51
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Morishita M, Mevius D, di Luccio E. In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L. BMC STRUCTURAL BIOLOGY 2014; 14:25. [PMID: 25494638 PMCID: PMC4280037 DOI: 10.1186/s12900-014-0025-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Abstract
Background Histone lysine methylation has a pivotal role in regulating the chromatin. Histone modifiers, including histone methyl transferases (HMTases), have clear roles in human carcinogenesis but the extent of their functions and regulation are not well understood. The NSD family of HMTases comprised of three members (NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L) are oncogenes aberrantly expressed in several cancers, suggesting their potential to serve as novel therapeutic targets. However, the substrate specificity of the NSDs and the molecular mechanism of histones H3 and H4 recognition and methylation have not yet been established. Results Herein, we investigated the in vitro mechanisms of histones H3 and H4 recognition and modifications by the catalytic domain of NSD family members. In this study, we quantified in vitro mono-, di- and tri- methylations on H3K4, H3K9, H3K27, H3K36, H3K79, and H4K20 by the carboxyl terminal domain (CTD) of NSD1, NSD2 and NSD3, using histone as substrate. Next, we used a molecular modelling approach and docked 6-mer peptides H3K4 a.a. 1-7; H3K9 a.a. 5-11; H3K27 a.a. 23-29; H3K36 a.a. 32-38; H3K79 a.a. 75-81; H4K20 a.a. 16-22 with the catalytic domain of the NSDs to provide insight into lysine-marks recognition and methylation on histones H3 and H4. Conclusions Our data highlight the versatility of NSD1, NSD2, and NSD3 for recognizing and methylating several histone lysine marks on histones H3 and H4. Our work provides a basis to design selective and specific NSDs inhibitors. We discuss the relevance of our findings for the development of NSD inhibitors amenable for novel chemotherapies. Electronic supplementary material The online version of this article (doi:10.1186/s12900-014-0025-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masayo Morishita
- Kyungpook National University, School of Applied Biosciences, Life Sciences and Agriculture building #3, room 309, 80 Daehak-ro, Daegu, Buk-gu, 702-701, Republic of Korea.
| | - Damiaan Mevius
- Kyungpook National University, School of Applied Biosciences, Life Sciences and Agriculture building #3, room 309, 80 Daehak-ro, Daegu, Buk-gu, 702-701, Republic of Korea.
| | - Eric di Luccio
- Kyungpook National University, School of Applied Biosciences, Life Sciences and Agriculture building #3, room 309, 80 Daehak-ro, Daegu, Buk-gu, 702-701, Republic of Korea.
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52
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Sun Y, Wei M, Ren SC, Chen R, Xu WD, Wang FB, Lu J, Shen J, Yu YW, Hou JG, Xu CL, Huang JT, Sun YH. Histone methyltransferase SETDB1 is required for prostate cancer cell proliferation, migration and invasion. Asian J Androl 2014; 16:319-24. [PMID: 24556744 PMCID: PMC3955348 DOI: 10.4103/1008-682x.122812] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
SETDB1 has been established as an oncogene in a number of human carcinomas. The present study was to evaluate the expression of SETDB1 in prostate cancer (PCa) tissues and cells and to preliminarily investigate the role of SETDB1 in prostate tumorigenesis in vitro. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) were used to detect the expression of SETDB1 in PCa tissues, adjacent normal tissues, benign prostatic hyperplasia (BPH) tissues, PCa cell lines and normal prostate epithelial cells. The results suggested that SETDB1 was upregulated in human PCa tissues compared with normal tissues at the mRNA and protein levels. The role of SETDB1 in proliferation was analyzed with cell counting kit-8, colony-forming efficiency and flow cytometry assays. The results indicated that downregulation of SETDB1 by siRNA inhibited PCa cell growth, and induced G0/G1 cell cycle arrest. The PCa cell migration and invasion decreased by silcencing SETDB1 which were assessed by using in vitro scratch and transwell invasion assay respectively. Our data suggested that SETDB1 is overexpressed in human PCa. Silencing SETDB1 inhibited PCa cell proliferation, migration and invasion.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Ying-Hao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
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53
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Clifton MK, Westman BJ, Thong SY, O’Connell MR, Webster MW, Shepherd NE, Quinlan KG, Crossley M, Blobel GA, Mackay JP. The identification and structure of an N-terminal PR domain show that FOG1 is a member of the PRDM family of proteins. PLoS One 2014; 9:e106011. [PMID: 25162672 PMCID: PMC4146578 DOI: 10.1371/journal.pone.0106011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/26/2014] [Indexed: 11/19/2022] Open
Abstract
FOG1 is a transcriptional regulator that acts in concert with the hematopoietic master regulator GATA1 to coordinate the differentiation of platelets and erythrocytes. Despite considerable effort, however, the mechanisms through which FOG1 regulates gene expression are only partially understood. Here we report the discovery of a previously unrecognized domain in FOG1: a PR (PRD-BF1 and RIZ) domain that is distantly related in sequence to the SET domains that are found in many histone methyltransferases. We have used NMR spectroscopy to determine the solution structure of this domain, revealing that the domain shares close structural similarity with SET domains. Titration with S-adenosyl-L-homocysteine, the cofactor product synonymous with SET domain methyltransferase activity, indicated that the FOG PR domain is not, however, likely to function as a methyltransferase in the same fashion. We also sought to define the function of this domain using both pulldown experiments and gel shift assays. However, neither pulldowns from mammalian nuclear extracts nor yeast two-hybrid assays reproducibly revealed binding partners, and we were unable to detect nucleic-acid-binding activity in this domain using our high-diversity Pentaprobe oligonucleotides. Overall, our data demonstrate that FOG1 is a member of the PRDM (PR domain containing proteins, with zinc fingers) family of transcriptional regulators. The function of many PR domains, however, remains somewhat enigmatic for the time being.
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Affiliation(s)
- Molly K. Clifton
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Belinda J. Westman
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Sock Yue Thong
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | | | - Michael W. Webster
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | | | - Kate G. Quinlan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Merlin Crossley
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Gerd A. Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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54
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Characterization of the histone methyltransferase PRDM9 using biochemical, biophysical and chemical biology techniques. Biochem J 2014; 461:323-34. [PMID: 24785241 DOI: 10.1042/bj20140374] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PRDM proteins have emerged as important regulators of disease and developmental processes. To gain insight into the mechanistic actions of the PRDM family, we have performed comprehensive characterization of a prototype member protein, the histone methyltransferase PRDM9, using biochemical, biophysical and chemical biology techniques. In the present paper we report the first known molecular characterization of a PRDM9-methylated recombinant histone octamer and the identification of new histone substrates for the enzyme. A single C321P mutant of the PR/SET domain was demonstrated to significantly weaken PRDM9 activity. Additionally, we have optimized a robust biochemical assay amenable to high-throughput screening to facilitate the generation of small-molecule chemical probes for this protein family. The present study has provided valuable insight into the enzymology of an intrinsically active PRDM protein.
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55
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Fang L, Zhang L, Wei W, Jin X, Wang P, Tong Y, Li J, Du JX, Wong J. A methylation-phosphorylation switch determines Sox2 stability and function in ESC maintenance or differentiation. Mol Cell 2014; 55:537-51. [PMID: 25042802 DOI: 10.1016/j.molcel.2014.06.018] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/08/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022]
Abstract
Sox2 is a key factor for maintaining embryonic stem cell (ESS) pluripotency, but little is known about its posttranslational regulation. Here we present evidence that the precise level of Sox2 proteins in ESCs is regulated by a balanced methylation and phosphorylation switch. Set7 monomethylates Sox2 at K119, which inhibits Sox2 transcriptional activity and induces Sox2 ubiquitination and degradation. The E3 ligase WWP2 specifically interacts with K119-methylated Sox2 through its HECT domain to promote Sox2 ubiquitination. In contrast, AKT1 phosphorylates Sox2 at T118 and stabilizes Sox2 by antagonizing K119me by Set7 and vice versa. In mouse ESCs, AKT1 activity toward Sox2 is greater than that of Set7, leading to Sox2 stabilization and ESC maintenance. In early development, increased Set7 expression correlates with Sox2 downregulation and appropriate differentiation. Our study highlights the importance of a Sox2 methylation-phosphorylation switch in determining ESC fate.
