2011; 31:4405-16. [PMID: 21930785 DOI: 10.1128/mcb.06163-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA replication is tightly coordinated both with cell cycle cues and with responses to extracellular signals to maintain genome stability. We discovered that human Cdt1, an essential origin licensing protein whose activity must be restricted to G(1) phase, is a substrate of the stress-activated mitogen-activated protein (MAP) kinases p38 and c-Jun N-terminal kinase (JNK). These MAP kinases phosphorylate Cdt1 both during unperturbed G(2) phase and during an acute stress response. Phosphorylation renders Cdt1 resistant to ubiquitin-mediated degradation during S phase and after DNA damage by blocking Cdt1 binding to the Cul4 adaptor, Cdt2. Mutations that block normal cell cycle-regulated MAP kinase-mediated phosphorylation interfere with rapid Cdt1 reaccumulation at the end of S phase. Phosphomimetic mutations recapitulate the stabilizing effects of Cdt1 phosphorylation but also reduce the ability of Cdt1 to support origin licensing. Two other CRL4(Cdt2) targets, the cyclin-dependent kinase (CDK) inhibitor p21 and the methyltransferase PR-Set7/Set8, are similarly stabilized by MAP kinase activity. These findings support a model in which MAP kinase activity in G(2) promotes reaccumulation of a low-activity Cdt1 isoform after replication is complete.
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