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Crain AT, Butler MB, Hill CA, Huynh M, McGinty RK, Duronio RJ. Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584710. [PMID: 38559189 PMCID: PMC10980064 DOI: 10.1101/2024.03.12.584710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8 null , H4 K20R/A , and l(3)mbt mutant Drosophila melanogaster . We found that the gene expression profiles of H4 K20A and H4 K20R larvae are markedly different than Set8 null larvae despite similar reductions in H4K20me1. Set8 null mutant cells have a severely disrupted transcriptome and fail to proliferate in vivo , but these phenotypes are not recapitulated by mutation of H4 K20 indicating that the developmental defects of Set8 null animals are largely due to H4K20me1-independent effects on gene expression. Further, the H4K20me1 binding protein L(3)mbt is recruited to the transcription start sites of most genes independently of H4K20me even though genes bound by L(3)mbt have high levels of H4K20me1. Moreover, both Set8 and L(3)mbt bind to purified H4K20R nucleosomes in vitro. We conclude that gene expression changes in Set8 null and H4 K20 mutants cannot be explained by loss of H4K20me1 or L(3)mbt binding to chromatin, and therefore that H4K20me1 does not play a large role in gene expression.
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2
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Li Y, Cheng M, Jin J, Zhang D, Zhang S, Bai Y, Xu J. Interaction of Sp1 and Setd8 promotes vascular smooth muscle cells apoptosis by activating Mark4 in vascular calcification. Aging (Albany NY) 2024; 16:2438-2456. [PMID: 38301049 PMCID: PMC10911351 DOI: 10.18632/aging.205492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
Vascular calcification (VC) is directly related to high mortality in chronic kidney disease (CKD), and cellular apoptosis of vascular smooth muscle cells (VSMCs) is a crucial process in the initiation of VC. Microtubule affinity-regulating kinase 4 (Mark4), known as a serine/threonine protein kinase, can induce cell apoptosis and autophagy by modulating Akt phosphorylation. However, the potential functions and molecular mechanisms of Mark4 in VSMCs apoptosis and calcification need to be further explored. Initially, our data indicated that the mRNA expression of Mark4 was prominently elevated in high phosphorus-stimulated human VSMCs compared with the other members in Marks. Consistently, Mark4 expression was found to be significantly increased in the calcified arteries of both CKD patients and rats. In vitro, silencing Mark4 suppressed apoptosis-specific marker expression by promoting Akt phosphorylation, finally attenuating VSMCs calcification induced by high phosphate. Mechanically, the transcription factor Sp1 was enriched in the Mark4 promoter region and modulated Mark4 transcription. Moreover, SET domain-containing protein 8 (Setd8) was proved to interact with Sp1 and jointly participated in the transcriptional regulation of Mark4. Finally, rescue experiments revealed that Setd8 contributed to VSMCs apoptosis and calcification by modulating Mark4 expression. In conclusion, these findings reveal that Mark4 is transcriptionally activated by Sp1, which is interacted with Setd8, to promote VSMCs calcification through Akt-mediated antiapoptotic effects, suggesting that Mark4 represents a potent and promising therapeutic target for VC in CKD.
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Affiliation(s)
- Yun Li
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Meijuan Cheng
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Jingjing Jin
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Dongxue Zhang
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Shenglei Zhang
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Yaling Bai
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
| | - Jinsheng Xu
- Department of Nephrology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, People’s Republic of China
- Hebei Clinical Research Center for Chronic Kidney Disease, Hebei Key Laboratory of Vascular Calcification in Kidney Disease, Shijiazhuang, People’s Republic of China
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3
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Möller M, Ridenour JB, Wright DF, Martin FA, Freitag M. H4K20me3 is important for Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin in a fungal pathogen. PLoS Genet 2023; 19:e1010945. [PMID: 37747878 PMCID: PMC10553808 DOI: 10.1371/journal.pgen.1010945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/05/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023] Open
Abstract
Facultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungus Zymoseptoria tritici, a globally important pathogen of wheat. Deletion of kmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Derepression in the absence of H4K20me3 not only affected known genes but also a large number of novel, previously undetected transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation in kmt5 deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with H4K20L, M or Q mutations in the single histone H4 gene of Z. tritici recapitulated these chromatin changes, suggesting that H4K20me3 is important for Ash1-mediated H3K36me3. The ∆kmt5 mutants we obtained were more sensitive to genotoxic stressors than wild type and both, ∆kmt5 and ∆ash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into an unsuspected mechanism involved in the assembly and maintenance of facultative heterochromatin.
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Affiliation(s)
- Mareike Möller
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - John B. Ridenour
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Devin F. Wright
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Faith A. Martin
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
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4
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Kukita A, Sone K, Kaneko S, Kawakami E, Oki S, Kojima M, Wada M, Toyohara Y, Takahashi Y, Inoue F, Tanimoto S, Taguchi A, Fukuda T, Miyamoto Y, Tanikawa M, Mori-Uchino M, Tsuruga T, Iriyama T, Matsumoto Y, Nagasaka K, Wada-Hiraike O, Oda K, Hamamoto R, Osuga Y. The Histone Methyltransferase SETD8 Regulates the Expression of Tumor Suppressor Genes via H4K20 Methylation and the p53 Signaling Pathway in Endometrial Cancer Cells. Cancers (Basel) 2022; 14:5367. [PMID: 36358786 PMCID: PMC9655767 DOI: 10.3390/cancers14215367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 08/01/2023] Open
Abstract
The histone methyltransferase SET domain-containing protein 8 (SETD8), which methylates histone H4 lysine 20 (H4K20) and non-histone proteins such as p53, plays key roles in human carcinogenesis. Our aim was to determine the involvement of SETD8 in endometrial cancer and its therapeutic potential and identify the downstream genes regulated by SETD8 via H4K20 methylation and the p53 signaling pathway. We examined the expression profile of SETD8 and evaluated whether SETD8 plays a critical role in the proliferation of endometrial cancer cells using small interfering RNAs (siRNAs). We identified the prognostically important genes regulated by SETD8 via H4K20 methylation and p53 signaling using chromatin immunoprecipitation sequencing, RNA sequencing, and machine learning. We confirmed that SETD8 expression was elevated in endometrial cancer tissues. Our in vitro results suggest that the suppression of SETD8 using siRNA or a selective inhibitor attenuated cell proliferation and promoted the apoptosis of endometrial cancer cells. In these cells, SETD8 regulates genes via H4K20 methylation and the p53 signaling pathway. We also identified the prognostically important genes related to apoptosis, such as those encoding KIAA1324 and TP73, in endometrial cancer. SETD8 is an important gene for carcinogenesis and progression of endometrial cancer via H4K20 methylation.