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Affiliation(s)
- Lan Fang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ling Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xueling Jin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ping Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yufeng Tong
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
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56
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Kupershmit I, Khoury-Haddad H, Awwad SW, Guttmann-Raviv N, Ayoub N. KDM4C (GASC1) lysine demethylase is associated with mitotic chromatin and regulates chromosome segregation during mitosis. Nucleic Acids Res 2014; 42:6168-82. [PMID: 24728997 PMCID: PMC4041427 DOI: 10.1093/nar/gku253] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 03/11/2014] [Accepted: 03/15/2014] [Indexed: 12/11/2022] Open
Abstract
Various types of human cancers exhibit amplification or deletion of KDM4A-D members, which selectively demethylate H3K9 and H3K36, thus implicating their activity in promoting carcinogenesis. On this basis, it was hypothesized that dysregulated expression of KDM4A-D family promotes chromosomal instabilities by largely unknown mechanisms. Here, we show that unlike KDM4A-B, KDM4C is associated with chromatin during mitosis. This association is accompanied by a decrease in the mitotic levels of H3K9me3. We also show that the C-terminal region, containing the Tudor domains of KDM4C, is essential for its association with mitotic chromatin. More specifically, we show that R919 residue on the proximal Tudor domain of KDM4C is critical for its association with chromatin during mitosis. Interestingly, we demonstrate that depletion or overexpression of KDM4C, but not KDM4B, leads to over 3-fold increase in the frequency of abnormal mitotic cells showing either misaligned chromosomes at metaphase, anaphase-telophase lagging chromosomes or anaphase-telophase bridges. Furthermore, overexpression of KDM4C demethylase-dead mutant has no detectable effect on mitotic chromosome segregation. Altogether, our findings implicate KDM4C demethylase activity in regulating the fidelity of mitotic chromosome segregation by a yet unknown mechanism.
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Affiliation(s)
- Ilana Kupershmit
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Hanan Khoury-Haddad
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Samah W Awwad
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Noga Guttmann-Raviv
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
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57
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Hamamoto R, Toyokawa G, Nakakido M, Ueda K, Nakamura Y. SMYD2-dependent HSP90 methylation promotes cancer cell proliferation by regulating the chaperone complex formation. Cancer Lett 2014; 351:126-33. [PMID: 24880080 DOI: 10.1016/j.canlet.2014.05.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/30/2014] [Accepted: 05/11/2014] [Indexed: 02/07/2023]
Abstract
Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that facilitates the maturation of a wide range of proteins, and it has been recognized as a crucial facilitator of oncogene addiction and cancer cell survival. Although HSP90 function is regulated by a variety of post-translational modifications, the physiological significance of methylation has not fully been elucidated. Here we demonstrate that HSP90AB1 is methylated by the histone methyltransferase SMYD2 and that it plays a critical role in human carcinogenesis. HSP90AB1 and SMYD2 can interact through the C-terminal region of HSP90AB1 and the SET domain of SMYD2. Both in vitro and in vivo methyltransferase assays revealed that SMYD2 could methylate HSP90AB1 and mass spectrometry analysis indicated lysines 531 and 574 of HSP90AB1 to be methylated. These methylation sites were shown to be important for the dimerization and chaperone complex formation of HSP90AB1. Furthermore, methylated HSP90AB1 accelerated the proliferation of cancer cells. Our study reveals a novel mechanism for human carcinogenesis via methylation of HSP90AB1 by SMYD2, and additional functional studies may assist in developing novel strategies for cancer therapy.
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Affiliation(s)
- Ryuji Hamamoto
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC2115 Chicago, IL 60637, United States; Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Gouji Toyokawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Nakakido
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC2115 Chicago, IL 60637, United States
| | - Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC2115 Chicago, IL 60637, United States
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58
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O'Neill DJ, Williamson SC, Alkharaif D, Monteiro ICM, Goudreault M, Gaughan L, Robson CN, Gingras AC, Binda O. SETD6 controls the expression of estrogen-responsive genes and proliferation of breast carcinoma cells. Epigenetics 2014; 9:942-50. [PMID: 24751716 PMCID: PMC4143409 DOI: 10.4161/epi.28864] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The lysine methyltransferase SETD6 modifies the histone variant H2AZ, a key component of nuclear receptor-dependent transcription. Herein, we report the identification of several factors that associate with SETD6 and are implicated in nuclear hormone receptor signaling. Specifically, SETD6 associates with the estrogen receptor α (ERα), histone deacetylase HDAC1, metastasis protein MTA2, and the transcriptional co-activator TRRAP. Luciferase reporter assays identify SETD6 as a transcriptional repressor, in agreement with its association with HDAC1 and MTA2. However, SETD6 behaves as a co-activator of several estrogen-responsive genes, such as PGR and TFF1. Consistent with these results, silencing of SETD6 in several breast carcinoma cell lines induced cellular proliferation defects accompanied by enhanced expression of the cell cycle inhibitor CDKN1A and induction of apoptosis. Herein, we have identified several chromatin proteins that associate with SETD6 and described SETD6 as an essential factor for nuclear receptor signaling and cellular proliferation.
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Affiliation(s)
- Daniel J O'Neill
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | | | - Dhuha Alkharaif
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | | | - Marilyn Goudreault
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto, ON Canada
| | - Luke Gaughan
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | - Craig N Robson
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto, ON Canada; Department of Molecular Genetics; University of Toronto; Toronto, ON Canada
| | - Olivier Binda
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
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59
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Savickiene J, Treigyte G, Stirblyte I, Valiuliene G, Navakauskiene R. Euchromatic histone methyltransferase 2 inhibitor, BIX-01294, sensitizes human promyelocytic leukemia HL-60 and NB4 cells to growth inhibition and differentiation. Leuk Res 2014; 38:822-9. [PMID: 24832370 DOI: 10.1016/j.leukres.2014.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 11/26/2022]
Abstract
The involvement of histone lysine methyltransferases (HMT) in carcinogenesis is not well understood. Here, we describe a dose-dependent growth and survival inhibitory effects of BIX-01294, a specific inhibitor of euchromatic HMT2, in promyelocytic leukemia HL-60 and NB4 cells. BIX-01294 combined with all-trans retinoic acid or together with histone deacetylase and DNA methyltransferase inhibitors enhanced cell differentiation to granulocytes and induced cell line-specific changes in the expression of cell cycle-, survival- and differentiation regulating genes and proteins in association with histone modification state. Our results suggest that targeting EHMT2 may be of therapeutical benefits in myeloid leukemia.
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Affiliation(s)
- Jurate Savickiene
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, LT 08662 Vilnius, Lithuania
| | - Grazina Treigyte
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, LT 08662 Vilnius, Lithuania
| | - Ieva Stirblyte
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, LT 08662 Vilnius, Lithuania
| | - Giedre Valiuliene
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, LT 08662 Vilnius, Lithuania
| | - Ruta Navakauskiene
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, LT 08662 Vilnius, Lithuania.
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60
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Zhang W, Hu D, Ji W, Yang L, Yang J, Yuan J, Xuan A, Zou F, Zhuang Z. Histone modifications contribute to cellular replicative and hydrogen peroxide-induced premature senescence in human embryonic lung fibroblasts. Free Radic Res 2014; 48:550-9. [PMID: 24528089 DOI: 10.3109/10715762.2014.893580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Histone modifications are major post-translational mechanisms responsible for regulation of gene transcription involved in cellular senescence. By using immunofluorescence and Western blot, we showed that the global acetylated levels of histone H3 and H4 were significantly reduced in both replicative and premature senescence of human embryonic lung fibroblasts. However the whole trimethylated level of histone H4 lysine 20 was higher in senescent cells. The alterations in the mRNA and protein levels of histone acetyltransferases (HATs), histone methyltransferase (HMT), and histone deacetylases (HDACs) indicate that differential expression exists between replicative and premature senescent cells. Meanwhile, the reduced activity of HDACs was accompanied by cellular senescence. By employing the quantitative chromatin immunoprecipitation assay in detecting specific histone modifications in senescence-related genes including p53 and p16, it was demonstrated that the mRNA expression of p53 was associated with increased H4 acetylation in replicative senescence and increased H4 acetylation and trimethylation of histone H3 at lysine 4 (H3K4me3) in premature senescence. Both acetylation and trimethylation of H3 were involved in replicative senescence, while the acetylation of histone H3 and H4 was predominant in premature senescence, contributing to the mRNA expression of p16. In summary, the global hypoacetylation of histone H3 and H4 and the hypertrimethylation of histone H4 lysine 20 account for epigenetic characteristics in senescence, controlled by HATs, HMT, and HDACs differentially between replicative and premature senescence. Taken together, these findings suggest that the specific histone modifications are involved in regulating the expression of genes related to senescence of human embryonic lung fibroblasts.