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Affiliation(s)
- Asako Kukita
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Eiryo Kawakami
- Graduate School of Medicine, Chiba University, Chiba 263-8522, Japan
| | - Shinya Oki
- National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan
| | - Machiko Kojima
- Tazuke Kofukai, Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
| | - Miku Wada
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yusuke Toyohara
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yu Takahashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Futaba Inoue
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Saki Tanimoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ayumi Taguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Tomohiko Fukuda
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yuichiro Miyamoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Mayuyo Mori-Uchino
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Tetsushi Tsuruga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takayuki Iriyama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yoko Matsumoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kazunori Nagasaka
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Tokyo 173-0003, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Katsutoshi Oda
- Division of Integrated Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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5
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Crain AT, Klusza S, Armstrong RL, Santa Rosa P, Temple BRS, Strahl BD, McKay DJ, Matera AG, Duronio RJ. Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. Genetics 2022; 221:iyac054. [PMID: 35404465 PMCID: PMC9157153 DOI: 10.1093/genetics/iyac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Mono-methylation of histone H4 lysine 20 (H4K20me1) is catalyzed by Set8/KMT5A and regulates numerous aspects of genome organization and function. Loss-of-function mutations in Drosophila melanogaster Set8 or mammalian KMT5A prevent H4K20me1 and disrupt development. Set8/KMT5A also has non-histone substrates, making it difficult to determine which developmental functions of Set8/KMT5A are attributable to H4K20me1 and which to other substrates or to non-catalytic roles. Here, we show that human KMT5A can functionally substitute for Set8 during Drosophila development and that the catalytic SET domains of the two enzymes are fully interchangeable. We also uncovered a role in eye development for the N-terminal domain of Set8 that cannot be complemented by human KMT5A. Whereas Set820/20 null mutants are inviable, we found that an R634G mutation in Set8 predicted from in vitro experiments to ablate catalytic activity resulted in viable adults. Additionally, Set8(R634G) mutants retain significant, albeit reduced, H4K20me1, indicating that the R634G mutation does not eliminate catalytic activity in vivo and is functionally hypomorphic rather than null. Flies engineered to express only unmodifiable H4 histones (H4K20A) can also complete development, but are phenotypically distinct from H4K20R, Set820/20 null, and Set8R634G mutants. Taken together, our results demonstrate functional conservation of KMT5A and Set8 enzymes, as well as distinct roles for Set8 and H4K20me1 in Drosophila development.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Stephen Klusza
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
| | | | - Brenda R S Temple
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599 USA
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6
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Shoaib M, Chen Q, Shi X, Nair N, Prasanna C, Yang R, Walter D, Frederiksen KS, Einarsson H, Svensson JP, Liu CF, Ekwall K, Lerdrup M, Nordenskiöld L, Sørensen CS. Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. Nat Commun 2021; 12:4800. [PMID: 34417450 PMCID: PMC8379281 DOI: 10.1038/s41467-021-25051-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
Histone lysine methylations have primarily been linked to selective recruitment of reader or effector proteins that subsequently modify chromatin regions and mediate genome functions. Here, we describe a divergent role for histone H4 lysine 20 mono-methylation (H4K20me1) and demonstrate that it directly facilitates chromatin openness and accessibility by disrupting chromatin folding. Thus, accumulation of H4K20me1 demarcates highly accessible chromatin at genes, and this is maintained throughout the cell cycle. In vitro, H4K20me1-containing nucleosomal arrays with nucleosome repeat lengths (NRL) of 187 and 197 are less compact than unmethylated (H4K20me0) or trimethylated (H4K20me3) arrays. Concordantly, and in contrast to trimethylated and unmethylated tails, solid-state NMR data shows that H4K20 mono-methylation changes the H4 conformational state and leads to more dynamic histone H4-tails. Notably, the increased chromatin accessibility mediated by H4K20me1 facilitates gene expression, particularly of housekeeping genes. Altogether, we show how the methylation state of a single histone H4 residue operates as a focal point in chromatin structure control. While H4K20me1 directly promotes chromatin openness at highly transcribed genes, it also serves as a stepping-stone for H4K20me3-dependent chromatin compaction. The effect of histone H4 lysine 20 methylation (H4K20me) on chromatin accessibility are not well established. Here the authors show how H4K20 methylation regulates chromatin structure and accessibility to ensure precise transcriptional outputs through the cell cycle using genome-wide approaches, in vitro biophysical assays, and NMR.
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Affiliation(s)
- Muhammad Shoaib
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nidhi Nair
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Wilmar International Limited, Jurong Island, Singapore
| | - David Walter
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Hjorleifur Einarsson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Mads Lerdrup
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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7
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Histone lysine methyltransferase SET8 is a novel therapeutic target for cancer treatment. Drug Discov Today 2021; 26:2423-2430. [PMID: 34022460 DOI: 10.1016/j.drudis.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 12/24/2022]
Abstract
SET8 is the only lysine methyltransferase that can specifically monomethylate the histone H4K20. SET8-mediated protein modifications are largely involved in the regulation of cell cycle, DNA repair, gene transcription, cell apoptosis, and other vital physiological processes. The aberrant expression of SET8 is closely linked to the proliferation, invasion, metastasis, and prognosis of a variety of cancers. As a consequence, targeting SET8 could be an appealing strategy for cancer therapy. In this article, we introduce the molecular structure of SET8, followed by summarizing its roles in various biological pathways. Crucially, we highlight the potential functions of SET8 in tumors, as well as progress in the development of SET inhibitors for cancer treatment.
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8
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Huang J, Gujar MR, Deng Q, Y Chia S, Li S, Tan P, Sung W, Wang H. Histone lysine methyltransferase Pr-set7/SETD8 promotes neural stem cell reactivation. EMBO Rep 2021; 22:e50994. [PMID: 33565211 PMCID: PMC8024890 DOI: 10.15252/embr.202050994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 01/07/2023] Open
Abstract
The ability of neural stem cells (NSCs) to switch between quiescence and proliferation is crucial for brain development and homeostasis. Increasing evidence suggests that variants of histone lysine methyltransferases including KMT5A are associated with neurodevelopmental disorders. However, the function of KMT5A/Pr-set7/SETD8 in the central nervous system is not well established. Here, we show that Drosophila Pr-Set7 is a novel regulator of NSC reactivation. Loss of function of pr-set7 causes a delay in NSC reactivation and loss of H4K20 monomethylation in the brain. Through NSC-specific in vivo profiling, we demonstrate that Pr-set7 binds to the promoter region of cyclin-dependent kinase 1 (cdk1) and Wnt pathway transcriptional co-activator earthbound1/jerky (ebd1). Further validation indicates that Pr-set7 is required for the expression of cdk1 and ebd1 in the brain. Similar to Pr-set7, Cdk1 and Ebd1 promote NSC reactivation. Finally, overexpression of Cdk1 and Ebd1 significantly suppressed NSC reactivation defects observed in pr-set7-depleted brains. Therefore, Pr-set7 promotes NSC reactivation by regulating Wnt signaling and cell cycle progression. Our findings may contribute to the understanding of mammalian KMT5A/PR-SET7/SETD8 during brain development.
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Affiliation(s)
- Jiawen Huang
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Mahekta R Gujar
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Qiannan Deng
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Sook Y Chia
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
- Present address:
National Neuroscience InstituteSingaporeSingapore
| | - Song Li
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
| | - Patrick Tan
- Genome Institute of SingaporeSingaporeSingapore
- Cancer & Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingaporeSingapore
- Cellular and Molecular ResearchNational Cancer CentreSingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
| | - Wing‐Kin Sung
- Genome Institute of SingaporeSingaporeSingapore
- Department of Computer ScienceNational University of SingaporeSingaporeSingapore
| | - Hongyan Wang
- Neuroscience & Behavioral Disorders ProgrammeDuke‐NUS Medical SchoolSingaporeSingapore
- Department of PhysiologyYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Integrative Sciences and Engineering ProgrammeNational University of SingaporeSingaporeSingapore
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9
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Corvalan AZ, Coller HA. Methylation of histone 4's lysine 20: a critical analysis of the state of the field. Physiol Genomics 2020; 53:22-32. [PMID: 33197229 DOI: 10.1152/physiolgenomics.00128.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin is a highly dynamic structure whose plasticity is achieved through multiple processes including the posttranslational modification of histone tails. Histone modifications function through the recruitment of nonhistone proteins to chromatin and thus have the potential to influence many fundamental biological processes. Here, we focus on the function and regulation of lysine 20 of histone H4 (H4K20) methylation in multiple biological processes including DNA repair, cell cycle regulation, and DNA replication. The purpose of this review is to highlight recent studies that elucidate the functions associated with each of the methylation states of H4K20, their modifying enzymes, and their protein readers. Based on our current knowledge of H4K20 methylation, we critically analyze the data supporting these functions and outline questions for future research.
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Affiliation(s)
- Adriana Z Corvalan
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, California
| | - Hilary A Coller
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, California
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10
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Mori L, Valente ST. Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:E529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The "block-and-lock" approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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Affiliation(s)
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA;
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11
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Niu C, Guo J, Shen X, Ma S, Xia M, Xia J, Zheng Y. Meiotic gatekeeper STRA8 regulates cell cycle by interacting with SETD8 during spermatogenesis. J Cell Mol Med 2020; 24:4194-4211. [PMID: 32090428 PMCID: PMC7171306 DOI: 10.1111/jcmm.15080] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 12/11/2022] Open
Abstract
STRA8 (Stimulated By Retinoic Acid Gene 8) is a retinoic acid (RA) induced gene that plays vital roles in spermatogonial proliferation, differentiation and meiosis. The SETD8 and STRA8 protein interaction was discovered using the yeast two-hybrid technique using a mouse spermatogonial stem cell (SSC) cDNA library. The interaction of these two proteins was confirmed using co-immunoprecipitation and identification of key domains governing the protein: protein complex. STRA8 and SETD8 showed a mutual transcriptional regulation pattern that provided evidence that SETD8 negatively regulated transcriptional activity of the STRA8 promoter. The SETD8 protein directly bound to the proximal promoter of the STRA8 gene. STRA8 increased the transcriptional activity of SETD8 promoter in a dose-dependent manner. For the first time, we have discovered that STRA8 and SETD8 display a cell cycle-dependent expression pattern in germline cells. Expression levels of SETD8 and H4K20me1 in S phase of STRA8 overexpression GC1 cells were different from that previously observed in tumour cell lines. In wild-type mice testis, SETD8, H4K20me1 and PCNA co-localized with STRA8 in spermatogonia. Further, our studies quantitated abnormal expression levels of cell cycle and ubiquitination-related factors in STRA8 dynamic models. STRA8 and SETD8 may regulate spermatogenesis via Cdl4-Clu4A-Ddb1 ubiquitinated degradation axis in a PCNA-dependent manner.
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Affiliation(s)
- Changmin Niu
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
| | - Jiaqian Guo
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
| | - Xueyi Shen
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
| | - Shikun Ma
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
| | - Mengmeng Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
| | - Jing Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
| | - Ying Zheng
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou, China
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12
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Kim JE. Bookmarking by histone methylation ensures chromosomal integrity during mitosis. Arch Pharm Res 2019; 42:466-480. [PMID: 31020544 DOI: 10.1007/s12272-019-01156-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022]
Abstract
The cell cycle is an orchestrated process that replicates DNA and transmits genetic information to daughter cells. Cell cycle progression is governed by diverse histone modifications that control gene transcription in a timely fashion. Histone modifications also regulate cell cycle progression by marking specific chromatic regions. While many reviews have covered histone phosphorylation and acetylation as regulators of the cell cycle, little attention has been paid to the roles of histone methylation in the faithful progression of mitosis. Indeed, specific histone methylations occurring before, during, or after mitosis affect kinetochore assembly and chromosome condensation and segregation. In addition to timing, histone methylations specify the chromatin regions such as chromosome arms, pericentromere, and centromere. Therefore, spatiotemporal programming of histone methylations ensures epigenetic inheritance through mitosis. This review mainly discusses histone methylations and their relevance to mitotic progression.