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Affiliation(s)
- Wenjuan Zhang
- Department of Toxicology, School of Public Health and Tropical Medicine, Southern Medical University , Guangzhou , P. R. China
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61
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Sweis RF, Pliushchev M, Brown PJ, Guo J, Li F, Maag D, Petros AM, Soni NB, Tse C, Vedadi M, Michaelides MR, Chiang GG, Pappano WN. Discovery and development of potent and selective inhibitors of histone methyltransferase g9a. ACS Med Chem Lett 2014; 5:205-9. [PMID: 24900801 DOI: 10.1021/ml400496h] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/02/2014] [Indexed: 12/12/2022] Open
Abstract
G9a is a histone lysine methyltransferase responsible for the methylation of histone H3 lysine 9. The discovery of A-366 arose from a unique diversity screening hit, which was optimized by incorporation of a propyl-pyrrolidine subunit to occupy the enzyme lysine channel. A-366 is a potent inhibitor of G9a (IC50: 3.3 nM) with greater than 1000-fold selectivity over 21 other methyltransferases.
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Affiliation(s)
- Ramzi F. Sweis
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Marina Pliushchev
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Peter J. Brown
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Jun Guo
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Fengling Li
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - David Maag
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Andrew M. Petros
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Nirupama B. Soni
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Chris Tse
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Masoud Vedadi
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Michael R. Michaelides
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Gary G. Chiang
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - William N. Pappano
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
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62
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Gewies A, Castineiras-Vilarino M, Ferch U, Jährling N, Heinrich K, Hoeckendorf U, Przemeck GKH, Munding M, Groß O, Schroeder T, Horsch M, Karran EL, Majid A, Antonowicz S, Beckers J, Hrabé de Angelis M, Dodt HU, Peschel C, Förster I, Dyer MJS, Ruland J. Prdm6 is essential for cardiovascular development in vivo. PLoS One 2013; 8:e81833. [PMID: 24278461 PMCID: PMC3836774 DOI: 10.1371/journal.pone.0081833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 10/28/2013] [Indexed: 11/18/2022] Open
Abstract
Members of the PRDM protein family have been shown to play important roles during embryonic development. Previous in vitro and in situ analyses indicated a function of Prdm6 in cells of the vascular system. To reveal physiological functions of Prdm6, we generated conditional Prdm6-deficient mice. Complete deletion of Prdm6 results in embryonic lethality due to cardiovascular defects associated with aberrations in vascular patterning. However, smooth muscle cells could be regularly differentiated from Prdm6-deficient embryonic stem cells and vascular smooth muscle cells were present and proliferated normally in Prdm6-deficient embryos. Conditional deletion of Prdm6 in the smooth muscle cell lineage using a SM22-Cre driver line resulted in perinatal lethality due to hemorrhage in the lungs. We thus identified Prdm6 as a factor that is essential for the physiological control of cardiovascular development.
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Affiliation(s)
- Andreas Gewies
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory of Signaling in the Immune System, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mercedes Castineiras-Vilarino
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Uta Ferch
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Nina Jährling
- Department of Bioelectronics, Institute of Solid State Electronics, Vienna University of Technology, Vienna, Austria
- Center for Brain Research, Section of Bioelectronics, Medical University of Vienna, Vienna, Austria
- Department of Neurobiology, University of Oldenburg, Oldenburg, Germany
| | - Katja Heinrich
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Ulrike Hoeckendorf
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- Department of Internal Medicine III, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Gerhard K. H. Przemeck
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Munding
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Stem Cell Dynamics, Neuherberg, Germany
| | - Olaf Groß
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Timm Schroeder
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Stem Cell Dynamics, Neuherberg, Germany
| | - Marion Horsch
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - E. Loraine Karran
- MRC Toxicology Unit and Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Aneela Majid
- MRC Toxicology Unit and Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Stefan Antonowicz
- MRC Toxicology Unit and Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, Freising-Weihenstephan, Germany
| | - Martin Hrabé de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, Freising-Weihenstephan, Germany
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, Institute of Solid State Electronics, Vienna University of Technology, Vienna, Austria
- Center for Brain Research, Section of Bioelectronics, Medical University of Vienna, Vienna, Austria
| | - Christian Peschel
- Department of Internal Medicine III, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Irmgard Förster
- Institute of Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martin J. S. Dyer
- MRC Toxicology Unit and Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Jürgen Ruland
- Institut für Klinische Chemie und Pathobiochemie, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Laboratory of Signaling in the Immune System, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Infection Research (DZIF), partner site München, Munich, Germany
- * E-mail:
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Pachaiyappan B, Woster PM. Design of small molecule epigenetic modulators. Bioorg Med Chem Lett 2013; 24:21-32. [PMID: 24300735 DOI: 10.1016/j.bmcl.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 10/28/2013] [Accepted: 11/04/2013] [Indexed: 12/16/2022]
Abstract
The field of epigenetics has expanded rapidly to reveal multiple new targets for drug discovery. The functional elements of the epigenomic machinery can be categorized as writers, erasers and readers, and together these elements control cellular gene expression and homeostasis. It is increasingly clear that aberrations in the epigenome can underly a variety of diseases, and thus discovery of small molecules that modulate the epigenome in a specific manner is a viable approach to the discovery of new therapeutic agents. In this Digest, the components of epigenetic control of gene expression will be briefly summarized, and efforts to identify small molecules that modulate epigenetic processes will be described.
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Affiliation(s)
- Boobalan Pachaiyappan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Patrick M Woster
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States.
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64
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Li B, Li S, Yin J, Zhong J. Identification and characterization of the Spodoptera Su(var) 3-9 histone H3K9 trimethyltransferase and its effect in AcMNPV infection. PLoS One 2013; 8:e69442. [PMID: 23894480 PMCID: PMC3722159 DOI: 10.1371/journal.pone.0069442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 06/14/2013] [Indexed: 11/19/2022] Open
Abstract
Histone H3-lysine9 (H3K9) trimethyltransferase gene Su(var) 3-9 was cloned and identified in three Spodoptera insects, Spodopterafrugiperda (S. frugiperda), S. exigua and S. litura. Sequence analysis showed that Spodoptera Su(var) 3-9 is highly conserved evolutionarily. Su(var) 3-9 protein was found to be localized in the nucleus in Sf9 cells, and interact with histone H3, and the heterochromatin protein 1a (HP1a) and HP1b. A dose-dependent enzymatic activity was found at both 27 °C and 37 °C in vitro, with higher activity at 27 °C. Addition of specific inhibitor chaetocin resulted in decreased histone methylation level and host chromatin relaxation. In contrast, overexpression of Su(var) 3-9 caused increased histone methylation level and cellular genome compaction. In AcMNV-infected Sf9 cells, the transcription of Su(var) 3-9 increased at late time of infection, although the mRNA levels of most cellular genes decreased. Pre-treatment of Sf9 cells with chaetocin speeded up viral DNA replication, and increased the transcription level of a variety of virus genes, whereas in Sf9 cells pre-transformed with Su(var) 3-9 expression vector, viral DNA replication slow down slightly. These findings suggest that Su(var) 3-9 might participate in the viral genes expression an genome replication repression during AcMNPV infection. It provided a new insight for the understanding virus–host interaction mechanism.
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Affiliation(s)
- Binbin Li
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Sisi Li
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Juan Yin
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jiang Zhong
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- * E-mail:
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Rodriguez-Paredes M, Martinez de Paz A, Simó-Riudalbas L, Sayols S, Moutinho C, Moran S, Villanueva A, Vázquez-Cedeira M, Lazo PA, Carneiro F, Moura CS, Vieira J, Teixeira MR, Esteller M. Gene amplification of the histone methyltransferase SETDB1 contributes to human lung tumorigenesis. Oncogene 2013; 33:2807-13. [PMID: 23770855 PMCID: PMC4031636 DOI: 10.1038/onc.2013.239] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 12/14/2022]
Abstract
Disruption of the histone modification patterns is one of the most common features of human tumors. However, few genetic alterations in the histone modifier genes have been described in tumorigenesis. Herein we show that the histone methyltransferase SETDB1 undergoes gene amplification in non-small and small lung cancer cell lines and primary tumors. The existence of additional copies of the SETDB1 gene in these transformed cells is associated with higher levels of the corresponding mRNA and protein. From a functional standpoint, the depletion of SETDB1 expression in amplified cells reduces cancer growth in cell culture and nude mice models, whereas its overexpression increases the tumor invasiveness. The increased gene dosage of SETDB1 is also associated with enhanced sensitivity to the growth inhibitory effect mediated by the SETDB1-interfering drug mithramycin. Overall, the findings identify SETDB1 as a bona fide oncogene undergoing gene amplification-associated activation in lung cancer and suggest its potential for new therapeutic strategies.
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Affiliation(s)
- M Rodriguez-Paredes
- Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - A Martinez de Paz
- Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - L Simó-Riudalbas
- Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - S Sayols
- Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - C Moutinho
- Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - S Moran
- Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - A Villanueva
- Translational Research Laboratory, IDIBELL-Institut Catala d'Oncologia, Barcelona, Spain
| | - M Vázquez-Cedeira
- 1] Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, Spain [2] Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - P A Lazo
- 1] Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, Spain [2] Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - F Carneiro
- Department of Pathology, Centro Hospitalar São João/Medical Faculty and Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - C S Moura
- Department of Pathology, Centro Hospitalar São João/Medical Faculty and Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - J Vieira
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - M R Teixeira
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - M Esteller
- 1] Cancer Epigenetics and Biology Progrm (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain [2] Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain [3] Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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66
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Lu Z, Huang X, Ouyang Y, Yao J. Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice. PLoS One 2013; 8:e65426. [PMID: 23762371 PMCID: PMC3676427 DOI: 10.1371/journal.pone.0065426] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 04/23/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited. METHODOLOGY/PRINCIPAL FINDINGS In this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback. CONCLUSIONS/SIGNIFICANCE This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.
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Affiliation(s)
- Zhanhua Lu
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, PR China
| | - Xiaolong Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, PR China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
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67
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Abstract
Lysine methylation of histones and non-histone proteins has emerged in recent years as a posttranslational modification with wide-ranging cellular implications beyond epigenetic regulation. The molecular interactions between lysine methyltransferases and their substrates appear to be regulated by posttranslational modifications surrounding the lysine methyl acceptor. Two very interesting examples of this cross-talk between methyl-lysine sites are found in the SET (Su(var)3–9, Enhancer-of-zeste, Trithorax) domain-containing lysine methyltransferases SET7 and SETDB1, whereby the histone H3 trimethylated on lysine 4 (H3K4me3) modification prevents methylation by SETDB1 on H3 lysine 9 (H3K9) and the histone H3 trimethylated on lysine 9 (H3K9me3) modification prevents methylation by SET7 on H3K4. A similar cross-talk between posttranslational modifications regulates the functions of non-histone proteins such as the tumor suppressor p53 and the DNA methyltransferase DNMT1. Herein, in cis effects of acetylation, phosphorylation, as well as arginine and lysine methylation on lysine methylation events will be discussed.
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Affiliation(s)
- Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research; Newcastle University, Newcastle upon Tyne, England.
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68
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Binda O, Sevilla A, LeRoy G, Lemischka IR, Garcia BA, Richard S. SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal. Epigenetics 2013; 8:177-83. [PMID: 23324626 DOI: 10.4161/epi.23416] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The histone H2A variant H2AZ is an essential chromatin signaling factor. Herein, we report that H2AZ is monomethylated at lysine 7 (H2AZK7me1) by the lysine methyltransferase SETD6. We observed that methylation of H2AZ increased noticeably upon cellular differentiation of mouse embryonic stem cells (mESCs). H2AZK7me1 and the repressive H3K27me3 mark were found near the transcriptional start sites of differentiation marker genes, but were removed upon retinoic acid-induced cellular differentiation. The depletion of Setd6 in mESCs led to cellular differentiation, compromised self-renewal, and poor clonogenicity. These findings demonstrate that mESCs require Setd6 for self-renewal and portray H2AZK7me1 as a marker of cellular differentiation.
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Affiliation(s)
- Olivier Binda
- Terry Fox Molecular Oncology Group, Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Department of Oncology, McGill University, Montréal, QC, Canada
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Ghorab MM, Al-Said MS, Nissan YM. Dapson in heterocyclic chemistry, part V: synthesis, molecular docking and anticancer activity of some novel sulfonylbiscompounds carrying biologically active dihydropyridine, dihydroisoquinoline, 1,3-dithiolan, 1,3-dithian, acrylamide, pyrazole, pyrazolopyrimidine and benzochromenemoieties. Chem Pharm Bull (Tokyo) 2012; 60:1019-28. [PMID: 22863706 DOI: 10.1248/cpb.c12-00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
N,N'-(4,4'-Sulfonylbis(4,1-phenylene))bis(2-cyanoacetamid) 2 was utilized as a key intermediate for the synthesis of novel dihydropyridines 3, 4, 8, dihydroisoquinolines 5-7, dithiolan 10, dithian 11, acrylamide 12, benzochromenes 17 and 18 and chromenopyridones 19 and 20. Compound 2 was the starting material in the synthesis of the acrylamide derivative 14, the pyrazole derivative 15 and the pyrazolopyrimidine derivative 16. All the synthesized compounds were evaluated for their in vitro anticancer activity against human breast cancer cell line (MCF7). Compound 19 showed the best cytotoxic activity with IC(50) value 19.36 µM. In addition, molecular docking study of the synthesized compounds on the active sites of farnesyltransferase and arginine methyltransferase was performed in order to give a suggestion about the mechanism of action of their cytotoxic activity.
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Affiliation(s)
- Mostafa Mohammed Ghorab
- Medicinal, Aromatic and Poisonous Plants Research Center (MAPPRC), College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
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Fingerman IM, Zhang X, Ratzat W, Husain N, Cohen RF, Schuler GD. NCBI Epigenomics: what's new for 2013. Nucleic Acids Res 2012. [PMID: 23193265 PMCID: PMC3531100 DOI: 10.1093/nar/gks1171] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.
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Affiliation(s)
- Ian M Fingerman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA.
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71
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Chen Z, Yan CT, Dou Y, Viboolsittiseri SS, Wang JH. The role of a newly identified SET domain-containing protein, SETD3, in oncogenesis. Haematologica 2012; 98:739-43. [PMID: 23065515 DOI: 10.3324/haematol.2012.066977] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The SET domain is found in histone methyltransferases and other lysine methyltransferases. SET domain-containing proteins such as MLL1 play a critical role in leukemogenesis, while others such as SETD2 may function as a tumor suppressor in breast cancer and renal cell carcinoma. We recently discovered that SETD3, a well-conserved SET domain-containing protein, was involved in a translocation to the immunoglobulin lambda light chain locus in one of the non-homologous end-joining/p53-deficient peripheral B-cell lymphomas. We showed that a truncated mRNA lacking the SET domain sequences in Setd3 gene was highly expressed in the lymphoma. Furthermore, we found that the truncated SET-less protein displayed oncogenic potential while the full length SETD3 protein did not. Finally, SETD3 exhibits histone methyltransferases activity on nucleosomal histone 3 in a SET-domain dependent manner. We propose that this newly identified Setd3 gene may play an important role in carcinogenesis.
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Affiliation(s)
- Zhangguo Chen
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish Health, Denver, CO, USA
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72
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Chittka A, Nitarska J, Grazini U, Richardson WD. Transcription factor positive regulatory domain 4 (PRDM4) recruits protein arginine methyltransferase 5 (PRMT5) to mediate histone arginine methylation and control neural stem cell proliferation and differentiation. J Biol Chem 2012; 287:42995-3006. [PMID: 23048031 PMCID: PMC3522294 DOI: 10.1074/jbc.m112.392746] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During development of the cerebral cortex, neural stem cells (NSCs) undergo a temporal switch from proliferative (symmetric) to neuron-generating (asymmetric) divisions. We investigated the role of Schwann cell factor 1 (SC1/PRDM4), a member of the PRDM family of transcription factors, in this critical transition. We discovered that SC1 recruits the chromatin modifier PRMT5, an arginine methyltransferase that catalyzes symmetric dimethylation of histone H4 arginine 3 (H4R3me2s) and that this modification is preferentially associated with undifferentiated cortical NSCs. Overexpressing SC1 in embryonic NSCs led to an increase in the number of Nestin-expressing precursors; mutational analysis of SC1 showed that this was dependent on recruitment of PRMT5. We found that SC1 protein levels are down-regulated at the onset of neurogenesis and that experimental knockdown of SC1 in primary NSCs triggers precocious neuronal differentiation. We propose that SC1 and PRMT5 are components of an epigenetic regulatory complex that maintains the “stem-like” cellular state of the NSC by preserving their proliferative capacity and modulating their cell cycle progression. Our findings provide evidence that histone arginine methylation regulates NSC differentiation.
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Affiliation(s)
- Alexandra Chittka
- Wolfson Institute for Biomedical Research and Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom.