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Affiliation(s)
- Ja-Eun Kim
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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13
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Chen X, Ding X, Wu Q, Qi J, Zhu M, Miao C. Monomethyltransferase SET8 facilitates hepatocellular carcinoma growth by enhancing aerobic glycolysis. Cell Death Dis 2019; 10:312. [PMID: 30952833 PMCID: PMC6450876 DOI: 10.1038/s41419-019-1541-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/21/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most aggressive cancers worldwide. Despite such a public health importance, efficient therapeutic agents are still lacking for this malignancy. Most tumor cells use aerobic glycolysis to sustain anabolic growth, including HCC, and the preference of glycolysis often leads to a close association with poorer clinical outcomes. The histone methyltransferase SET8 plays crucial roles in controlling cell-cycle progression, transcription regulation, and tumorigenesis. However, it remains largely undefined whether SET8 affects the glucose metabolism in HCC. Here, we report that upregulation of SET8 is positively correlated with a poor survival rate in HCC patients. Both in vitro and in vivo studies revealed that SET8 deficiency conferred an impaired glucose metabolism phenotype and thus inhibited the progression of HCC tumors. By contrast, SET8 overexpression aggravated the glycolytic alterations and tumor progression. Mechanistically, SET8 directly binds to and inactivates KLF4, resulting in suppression of its downstream SIRT4. We also provided further evidence that mutations in SET8 failed to restrain the transactivation of SIRT4 by KLF4. Our data collectively uncover a novel mechanism of SET8 in mediating glycolytic metabolism in HCC cells and may provide a basis for targeting SET8 as a therapeutic strategy in HCC.
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Affiliation(s)
- Xiangyuan Chen
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, shanghai, 200032, China
| | - Xiaowei Ding
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, shanghai, 200032, China
| | - Qichao Wu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, shanghai, 200032, China
| | - Jie Qi
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, shanghai, 200032, China
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, shanghai, 200032, China.
| | - Changhong Miao
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, shanghai, 200032, China.
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14
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Lin Z, Jia H, Hong L, Zheng Y, Shao W, Ren X, Zhu W, Lu L, Lu M, Zhang J, Chen J. Prognostic impact of SET domain-containing protein 8 and protein arginine methyltransferase 5 in patients with hepatocellular carcinoma following curative resection. Oncol Lett 2018; 16:3665-3673. [PMID: 30127976 PMCID: PMC6096198 DOI: 10.3892/ol.2018.9083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Histone methyltransferases are important determinants of the initiation and progression of hepatocellular carcinoma (HCC) and represent promising therapeutic targets. However, whether the expression profile of multiple histone methyltransferases represents a poorer prognosis is entirely unknown. The aim of the present study was to investigate the association between histone methylation and HCC phenotype, and the prognostic value of combining expression levels of SET domain-containing protein 8 (SET8) with protein arginine methyltransferase 5 (PRMT5) in patients with HCC following curative resection. The retrospective study included 195 consecutive patients who had undergone hepatectomy for HCC. Immunohistochemical staining for SET8 and PRMT5 was performed on paraffin-embedded tumor tissue microarrays. Expression was analyzed for correlations with clinicopathological features, marker co-expression and patients' survival by univariate and multivariate analyses. Positive SET8 expression was noted in 104 patients (53.3%), and was associated with PRMT5 expression (n=106, 54.4%, P<0.05). Immunohistochemical analysis demonstrated that high expression of SET8 and PRMT5 was significantly associated with poor overall survival (OS, P<0.001) and time to recurrence (TTR, P<0.001). Multivariate Cox analysis revealed that SET8 and PRMT5, along with vascular invasion, tumor size and tumor number, were independent prognostic factors for OS and TTR. The combination of SET8 and PRMT5 demonstrated an improved capacity to predict patient mortality and disease recurrence (P=0.002 and P=0.004, respectively), particularly for the prediction of early recurrence (P<0.001). In conclusion, high expression of SET8 combined with PRMT5 was associated with a high rate of recurrence and poor survival in patients with HCC. The independent pattern of histone methylation represents a novel insight into tumor progression and therapeutic targets for HCC.
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Affiliation(s)
- Zhifei Lin
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Huliang Jia
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Liang Hong
- Department of Infectious Diseases, Ruian People's Hospital, Wenzhou, Zhejiang 325200, P.R. China
| | - Yahui Zheng
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Weiqin Shao
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xudong Ren
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Wenwei Zhu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Lu Lu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Ming Lu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jubo Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jinhong Chen
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
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15
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Nikolaou KC, Moulos P, Harokopos V, Chalepakis G, Talianidis I. Kmt5a Controls Hepatic Metabolic Pathways by Facilitating RNA Pol II Release from Promoter-Proximal Regions. Cell Rep 2018; 20:909-922. [PMID: 28746875 PMCID: PMC5542855 DOI: 10.1016/j.celrep.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/23/2017] [Accepted: 06/30/2017] [Indexed: 01/02/2023] Open
Abstract
H4K20 monomethylation maintains genome integrity by regulating proper mitotic condensation, DNA damage response, and replication licensing. Here, we show that, in non-dividing hepatic cells, H4K20Me1 is specifically enriched in active gene bodies and dynamically regulated by the antagonistic action of Kmt5a methylase and Kdm7b demethylase. In liver-specific Kmt5a-deficient mice, reduced levels of H4K20Me1 correlated with reduced RNA Pol II release from promoter-proximal regions. Genes regulating glucose and fatty acid metabolism were most sensitive to impairment of RNA Pol II release. Downregulation of glycolytic genes resulted in an energy starvation condition partially compensated by AMP-activated protein kinase (AMPK) activation and increased mitochondrial activity. This metabolic reprogramming generated a highly sensitized state that, upon different metabolic stress conditions, quickly aggravated into a senescent phenotype due to ROS overproduction-mediated oxidative DNA damage. The results illustrate how defects in the general process of RNA Pol II transition into a productive elongation phase can trigger specific metabolic changes and genome instability. H4K20Me1 is dynamically deposited in the gene bodies of active genes Kmt5a regulates RNA Pol II release from promoter-proximal pause sites Kmt5a regulates metabolic gene transcription The transcription regulatory function of Kmt5a is important for genome integrity
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Affiliation(s)
- Kostas C Nikolaou
- Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - Panagiotis Moulos
- Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - Vangelis Harokopos
- Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - George Chalepakis
- Department of Biology, University of Crete, 71110 Herakleion, Crete, Greece
| | - Iannis Talianidis
- Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece; Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece.