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Shi SP, Qiu JD, Sun XY, Suo SB, Huang SY, Liang RP. A method to distinguish between lysine acetylation and lysine methylation from protein sequences. J Theor Biol 2012; 310:223-30. [DOI: 10.1016/j.jtbi.2012.06.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/21/2012] [Accepted: 06/25/2012] [Indexed: 01/21/2023]
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Guo N, Cheng D, Li ZH, Zhou QB, Zhou JJ, Lin Q, Zeng B, Liao Q, Chen RF. Transfection of HCVc improves hTERT expression through STAT3 pathway by epigenetic regulation in Huh7 cells. J Cell Biochem 2012; 113:3419-26. [PMID: 22688977 DOI: 10.1002/jcb.24218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ning Guo
- Department of Organ Transplant,Qi Lu hosptial of Shan Dong university,Jinan,250012, China
| | - Di Cheng
- Department of Oncology, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Zhi Hua Li
- Department of Oncology, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Quan Bo Zhou
- Department of Hepatobiliary Surgery, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Jia Jia Zhou
- Department of Hepatobiliary Surgery, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Qing Lin
- Department of Hepatobiliary Surgery, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Bing Zeng
- Department of Hepatobiliary Surgery, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Qiaofang Liao
- Department of Oncology, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
| | - Ru Fu Chen
- Department of Hepatobiliary Surgery, Sun Yat‐sen Memorial Hospital of Sun Yat‐sen University, Guangzhou 510120, China
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Jun HJ, Kim J, Hoang MH, Lee SJ. Hepatic lipid accumulation alters global histone h3 lysine 9 and 4 trimethylation in the peroxisome proliferator-activated receptor alpha network. PLoS One 2012; 7:e44345. [PMID: 22973438 PMCID: PMC3433434 DOI: 10.1371/journal.pone.0044345] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 08/02/2012] [Indexed: 12/24/2022] Open
Abstract
Recent data suggest that the etiology of several metabolic diseases is closely associated with transcriptome alteration by aberrant histone methylation. We performed DNA microarray and ChIP-on-chip analyses to examine transcriptome profiling and trimethylation alterations to identify the genomic signature of nonalcoholic fatty liver disease (NAFLD), the most common form of chronic liver disease. Transcriptome analysis showed that steatotic livers in high-fat diet-fed apolipoprotein E2 mice significantly altered the expression of approximately 70% of total genes compared with normal diet-fed control livers, suggesting that hepatic lipid accumulation induces dramatic alterations in gene expression in vivo. Also, pathway analysis suggested that genes encoding chromatin-remodeling enzymes, such as jumonji C-domain-containing histone demethylases that regulate histone H3K9 and H3K4 trimethylation (H3K9me3, H3K4me3), were significantly altered in steatotic livers. Thus, we further investigated the global H3K9me3 and H3K4me3 status in lipid-accumulated mouse primary hepatocytes by ChIP-on-chip analysis. Results showed that hepatic lipid accumulation induced aberrant H3K9me3 and H3K4me3 status in peroxisome proliferator-activated receptor alpha and hepatic lipid catabolism network genes, reducing their mRNA expression compared with non-treated control hepatocytes. This study provides the first evidence that epigenetic regulation by H3K9me3 and H3K4me3 in hepatocytes may be involved in hepatic steatosis and the pathogenesis of NAFLD. Thus, control of H3K9me3 and H3K4me3 represents a potential novel NAFLD prevention and treatment strategy.
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Affiliation(s)
- Hee-Jin Jun
- Department of Biotechnology, Graduate School of Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jinyoung Kim
- Department of Biotechnology, Graduate School of Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Minh-Hien Hoang
- Department of Biotechnology, Graduate School of Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Sung-Joon Lee
- Department of Biotechnology, Graduate School of Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- * E-mail:
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76
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Hazeldine S, Pachaiyappan B, Steinbergs N, Nowotarski S, Hanson AS, Casero RA, Woster PM. Low molecular weight amidoximes that act as potent inhibitors of lysine-specific demethylase 1. J Med Chem 2012; 55:7378-91. [PMID: 22876979 DOI: 10.1021/jm3002845] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered enzyme lysine-specific demethylase 1 (LSD1) plays an important role in the epigenetic control of gene expression, and aberrant gene silencing secondary to LSD1 dysregulation is thought to contribute to the development of cancer. We reported that (bis)guanidines, (bis)biguanides, and their urea- and thiourea isosteres are potent inhibitors of LSD1 and induce the re-expression of aberrantly silenced tumor suppressor genes in tumor cells in vitro. We now report a series of small molecule amidoximes that are moderate inhibitors of recombinant LSD1 but that produce dramatic changes in methylation at the histone 3 lysine 4 (H3K4) chromatin mark, a specific target of LSD1, in Calu-6 lung carcinoma cells. In addition, these analogues increase cellular levels of secreted frizzle-related protein (SFRP) 2, H-cadherin (HCAD), and the transcription factor GATA4. These compounds represent leads for an important new series of drug-like epigenetic modulators with the potential for use as antitumor agents.
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Affiliation(s)
- Stuart Hazeldine
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, Michigan 48202, USA
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77
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Hohenauer T, Moore AW. The Prdm family: expanding roles in stem cells and development. Development 2012; 139:2267-82. [PMID: 22669819 DOI: 10.1242/dev.070110] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Members of the Prdm family are characterized by an N-terminal PR domain that is related to the SET methyltransferase domain, and multiple zinc fingers that mediate sequence-specific DNA binding and protein-protein interactions. Prdm factors either act as direct histone methyltransferases or recruit a suite of histone-modifying enzymes to target promoters. In this way, they function in many developmental contexts to drive and maintain cell state transitions and to modify the activity of developmental signalling pathways. Here, we provide an overview of the structure and function of Prdm family members and discuss the roles played by these proteins in stem cells and throughout development.
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Affiliation(s)
- Tobias Hohenauer
- Disease Mechanism Research Core, RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
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78
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Zou Y, Ma X, Huang Y, Hong L, Chiao JW. Effect of phenylhexyl isothiocyanate on aberrant histone H3 methylation in primary human acute leukemia. J Hematol Oncol 2012; 5:36. [PMID: 22747680 PMCID: PMC3413588 DOI: 10.1186/1756-8722-5-36] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/07/2012] [Indexed: 11/29/2022] Open
Abstract
Background We have previously studied the histone acetylation in primary human leukemia cells. However, histone H3 methylation in these cells has not been characterized. Methods This study examined the methylation status at histone H3 lysine 4 (H3K4) and histone H3 lysine 9 (H3K9) in primary acute leukemia cells obtained from patients and compared with those in the non-leukemia and healthy cells. We further characterized the effect of phenylhexyl isothiocyanate (PHI), Trichostatin A (TSA), and 5-aza-2’-deoxycytidine (5-Aza) on the cells. Results We found that methylation of histone H3K4 was virtually undetectable, while methylation at H3K9 was significantly higher in primary human leukemia cells. The histone H3K9 hypermethylation and histone H3K4 hypomethylation were observed in both myeloid and lymphoid leukemia cells. PHI was found to be able to normalize the methylation level in the primary leukemia cells. We further showed that PHI was able to enhance the methyltransferase activity of H3K4 and decrease the activity of H3K9 methyltransferase. 5-Aza had similar effect on H3K4, but minimal effect on H3K9, whereas TSA had no effect on H3K4 and H3K9 methyltransferases. Conclusions This study revealed opposite methylation level of H3K4 and H3K9 in primary human leukemia cells and demonstrated for the first time that PHI has different effects on the methyltransferases for H3K4 and H3K9.
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Affiliation(s)
- Yong Zou
- Department of Hematology, Zhangzhou Hospital of Fujian Medical University, Zhangzhou, Fujian Province, 363000, China
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79
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Cho HS, Hayami S, Toyokawa G, Maejima K, Yamane Y, Suzuki T, Dohmae N, Kogure M, Kang D, Neal DE, Ponder BAJ, Yamaue H, Nakamura Y, Hamamoto R. RB1 methylation by SMYD2 enhances cell cycle progression through an increase of RB1 phosphorylation. Neoplasia 2012; 14:476-86. [PMID: 22787429 PMCID: PMC3394190 DOI: 10.1593/neo.12656] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/05/2012] [Accepted: 05/07/2012] [Indexed: 12/13/2022]
Abstract
It is well known that RB functions are regulated by posttranslational modifications such as phosphorylation and acetylation, but the significance of lysine methylation on RB has not been fully elucidated. Our expression analysis of SMYD2 by quantitative real-time polymerase chain reaction showed that expression levels of SMYD2 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (P < .0001), and its expression levels in tumor tissues were much higher than those of any other normal tissues. SMYD2 knockdown resulted in the suppression of cancer cell growth, and cell cycle analysis indicated that SMYD2 might play a crucial role in the G(1)/S transition. According to an in vitro methyltransferase assay, we found that SMYD2 methylates RB1 protein, and liquid chromatography-tandem mass spectrometry analysis revealed lysine 810 of RB1 to be methylated by SMYD2. Importantly, this methylation enhanced Ser 807/811 phosphorylation of RB1 both in vitro and in vivo. Furthermore, we demonstrated that methylated RB1 accelerates E2F transcriptional activity and promotes cell cycle progression. SMYD2 is an important oncoprotein in various types of cancer, and SMYD2-dependent RB1 methylation at lysine 810 promotes cell cycle progression of cancer cells. Further study may explore SMYD2-dependent RB1 methylation as a potential therapeutic target in human cancer.
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Affiliation(s)
- Hyun-Soo Cho
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinya Hayami
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Second Department of Surgery, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Gouji Toyokawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuka Yamane
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Naoshi Dohmae
- Biomolecular Characterization Team, RIKEN, Saitama, Japan
| | - Masaharu Kogure
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daechun Kang
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - David E Neal
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Bruce AJ Ponder
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Hiroki Yamaue
- Second Department of Surgery, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ryuji Hamamoto
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
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Khorshidi A, Russell L, Bamforth S, Drummond G, Johnson R, Lehmann OJ. Homozygosity mapping in an anophthalmic pedigree provides evidence of additional genetic heterogeneity. Ophthalmic Genet 2012; 33:208-20. [DOI: 10.3109/13816810.2011.648364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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81
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Abstract
Posttranslational modifications (PTMs) of histone proteins, such as acetylation, methylation, phosphorylation, and ubiquitylation, play essential roles in regulating chromatin dynamics. Combinations of different modifications on the histone proteins, termed 'histone code' in many cases, extend the information potential of the genetic code by regulating DNA at the epigenetic level. Many PTMs occur on non-histone proteins as well as histones, regulating protein-protein interactions, stability, localization, and/or enzymatic activities of proteins involved in diverse cellular processes. Although protein phosphorylation, ubiquitylation, and acetylation have been extensively studied, only a few proteins other than histones have been reported that can be modified by lysine methylation. This review summarizes the current progress on lysine methylation of non-histone proteins, and we propose that lysine methylation, like phosphorylation and acetylation, is a common PTM that regulates proteins in diverse cellular processes.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, 77030, USA
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82
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Shi SP, Qiu JD, Sun XY, Suo SB, Huang SY, Liang RP. PLMLA: prediction of lysine methylation and lysine acetylation by combining multiple features. MOLECULAR BIOSYSTEMS 2012; 8:1520-7. [DOI: 10.1039/c2mb05502c] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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83
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Toyokawa G, Cho HS, Iwai Y, Yoshimatsu M, Takawa M, Hayami S, Maejima K, Shimizu N, Tanaka H, Tsunoda T, Field HI, Kelly JD, Neal DE, Ponder BAJ, Maehara Y, Nakamura Y, Hamamoto R. The histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6. Cancer Prev Res (Phila) 2011; 4:2051-61. [PMID: 21930796 DOI: 10.1158/1940-6207.capr-11-0290] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Histone methyltransferases and demethylases are known to regulate transcription by altering the epigenetic marks on histones, but the pathologic roles of their dysfunction in human diseases, such as cancer, still remain to be elucidated. Herein, we show that the histone demethylase JMJD2B is involved in human carcinogenesis. Quantitative real-time PCR showed notably elevated levels of JMJD2B expression in bladder cancers, compared with corresponding nonneoplastic tissues (P < 0.0001), and elevated protein expression was confirmed by immunohistochemistry. In addition, cDNA microarray analysis revealed transactivation of JMJD2B in lung cancer, and immunohistochemical analysis showed protein overexpression in lung cancer. siRNA-mediated reduction of expression of JMJD2B in bladder and lung cancer cell lines significantly suppressed the proliferation of cancer cells, and suppressing JMJD2B expression lead to a decreased population of cancer cells in S phase, with a concomitant increase of cells in G(1) phase. Furthermore, a clonogenicity assay showed that the demethylase activity of JMJD2B possesses an oncogenic activity. Microarray analysis after knockdown of JMJD2B revealed that JMJD2B could regulate multiple pathways which contribute to carcinogenesis, including the cell-cycle pathway. Of the downstream genes, chromatin immunoprecipitation showed that CDK6 (cyclin-dependent kinase 6), essential in G(1)-S transition, was directly regulated by JMJD2B, via demethylation of histone H3-K9 in its promoter region. Expression levels of JMJD2B and CDK6 were significantly correlated in various types of cell lines. Deregulation of histone demethylation resulting in perturbation of the cell cycle, represents a novel mechanism for human carcinogenesis and JMJD2B is a feasible molecular target for anticancer therapy.
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Affiliation(s)
- Gouji Toyokawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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84
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Duhoux FP, Ameye G, Montano-Almendras CP, Bahloula K, Mozziconacci MJ, Laibe S, Wlodarska I, Michaux L, Talmant P, Richebourg S, Lippert E, Speleman F, Herens C, Struski S, Raynaud S, Auger N, Nadal N, Rack K, Mugneret F, Tigaud I, Lafage M, Taviaux S, Roche-Lestienne C, Latinne D, Libouton JM, Demoulin JB, Poirel HA. PRDM16 (1p36) translocations define a distinct entity of myeloid malignancies with poor prognosis but may also occur in lymphoid malignancies. Br J Haematol 2011; 156:76-88. [DOI: 10.1111/j.1365-2141.2011.08918.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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85
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Ahrens T, Bergner A, Sheppard D, Hafenbradl D. Efficient Hit-Finding Approaches for Histone Methyltransferases. ACTA ACUST UNITED AC 2011; 17:85-98. [DOI: 10.1177/1087057111422823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
For many novel epigenetics targets the chemical ligand space and structural information were limited until recently and are still largely unknown for some targets. Hit-finding campaigns are therefore dependent on large and chemically diverse libraries. In the specific case of the histone methyltransferase G9a, the authors have been able to apply an efficient process of intelligent selection of compounds for primary screening, rather than screening the full diverse deck of 900 000 compounds to identify hit compounds. A number of different virtual screening methods have been applied for the compound selection, and the results have been analyzed in the context of their individual success rates. For the primary screening of 2112 compounds, a FlashPlate assay format and full-length histone H3.1 substrate were employed. Validation of hit compounds was performed using the orthogonal fluorescence lifetime technology. Rated by purity and IC50 value, 18 compounds (0.9% of compound screening deck) were finally considered validated primary G9a hits. The hit-finding approach has led to novel chemotypes being identified, which can facilitate hit-to-lead projects. This study demonstrates the power of virtual screening technologies for novel, therapeutically relevant epigenetics protein targets.
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86
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87
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Morishita M, di Luccio E. Structural insights into the regulation and the recognition of histone marks by the SET domain of NSD1. Biochem Biophys Res Commun 2011; 412:214-9. [PMID: 21806967 DOI: 10.1016/j.bbrc.2011.07.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 07/18/2011] [Indexed: 12/11/2022]
Abstract
The development of epigenetic therapies fuels cancer hope. DNA-methylation inhibitors, histone-deacetylase and histone-methyltransferase (HMTase) inhibitors are being developed as the utilization of epigenetic targets is emerging as an effective and valuable approach to chemotherapy as well as chemoprevention of cancer. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1 that are critical in maintaining the chromatin integrity. A growing number of studies have reported alterations or amplifications of NSD1, NSD2, or NSD3 in numerous carcinogenic events. Reducing NSDs activity through specific lysine-HMTase inhibitors appears promising to help suppressing cancer growth. However, little is known about the NSD pathways and our understanding of the histone lysine-HMTase mechanism is partial. To shed some light on both the recognition and the regulation of epigenetic marks by the SET domain of the NSD family, we investigate the structural mechanisms of the docking of the histone-H4 tail on the SET domain of NSD1. Our finding exposes a key regulatory and recognition mechanism driven by the flexibility of a loop at the interface of the SET and postSET region. Finally, we prospect the special value of this regulatory region for developing specific and selective NSD inhibitors for the epigenetic therapy of cancers.
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Affiliation(s)
- Masayo Morishita
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea
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88
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Richon VM, Johnston D, Sneeringer CJ, Jin L, Majer CR, Elliston K, Jerva LF, Scott MP, Copeland RA. Chemogenetic analysis of human protein methyltransferases. Chem Biol Drug Des 2011; 78:199-210. [PMID: 21564555 DOI: 10.1111/j.1747-0285.2011.01135.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A survey of the human genome was performed to understand the constituency of protein methyltransferases (both protein arginine and lysine methyltransferases) and the relatedness of their catalytic domains. We identified 51 protein lysine methyltransferase proteins based on similarity to the canonical Drosophila Su(var)3-9, enhancer of zeste (E(z)), and trithorax (trx) domain. Disruptor of telomeric silencing-1-like, a known protein lysine methyltransferase, did not fit within the protein lysine methyltransferase family, but did group with the protein arginine methyltransferases, along with 44 other proteins, including the METTL and NOP2/Sun domain family proteins. We show that a representative METTL, METTL11A, demonstrates catalytic activity as a histone methyltransferase. We also solved the co-crystal structures of disruptor of telomeric silencing-1-like with S-adenosylmethionine and S-adenosylhomocysteine bound in its active site. The conformation of both ligands is virtually identical to that found in known protein arginine methyltransferases, METTL and NOP2/Sun domain family proteins and is distinct from that seen in the Drosophila Su(var)3-9, enhancer of zeste (E(z)), and trithorax (trx) domain protein lysine methyltransferases. We have developed biochemical assays for 11 members of the protein methyltransferase target class and have profiled the affinity of three ligands for these enzymes: the common methyl-donating substrate S-adenosylmethionine; the common reaction product S-adenosylhomocysteine; and the natural product sinefungin. The affinity of each of these ligands is mapped onto the family trees of the protein lysine methyltransferases and protein arginine methyltransferases to reveal patterns of ligand recognition by these enzymes.