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16
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Liu B, Zhang X, Song F, Liu Q, Dai H, Zheng H, Cui P, Zhang L, Zhang W, Chen K. A functional single nucleotide polymorphism of SET8 is prognostic for breast cancer. Oncotarget 2018; 7:34277-87. [PMID: 27144429 PMCID: PMC5085155 DOI: 10.18632/oncotarget.9099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/10/2016] [Indexed: 01/28/2023] Open
Abstract
A single-nucleotide polymorphism (SNP) locus rs16917496 (T > C) within the 3′-untranslated region (3′-UTR) of SET8 was associated with susceptibility in several malignancies including breast cancer. To further elucidate the prognostic relevance of this SNP in breast cancer, we conducted a clinical study as well as SET8 expression analysis in a cohort of 1,190 breast cancer patients. We demonstrated the expression levels of SET8 in TT genotype were higher than in CC genotypes, and high levels of SET8 were associated with poor survival. SET8 expression was significantly higher in breast tumor tissue than in paired adjacent normal tissue. In addition, survival analysis in 315 patients showed SNP rs16917496 was an independent prognostic factor of breast cancer outcome with TT genotype associated with poor survival compared with CC/CT genotypes. Thus, this SNP may serve as a genetic prognostic factor and a treatment target for breast cancer. Future studies are warranted.
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Affiliation(s)
- Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Xining Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Qun Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.,Department of Neurosurgery, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Ping Cui
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Lina Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Wei Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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17
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Tanaka H, Takebayashi SI, Sakamoto A, Igata T, Nakatsu Y, Saitoh N, Hino S, Nakao M. The SETD8/PR-Set7 Methyltransferase Functions as a Barrier to Prevent Senescence-Associated Metabolic Remodeling. Cell Rep 2017; 18:2148-2161. [PMID: 28249161 DOI: 10.1016/j.celrep.2017.02.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/29/2016] [Accepted: 02/06/2017] [Indexed: 01/01/2023] Open
Abstract
Cellular senescence is an irreversible growth arrest that contributes to development, tumor suppression, and age-related conditions. Senescent cells show active metabolism compared with proliferating cells, but the underlying mechanisms remain unclear. Here we show that the SETD8/PR-Set7 methyltransferase, which catalyzes mono-methylation of histone H4 at lysine 20 (H4K20me1), suppresses nucleolar and mitochondrial activities to prevent cellular senescence. SETD8 protein was selectively downregulated in both oncogene-induced and replicative senescence. Inhibition of SETD8 alone was sufficient to trigger senescence. Under these states, the expression of genes encoding ribosomal proteins (RPs) and ribosomal RNAs as well as the cyclin-dependent kinase (CDK) inhibitor p16INK4A was increased, with a corresponding reduction of H4K20me1 at each locus. As a result, the loss of SETD8 concurrently stimulated nucleolar function and retinoblastoma protein-mediated mitochondrial metabolism. In conclusion, our data demonstrate that SETD8 acts as a barrier to prevent cellular senescence through chromatin-mediated regulation of senescence-associated metabolic remodeling.
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Affiliation(s)
- Hiroshi Tanaka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shin-Ichiro Takebayashi
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Akihisa Sakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Tomoka Igata
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yuko Nakatsu
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Noriko Saitoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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18
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Narouie B, Ziaee SAM, Basiri A, Hashemi M. Functional polymorphism at the miR-502-binding site in the 3' untranslated region of the SETD8 gene increased the risk of prostate cancer in a sample of Iranian population. Gene 2017; 626:354-357. [PMID: 28578017 DOI: 10.1016/j.gene.2017.05.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/20/2017] [Accepted: 05/31/2017] [Indexed: 12/30/2022]
Abstract
MicroRNAs (miRNAs), a class of non-coding RNAs, bind to the 3' untranslated regions (3'-UTRs) of target mRNAs and regulate gene expression. Genetic variations in miRNA binding domains influence the susceptibility to several diseases such as cancer. Several studies investigated the impact of single-nucleotide polymorphism (SNP) rs16917496 T>C within the 3'-UTR of SETD8 on cancer susceptibility, but the results were controversial. In addition, no study has been conducted to inspect the impact of this SNP in prostate cancer (PCa). Thus, the present study aimed to find out the possible association between rs16917496 polymorphism at the 3'UTR of SETD8 and PCa risk. This case-control study was done on 169 patients with pathologically confirmed PCa and 182 benign prostatic hyperplasia (BPH). Genotyping was done using PCR-RFLP method. The findings revealed that rs16917496 variant significantly increased the risk of PCa in codominant (OR=2.54, 95%CI=1.50-4.30, p<0.001, TC VS TT and OR=3.03, 95%CI=1.63-5.66, p<0.001, CC vs TT), dominant (OR=2.86, 95%CI=1.62-4.43, p<0.001, p<0.001). The C allele significantly increased the risk of PCa (OR=1.72, 95%CI=1.28-2.33, p<0.001) compared to T allele. In conclusion, the findings indicated that rs16917496 polymorphism may be a risk for predisposition to PCa in an Iranian population. Further studies with larger sample sizes and different ethnicities are required to confirm our findings.
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Affiliation(s)
- Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran 198396-3113, Iran
| | - Seyed Amir Mohsen Ziaee
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran 198396-3113, Iran
| | - Abbas Basiri
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran 198396-3113, Iran
| | - Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran; Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.
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19
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Luan X, Wang Y. Long non-coding RNA XLOC_006390 promotes cervical cancer proliferation and metastasis through the regulation of SET domain containing 8. Oncol Rep 2017; 38:159-166. [PMID: 28534991 DOI: 10.3892/or.2017.5663] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/24/2016] [Indexed: 11/06/2022] Open
Abstract
The long non-coding RNA (lncRNA) XLOC_006390 is increased in various human cancer tissues and it plays important roles in cell growth and migration. However, the role of lncRNA XLOC_006390 in the progression and metastasis of cervical cancer has not been evaluated and remains unclear. In the present study, we hypothesized that lncRNA XLOC_006390 is also increased in cervical cancer, and upregulation of lncRNA XLOC_006390 contributes to cervical cancer metastasis. The expression of lncRNA XLOC_006390 in cervical cancer tissues and cell lines was analyzed using quantitative reverse-transcription-polymerase chain reaction (qRT-PCR). RNA interference approach and an overexpression system were used to investigate the cellular functions of XLOC_006390 and SET domain containing 8 (SET8). Cell Counting Kit-8 (CCK-8) assay was performed to detect cell proliferation. Cell migration and invasion abilities were evaluated by Transwell assays. Western blotting and immunofluorescence were performed to detect SET8 protein expression. The results revealed that XLOC_006390 was increased in cervical cancer tissues. Patients with high XLOC_006390 expression were associated with FIGO stages III and IV (P=0.0170), lymphatic metastasis (P=0.0078) and distant metastasis (P=0.0025). Furthermore, SET8 was also increased in cervical cancer tissues and its expression was positively associated with XLOC_006390, and XLOC_006390 regulated SET8 expression. In addition, knockdown or overexpression of XLOC_006390 and SET8 expression suppressed or promoted cervical cancer cell proliferation, migration and invasion in vitro, respectively. In conclusion, our data suggest that lncRNA XLOC_006390 promotes cervical cancer cell growth and metastasis through the regulation of SET8, at least partly, which indicate the critical roles of XLOC_006390 and SET8 in cervical cancer progression and metastasis.