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Affiliation(s)
- Victoria M Richon
- Epizyme, Inc., 840 Memorial Drive, Cambridge, MA 02139, USA Genstruct Inc., One Alewife Center, Cambridge, MA 02140, USA
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89
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Morishita M, di Luccio E. Cancers and the NSD family of histone lysine methyltransferases. Biochim Biophys Acta Rev Cancer 2011; 1816:158-63. [PMID: 21664949 DOI: 10.1016/j.bbcan.2011.05.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 05/26/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
Abstract
Both genetic and epigenetic alterations are responsible for the stepwise initiation and progression of cancers. Only epigenetic aberrations can be reversible, allowing the malignant cell population to revert to a more benign phenotype. The epigenetic therapy of cancers is emerging as an effective and valuable approach to both the chemotherapy and the chemoprevention of cancer. The utilization of epigenetic targets that include histone methyltransferase (HMTase), Histone deacetylatase, and DNA methyltransferase, are emerging as key therapeutic targets. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, and plays a critical part in chromatin integrity as evidenced by a growing number of conditions linked to the alterations and/or amplification of NSD1, NSD2, and/or NSD3. NSD1, NSD2 and NSD3 are associated with multiple cancers. The amplification of either NSD1 or NSD2 triggers the cellular transformation and thus is key in the early carcinogenesis events. In most cases, reducing the levels of NSD proteins would suppress cancer growth. NSD1 and NSD2 were isolated as genes linked to developmental diseases, such as Sotos syndrome and Wolf-Hirschhorn syndrome, respectively, implying versatile aspects of the NSD proteins. The NSD pathways, however, are not well understood. It is noteworthy that the NSD family is phylogenetically distinct compared to other known lysine-HMTases, Here, we review the current knowledge on NSD1/NSD2/NSD3 in tumorigenesis and prospect their special value for developing novel anticancer drugs.
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Affiliation(s)
- Masayo Morishita
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
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90
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Guo N, Chen R, Li Z, Liu Y, Cheng D, Zhou Q, Zhou J, Lin Q. Hepatitis C virus core upregulates the methylation status of the RASSF1A promoter through regulation of SMYD3 in hilar cholangiocarcinoma cells. Acta Biochim Biophys Sin (Shanghai) 2011; 43:354-61. [PMID: 21450690 DOI: 10.1093/abbs/gmr021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Increasing evidence has been accumulated indicating the important role of epigenetic regulation in tumor genesis. Previously, we observed that the transfection of hepatitis C virus core (HCVc) protein led to malignant transformation in normal biliary cells, and that tumor suppressor gene RASSF1A was downregulated in many hilar cholangiocarcinoma patients by hypermethylation in the promoter region. In the present study, we found SET and MYND domain-containing protein 3 (SMYD3), a novel histone methyltransferase, was overexpressed in cholangiocarcinoma patients especially in those with HCV infection. Transfection of HCVc into hilar cholangiocarcinoma cell lines QBC939 and FRH0201 could upregulate the expression of SMYD3 and promote cell growth, which was consistent with the results of our clinical research. This phenomenon indicated that SMYD3 was related to the epigenetic regulation of cholangiocarcinoma genesis with HCV infection. Overexpression of SMYD3 could inhibit RASSF1A expression, whereas inhibition of SMYD3 by siRNA improved its expression. Methylation-specific polymerase chain reaction (MS-PCR) results showed the methylation status of RASSF1A promoter was regulated by SMYD3. In conclusion, HCVc could upregulate the methylation status of the RASSF1A promoter through regulation of SMYD3, and histone methylation may affect the DNA methylation of downstream gene by an unknown mechanism.
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Affiliation(s)
- Ning Guo
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou 510120, China
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91
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Binda O, LeRoy G, Bua DJ, Garcia BA, Gozani O, Richard S. Trimethylation of histone H3 lysine 4 impairs methylation of histone H3 lysine 9: regulation of lysine methyltransferases by physical interaction with their substrates. Epigenetics 2011; 5:767-75. [PMID: 21124070 DOI: 10.4161/epi.5.8.13278] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin is broadly compartmentalized in two defined states: euchromatin and heterochromatin. Generally, euchromatin is trimethylated on histone H3 lysine 4 (H3K4(me3)) while heterochromatin contains the H3K9(me3) marks. The H3K9(me3) modification is added by lysine methyltransferases (KMTs) such as SETDB1. Herein, we show that SETDB1 interacts with its substrate H3, but only in the absence of the euchromatic mark H3K4(me3). In addition, we show that SETDB1 fails to methylate substrates containing the H3K4(me3) mark. Likewise, the functionally related H3K9 KMTs G9A, GLP, and SUV39H1 also fail to bind and to methylate H3K4(me3) substrates. Accordingly, we provide in vivo evidence that H3K9(me2)-enriched histones are devoid of H3K4(me2/3) and that histones depleted of H3K4(me2/3) have elevated H3K9(me2/3). The correlation between the loss of interaction of these KMTs with H3K4 (me3) and concomitant methylation impairment leads to the postulate that, at least these four KMTs, require stable interaction with their respective substrates for optimal activity. Thus, novel substrates could be discovered via the identification of KMT interacting proteins. Indeed, we find that SETDB1 binds to and methylates a novel substrate, the inhibitor of growth protein ING2, while SUV39H1 binds to and methylates the heterochromatin protein HP1α. Thus, our observations suggest a mechanism of post-translational regulation of lysine methylation and propose a potential mechanism for the segregation of the biologically opposing marks, H3K4(me3) and H3K9(me3). Furthermore, the correlation between H3-KMTs interaction and substrate methylation highlights that the identification of novel KMT substrates may be facilitated by the identification of interaction partners.
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Affiliation(s)
- Olivier Binda
- Lady Davis Institute, Montréal Jewish Hospital, McGill University, Montréal, Québec, Canada.
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92
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Hayami S, Kelly JD, Cho HS, Yoshimatsu M, Unoki M, Tsunoda T, Field HI, Neal DE, Yamaue H, Ponder BAJ, Nakamura Y, Hamamoto R. Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers. Int J Cancer 2011; 128:574-86. [PMID: 20333681 DOI: 10.1002/ijc.25349] [Citation(s) in RCA: 369] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A number of histone demethylases have been identified and biochemically characterized, but the pathological roles of their dysfunction in human disease like cancer have not been well understood. Here, we demonstrate important roles of lysine-specific demethylase 1 (LSD1) in human carcinogenesis. Expression levels of LSD1 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (p < 0.0001). cDNA microarray analysis also revealed its transactivation in lung and colorectal carcinomas. LSD1-specific small interfering RNAs significantly knocked down its expression and resulted in suppression of proliferation of various bladder and lung cancer cell lines. Concordantly, introduction of exogenous LSD1 expression promoted cell cycle progression of human embryonic kidney fibroblast cells. Expression profile analysis showed that LSD1 could affect the expression of genes involved in various chromatin-modifying pathways such as chromatin remodeling at centromere, centromeric heterochromatin formation and chromatin assembly, indicating its essential roles in carcinogenesis through chromatin modification.
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Affiliation(s)
- Shinya Hayami
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
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93
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Binda O, Boyce M, Rush JS, Palaniappan KK, Bertozzi CR, Gozani O. A chemical method for labeling lysine methyltransferase substrates. Chembiochem 2011; 12:330-4. [PMID: 21243721 PMCID: PMC3056122 DOI: 10.1002/cbic.201000433] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Indexed: 01/07/2023]
Abstract
Several protein lysine methyltransferases (PKMTs) modify histones to regulate chromatin-dependent cellular processes, such as transcription, DNA replication and DNA damage repair. PKMTs are likely to have many additional substrates in addition to histones, but relatively few nonhistone substrates have been characterized, and the substrate specificity for many PKMTs has yet to be defined. Thus, new unbiased methods are needed to find PKMT substrates. Here, we describe a chemical biology approach for unbiased, proteome-wide identification of novel PKMT substrates. Our strategy makes use of an alkyne-bearing S-adenosylmethionine (SAM) analogue, which is accepted by the PKMT, SETDB1, as a cofactor, resulting in the enzymatic attachment of a terminal alkyne to its substrate. Such labeled proteins can then be treated with azide-functionalized probes to ligate affinity handles or fluorophores to the PKMT substrates. As a proof-of-concept, we have used SETDB1 to transfer the alkyne moiety from the SAM analogue onto a recombinant histone H3 substrate. We anticipate that this chemical method will find broad use in epigenetics to enable unbiased searches for new PKMT substrates by using recombinant enzymes and unnatural SAM cofactors to label and purify many substrates simultaneously from complex organelle or cell extracts.