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Affiliation(s)
- Xiaotian Luan
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yankui Wang
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
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20
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SUV4-20 activity in the preimplantation mouse embryo controls timely replication. Genes Dev 2016; 30:2513-2526. [PMID: 27920088 PMCID: PMC5159666 DOI: 10.1101/gad.288969.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/07/2016] [Indexed: 11/25/2022]
Abstract
Eid et al. show that ectopic expression of Suv4-20h2 leads to sustained levels of H4K20me3, developmental arrest, and defects in S-phase progression. The developmental phenotype can be partially overcome through inhibition of the ATR pathway, suggesting that the main function for the remodeling of H4K20me3 after fertilization is to allow the timely and coordinated progression of replication. Extensive chromatin remodeling after fertilization is thought to take place to allow a new developmental program to start. This includes dynamic changes in histone methylation and, in particular, the remodeling of constitutive heterochromatic marks such as histone H4 Lys20 trimethylation (H4K20me3). While the essential function of H4K20me1 in preimplantation mouse embryos is well established, the role of the additional H4K20 methylation states through the action of the SUV4-20 methyltransferases has not been addressed. Here we show that Suv4-20h1/h2 are mostly absent in mouse embryos before implantation, underscoring a rapid decrease of H4K20me3 from the two-cell stage onward. We addressed the functional significance of this remodeling by introducing Suv4-20h1 and Suv4-20h2 in early embryos. Ectopic expression of Suv4-20h2 leads to sustained levels of H4K20me3, developmental arrest, and defects in S-phase progression. The developmental phenotype can be partially overcome through inhibition of the ATR pathway, suggesting that the main function for the remodeling of H4K20me3 after fertilization is to allow the timely and coordinated progression of replication. This is in contrast to the replication program in somatic cells, where H4K20me3 has been shown to promote replication origin licensing, and anticipates a different regulation of replication during this early developmental time window.
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Milite C, Feoli A, Viviano M, Rescigno D, Cianciulli A, Balzano AL, Mai A, Castellano S, Sbardella G. The emerging role of lysine methyltransferase SETD8 in human diseases. Clin Epigenetics 2016; 8:102. [PMID: 27688818 PMCID: PMC5034662 DOI: 10.1186/s13148-016-0268-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/14/2016] [Indexed: 01/07/2023] Open
Abstract
SETD8/SET8/Pr-SET7/KMT5A is the only known lysine methyltransferase (KMT) that monomethylates lysine 20 of histone H4 (H4K20) in vivo. Lysine residues of non-histone proteins including proliferating cell nuclear antigen (PCNA) and p53 are also monomethylated. As a consequence, the methyltransferase activity of the enzyme is implicated in many essential cellular processes including DNA replication, DNA damage response, transcription modulation, and cell cycle regulation. This review aims to provide an overview of the roles of SETD8 in physiological and pathological pathways and to discuss the progress made to date in inhibiting the activity of SETD8 by small molecules, with an emphasis on their discovery, selectivity over other methyltransferases and cellular activity.
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Affiliation(s)
- Ciro Milite
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Alessandra Feoli
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Monica Viviano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Donatella Rescigno
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Agostino Cianciulli
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Amodio Luca Balzano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Programma di Dottorato di Ricerca in Scienze del Farmaco, Università degli studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
| | - Antonello Mai
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, I-00185 Rome, Italy
| | - Sabrina Castellano
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Dipartimento di Medicina e Chirurgia, Università degli Studi di Salerno, Via Salvador Allende, Baronissi, I-84081 Salerno, Italy
| | - Gianluca Sbardella
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy ; Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, Fisciano, I-84084 Salerno, Italy
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Käser-Pébernard S, Pfefferli C, Aschinger C, Wicky C. Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development. Epigenetics Chromatin 2016; 9:39. [PMID: 27651832 PMCID: PMC5024519 DOI: 10.1186/s13072-016-0091-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/06/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The nucleosome remodeling and deacetylase complex promotes cell fate decisions throughout embryonic development. Its core enzymatic subunit, the SNF2-like ATPase and Helicase Mi2, is well conserved throughout the eukaryotic kingdom and can be found in multiple and highly homologous copies in all vertebrates and some invertebrates. However, the reasons for such duplications and their implications for embryonic development are unknown. RESULTS Here we studied the two C. elegans Mi2 homologues, LET-418 and CHD-3, which displayed redundant activities during early embryonic development. At the transcriptional level, these two Mi2 homologues redundantly repressed the expression of a large gene population. We found that LET-418 physically accumulated at TSS-proximal regions on transcriptionally active genomic targets involved in growth and development. Moreover, LET-418 acted redundantly with CHD-3 to block H3K4me3 deposition at these genes. Our study also revealed that LET-418 was partially responsible for recruiting Polycomb to chromatin and for promoting H3K27me3 deposition. Surprisingly, CHD-3 displayed opposite activities on Polycomb, as it was capable of moderating its LET-418-dependent recruitment and restricted the amount of H3K27me3 on the studied target genes. CONCLUSION Although closely homologous, LET-418 and CHD-3 showed both redundant and opposite functions in modulating the chromatin environment at developmental target genes. We identified the interplay between LET-418 and CHD-3 to finely tune the levels of histone marks at developmental target genes. More than just repressors, Mi2-containing complexes appear as subtle modulators of gene expression throughout development. The study of such molecular variations in vertebrate Mi2 counterparts might provide crucial insights to our understanding of the epigenetic control of early development.