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Affiliation(s)
- Olivier Binda
- Department of Biology, Stanford UniversityStanford, CA 94305-5020 (USA), Fax: (+1) 650-725-8309 E-mail:
| | - Michael Boyce
- Department of Chemistry, University of CaliforniaBerkeley, CA 94720 (USA)
| | - Jason S Rush
- Department of Chemistry, University of CaliforniaBerkeley, CA 94720 (USA)
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of CaliforniaBerkeley, CA 94720 (USA)
- Department Molecular and Cellular Biology, University of CaliforniaBerkeley, CA 94720 (USA)
- Howard Hughes Medical Institute, University of CaliforniaBerkeley, CA 94720 (USA)
| | - Or Gozani
- Department of Biology, Stanford UniversityStanford, CA 94305-5020 (USA), Fax: (+1) 650-725-8309 E-mail:
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94
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Krishnan S, Horowitz S, Trievel RC. Structure and function of histone H3 lysine 9 methyltransferases and demethylases. Chembiochem 2011; 12:254-63. [PMID: 21243713 DOI: 10.1002/cbic.201000545] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Indexed: 12/20/2022]
Abstract
Histone lysine methylation is a dynamic chromatin modification that plays key regulatory roles in gene expression and other genomic functions. Methylation of Lys9 in histone H3 (H3K9) is a prominent modification that has been implicated in diverse processes, including transcriptional silencing, heterochromatin formation, and DNA methylation. In this review, we summarize recent advances in understanding the structure and substrate specificity of the H3K9-specific methyltransferases G9A and GLP and explore current efforts to develop inhibitors of these enzymes. In addition, we discuss the structure and specificity of the recently discovered PHF8 family of histone demethylases that target H3K9 as well as other methylation sites in histones H3 and H4. Finally, we conclude by comparing the H3K9 binding modes displayed by these enzymes and examine the relevance of these studies to their biological functions and to structure-based inhibitor design.
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Affiliation(s)
- Swathi Krishnan
- University of Michigan Medical School, Department of Biological Chemistry, Ann Arbor, MI 48109, USA
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95
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Ren X, McHale CM, Skibola CF, Smith AH, Smith MT, Zhang L. An emerging role for epigenetic dysregulation in arsenic toxicity and carcinogenesis. ENVIRONMENTAL HEALTH PERSPECTIVES 2011; 119:11-9. [PMID: 20682481 PMCID: PMC3018488 DOI: 10.1289/ehp.1002114] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/02/2010] [Indexed: 05/08/2023]
Abstract
BACKGROUND Exposure to arsenic, an established human carcinogen, through consumption of highly contaminated drinking water is a worldwide public health concern. Several mechanisms by which arsenical compounds induce tumorigenesis have been proposed, including oxidative stress, genotoxic damage, and chromosomal abnormalities. Recent studies have suggested that epigenetic mechanisms may also mediate toxicity and carcinogenicity resulting from arsenic exposure. OBJECTIVE We examined the evidence supporting the roles of the three major epigenetic mechanisms-DNA methylation, histone modification, and microRNA (miRNA) expression-in arsenic toxicity and, in particular, carcinogenicity. We also investigated future research directions necessary to clarify epigenetic and other mechanisms in humans. DATA SOURCES AND SYNTHESIS We conducted a PubMed search of arsenic exposure and epigenetic modification through April 2010 and summarized the in vitro and in vivo research findings, from both our group and others, on arsenic-associated epigenetic alteration and its potential role in toxicity and carcinogenicity. CONCLUSIONS Arsenic exposure has been shown to alter methylation levels of both global DNA and gene promoters; histone acetylation, methylation, and phosphorylation; and miRNA expression, in studies analyzing mainly a limited number of epigenetic end points. Systematic epigenomic studies in human populations exposed to arsenic or in patients with arsenic-associated cancer have not yet been performed. Such studies would help to elucidate the relationship between arsenic exposure, epigenetic dysregulation, and carcinogenesis and are becoming feasible because of recent technological advancements.
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Affiliation(s)
- Xuefeng Ren
- Division of Environmental Health Sciences, School of Public Health, University of California–Berkeley, Berkeley, California 94720, USA.
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96
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Duncan EM, Allis CD. Errors in erasure: links between histone lysine methylation removal and disease. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:69-90. [PMID: 21141725 DOI: 10.1007/978-3-7643-8989-5_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Many studies have demonstrated that covalent histone modifications are dynamically regulated to cause both chemical and physical changes to the chromatin template. Such changes in the chromatin template lead to biologically significant consequences, including differential gene expression. Histone lysine methylation, in particular, has been shown to correlate with gene expression both positively and negatively, depending on the specific site and degree (i.e., mono-, di-, or tri-) of methylation within the histone sequence. Although genetic alterations in the proteins that establish, or "write," methyl modifications and their effect in various human pathologies have been documented, connections between the misregulation of proteins that remove, or "erase," histone methylation and disease have emerged more recently. Here we discuss three mechanisms through which histone methylation can be removed from the chromatin template. We describe how these "erasure" mechanisms are linked to pathways that are known to be misregulated in diseases, such as cancer. We further describe how errors in the removal of histone methylation can and do lead to human pathologies, both directly and indirectly.
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Affiliation(s)
- Elizabeth M Duncan
- Department of Neurobiology and Anatomy, University of Utah, 20 North 1900 East, Salt Lake City, UT 84132, USA
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97
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Rao RC, Chen DF, Miller JW. An epigenetic approach toward understanding ocular α-herpesvirus pathogenesis and treatment. Int Ophthalmol Clin 2011; 51:117-133. [PMID: 21897145 DOI: 10.1097/iio.0b013e31822d6966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Rajesh C Rao
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114, USA
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98
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Fingerman IM, McDaniel L, Zhang X, Ratzat W, Hassan T, Jiang Z, Cohen RF, Schuler GD. NCBI Epigenomics: a new public resource for exploring epigenomic data sets. Nucleic Acids Res 2011; 39:D908-12. [PMID: 21075792 PMCID: PMC3013719 DOI: 10.1093/nar/gkq1146] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/14/2010] [Accepted: 10/25/2010] [Indexed: 12/21/2022] Open
Abstract
The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics.
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Affiliation(s)
| | | | | | | | | | | | | | - Gregory D. Schuler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
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99
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Dynamics of histone lysine methylation: structures of methyl writers and erasers. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:107-24. [PMID: 21141727 DOI: 10.1007/978-3-7643-8989-5_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In Eukarya, the packaging of DNA into chromatin provides a barrier that allows for regulation of access to the genome. Chromatin is refractory to processes acting on DNA. ATP-dependent chromatin remodeling machines and histone-modifying complexes can overcome this barrier (or strengthen it in silencing processes). Both components of chromatin (DNA and histones) are subject to postsynthetic covalent modifications, including methylation of lysines (the focus of this chapter). These lysine marks are generated by a host of histone lysine methyltransferases (writers) and can be removed by histone lysine demethylases (erasers). Importantly, epigenetic modifications impact chromatin structure directly or can be read by effector regulatory modules. Here, we summarize current knowledge on structural and functional properties of various histone lysine methyltransfereases and demethylases, with emphasis on their importance as druggable targets.
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100
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Sharma SK, Wu Y, Steinbergs N, Crowley ML, Hanson AS, Casero RA, Woster PM. (Bis)urea and (bis)thiourea inhibitors of lysine-specific demethylase 1 as epigenetic modulators. J Med Chem 2010; 53:5197-212. [PMID: 20568780 DOI: 10.1021/jm100217a] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The recently discovered enzyme lysine-specific demethylase 1 (LSD1) plays an important role in the epigenetic control of gene expression, and aberrant gene silencing secondary to LSD1 overexpression is thought to contribute to the development of cancer. We recently reported a series of (bis)guanidines and (bis)biguanides that are potent inhibitors of LSD1 and induce the re-expression of aberrantly silenced tumor suppressor genes in tumor cells in vitro. We now report a series of isosteric ureas and thioureas that are also potent inhibitors of LSD1. These compounds induce increases in methylation at the histone 3 lysine 4 (H3K4) chromatin mark, a specific target of LSD1, in Calu-6 lung carcinoma cells. In addition, these analogues increase cellular levels of secreted frizzle-related protein (SFRP) 2 and transcription factor GATA4. These compounds represent an important new series of epigenetic modulators with the potential for use as antitumor agents.
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Affiliation(s)
- Shiv K Sharma
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, Michigan 48202, USA
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