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Affiliation(s)
- Stéphanie Käser-Pébernard
- Biology Department, Zoology Institute, University of Fribourg, Ch. du musée 10, 1700 Fribourg, Switzerland ; Biology Department, Biochemistry Institute, University of Fribourg, Ch. du musée 10, 1700 Fribourg, Switzerland
| | - Catherine Pfefferli
- Biology Department, Zoology Institute, University of Fribourg, Ch. du musée 10, 1700 Fribourg, Switzerland
| | - Caroline Aschinger
- Biology Department, Zoology Institute, University of Fribourg, Ch. du musée 10, 1700 Fribourg, Switzerland
| | - Chantal Wicky
- Biology Department, Zoology Institute, University of Fribourg, Ch. du musée 10, 1700 Fribourg, Switzerland
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van Nuland R, Gozani O. Histone H4 Lysine 20 (H4K20) Methylation, Expanding the Signaling Potential of the Proteome One Methyl Moiety at a Time. Mol Cell Proteomics 2015; 15:755-64. [PMID: 26598646 DOI: 10.1074/mcp.r115.054742] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Indexed: 12/13/2022] Open
Abstract
Covalent post-translational modifications (PTMs) of proteins can regulate the structural and functional state of a protein in the absence of primary changes in the underlying sequence. Common PTMs include phosphorylation, acetylation, and methylation. Histone proteins are critical regulators of the genome and are subject to a highly abundant and diverse array of PTMs. To highlight the functional complexity added to the proteome by lysine methylation signaling, here we will focus on lysine methylation of histone proteins, an important modification in the regulation of chromatin and epigenetic processes. We review the signaling pathways and functions associated with a single residue, H4K20, as a model chromatin and clinically important mark that regulates biological processes ranging from the DNA damage response and DNA replication to gene expression and silencing.
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Affiliation(s)
- Rick van Nuland
- From the Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- From the Department of Biology, Stanford University, Stanford, California 94305
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24
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Abstract
Lysine methyltransferase which catalyze methylation of histone and non-histone proteins, play a crucial role in diverse biological processes and has emerged as a promising target for the development of various human diseases, including cancer, inflammation, and psychiatric disorders. However, inhibiting lysine methyltransferases selectively has presented many challenges to medicinal chemists. During the past decade, lysine methyltransferase inhibitors covering many different structural classes have been designed and developed. In this review, we describe the development of selective, small-molecule inhibitors of lysine methyltransferases with an emphasis on their discovery and chemical synthesis. We highlight the current state of lysine methyltransferase inhibitors and discuss future directions and opportunities for lysine methyltransferase inhibitor discovery.
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Affiliation(s)
| | - Tao Ye
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic UniversityHung Hom, Hong Kong
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25
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Yang SD, Cai YL, Jiang P, Li W, Tang JX. Association of a miR-502-binding site single nucleotide polymorphism in the 3'-untranslated region of SET8 and the TP53 codon 72 polymorphism with cervical cancer in the Chinese population. Asian Pac J Cancer Prev 2015; 15:6505-10. [PMID: 25169478 DOI: 10.7314/apjcp.2014.15.16.6505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This study was conducted to identify whether polymorphic variants of set domain-containing protein 8 (SET8) and tumor protein p53 (TP53) codon 72, either independently or jointly, might be associated with increased risk for cervical cancer. METHODS We genotyped SET8 and TP53 codon 72 polymorphisms of peripheral blood DNA from 114 cervical cancer patients and 200 controls using the polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) and direct DNA sequencing. RESULTS The frequency of SET8 CC (odds ratios (OR) = 2.717, 95% CI=1.436-5.141) or TP53 GG (OR=2.168, 95% CI=1.149-4.089) genotype was associated with an increased risk of cervical cancer on comparison with the SET8 TT or TP53 CC genotypes, respectively. In additional, interaction between the SET8 and TP53 polymorphisms increased the risk of cervical cancer in a synergistic manner, with the OR being 9.913 (95% CI=2.028-48.459) for subjects carrying both SET8 CC and TP53 GG genotypes. CONCLUSION These data suggest that there are significant associations between the miR-502-binding site SNP in the 3'-UTR of SET8 and the TP53 codon 72 polymorphism with cervical cancer in Chinese, and there is a gene-gene interaction.
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Affiliation(s)
- Shao-Di Yang
- Key Laboratory of Green Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, China E-mail :
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26
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Svensson JP, Shukla M, Menendez-Benito V, Norman-Axelsson U, Audergon P, Sinha I, Tanny JC, Allshire RC, Ekwall K. A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin. Genome Res 2015; 25:872-83. [PMID: 25778913 PMCID: PMC4448683 DOI: 10.1101/gr.188870.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/12/2015] [Indexed: 12/16/2022]
Abstract
Nucleosome composition actively contributes to chromatin structure and accessibility. Cells have developed mechanisms to remove or recycle histones, generating a landscape of differentially aged nucleosomes. This study aimed to create a high-resolution, genome-wide map of nucleosome turnover in Schizosaccharomyces pombe. The recombination-induced tag exchange (RITE) method was used to study replication-independent nucleosome turnover through the appearance of new histone H3 and the disappearance or preservation of old histone H3. The genome-wide location of histones was determined by chromatin immunoprecipitation-exonuclease methodology (ChIP-exo). The findings were compared with diverse chromatin marks, including histone variant H2A.Z, post-translational histone modifications, and Pol II binding. Finally, genome-wide mapping of the methylation states of H4K20 was performed to determine the relationship between methylation (mono, di, and tri) of this residue and nucleosome turnover. Our analysis showed that histone recycling resulted in low nucleosome turnover in the coding regions of active genes, stably expressed at intermediate levels. High levels of transcription resulted in the incorporation of new histones primarily at the end of transcribed units. H4K20 was methylated in low-turnover nucleosomes in euchromatic regions, notably in the coding regions of long genes that were expressed at low levels. This transcription-dependent accumulation of histone methylation was dependent on the histone chaperone complex FACT. Our data showed that nucleosome turnover is highly dynamic in the genome and that several mechanisms are at play to either maintain or suppress stability. In particular, we found that FACT-associated transcription conserves histones by recycling them and is required for progressive H4K20 methylation.
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Affiliation(s)
- J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
| | - Manu Shukla
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | | | - Ulrika Norman-Axelsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
| | - Pauline Audergon
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 57 Huddinge, Sweden
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Epigenetic Determinants of Erythropoiesis: Role of the Histone Methyltransferase SetD8 in Promoting Erythroid Cell Maturation and Survival. Mol Cell Biol 2015; 35:2073-87. [PMID: 25855754 DOI: 10.1128/mcb.01422-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
Erythropoiesis, in which committed progenitor cells generate millions of erythrocytes daily, involves dramatic changes in the chromatin structure and transcriptome of erythroblasts, prior to their enucleation. While the involvement of the master-regulatory transcription factors GATA binding protein 1 (GATA-1) and GATA-2 in this process is established, the mechanistic contributions of many chromatin-modifying/remodeling enzymes in red cell biology remain enigmatic. We demonstrated that SetD8, a histone methyltransferase that catalyzes monomethylation of histone H4 at lysine 20 (H4K20me1), is a context-dependent GATA-1 corepressor in erythroid cells. To determine whether SetD8 controls erythroid maturation and/or function, we used a small hairpin RNA (shRNA)-based loss-of-function strategy in a primary murine erythroblast culture system. In this system, SetD8 promoted erythroblast maturation and survival, and this did not involve upregulation of the established regulator of erythroblast survival Bcl-x(L). SetD8 catalyzed H4K20me1 at a critical Gata2 cis element and restricted occupancy by an enhancer of Gata2 transcription, Scl/TAL1, thereby repressing Gata2 transcription. Elevating GATA-2 levels in erythroid precursors yielded a maturation block comparable to that induced by SetD8 downregulation. As lowering GATA-2 expression in the context of SetD8 knockdown did not rescue erythroid maturation, we propose that SetD8 regulation of erythroid maturation involves multiple target genes. These results establish SetD8 as a determinant of erythroid cell maturation and provide a framework for understanding how a broadly expressed histone-modifying enzyme mediates cell-type-specific GATA factor function.
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Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation. Mol Cell Biol 2015; 35:2059-72. [PMID: 25848090 DOI: 10.1128/mcb.01413-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/27/2015] [Indexed: 11/20/2022] Open
Abstract
Setd8 is the sole histone methyltransferase in mammals capable of monomethylating histone H4 lysine 20 (H4K20me1). Setd8 is expressed at significantly higher levels in erythroid cells than any other cell or tissue type, suggesting that Setd8 has an erythroid-cell-specific function. To test this hypothesis, stable Setd8 knockdown was established in extensively self-renewing erythroblasts (ESREs), a well-characterized, nontransformed model of erythroid maturation. Knockdown of Setd8 resulted in impaired erythroid maturation characterized by a delay in hemoglobin accumulation, larger mean cell area, persistent ckit expression, incomplete nuclear condensation, and lower rates of enucleation. Setd8 knockdown did not alter ESRE proliferation or viability or result in accumulation of DNA damage. Global gene expression analyses following Setd8 knockdown demonstrated that in erythroid cells, Setd8 functions primarily as a repressor. Most notably, Gata2 expression was significantly higher in knockdown cells than in control cells and Gata2 knockdown rescued some of the maturation impairments associated with Setd8 disruption. Setd8 occupies critical regulatory elements in the Gata2 locus, and knockdown of Setd8 resulted in loss of H4K20me1 and gain of H4 acetylation at the Gata2 1S promoter. These results suggest that Setd8 is an important regulator of erythroid maturation that works in part through repression of Gata2 expression.
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SUV420H2 suppresses breast cancer cell invasion through down regulation of the SH2 domain-containing focal adhesion protein tensin-3. Exp Cell Res 2015; 334:90-9. [PMID: 25814362 DOI: 10.1016/j.yexcr.2015.03.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/12/2015] [Accepted: 03/14/2015] [Indexed: 11/20/2022]
Abstract
The genome-wide loss of histone H4 lysine 20 tri-methylation (H4K20me3) is observed in multiple types of cancer, including breast tumors. Since H4K20me3 is preferentially targeted to repetitive elements in the pericentromeric and telomeric heterochromatin and plays a role in chromatin integrity, the pathological effects of disrupted H4K20me3 in tumors have been attributed to genomic instability. However, in this report, we show that loss of H4K20me3 modulates gene expression profiles, leading to increased cell invasion. Reduced H4K20me3 levels in tumor cells are often accompanied by a decrease in the expression of the H4K20-specific methyltransferase, SUV420H2. Exogenous delivery of SUV420H2 into MDA-MB-231 human breast cancer cells induced selective and specific changes in the expression of cancer-related genes. One of the most downregulated genes in response to SUV420H2 expression was the Src substrate, tensin-3, a focal adhesion protein that contributes to cancer cell migration. Depletion of tensin-3 suppressed breast cancer cell invasiveness. Furthermore, silencing of tensin-3 was associated with enrichment of H4K20me3 immediately upstream of the tensin-3 transcription start site, suggesting that the loss of H4K20me3 in tumor cells induced the expression of cancer-promoting genes. These findings connect the loss of H4K20me3 with tumor progression, through the transcriptional activation of cancer-promoting genes.
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30
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Hashemi M, Sheybani-Nasab M, Naderi M, Roodbari F, Taheri M. Association of functional polymorphism at the miR-502-binding site in the 3' untranslated region of the SETD8 gene with risk of childhood acute lymphoblastic leukemia, a preliminary report. Tumour Biol 2014; 35:10375-9. [PMID: 25048968 DOI: 10.1007/s13277-014-2359-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/14/2014] [Indexed: 11/25/2022] Open
Abstract
MicroRNAs (miRNAs), a class of non-coding RNAs, bind to the 3' untranslated regions (UTRs) of mRNAs, where they interfere with translation of genes and are implicated in the pathogenesis of diverse diseases. In the present study, we evaluate the impact of rs16917496 polymorphism within the miR-502 miRNA seed region at the 3'UTR of SEDT8 on childhood acute lymphoblastic leukemia (ALL). This case-control study was done on 75 ALL and 115 healthy children. Genotyping of rs16917496 C/T polymorphism was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that CT as well as CT + TT decreased the risk of ALL in comparison with CC genotype (odds ratio (OR) = 0.29, 95 % confidence intervals (95 % CI) = 0.11-0.78, P = 0.014 and OR = 0.31, 95 % CI = 0.12-0.82, P = 0.016, respectively). Our results demonstrated that SETD8 rs16917496 C/T polymorphism was associated with decreased risk of developing pediatric ALL in Zahedan, southeast Iran. Larger studies with different ethnicities are desired to validate our findings.
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Affiliation(s)
- Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran,
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Abstract
Post-translational modifications provide a fine-tuned control of protein function(s) in the cell. The well-known tumour suppressor p53 is subject to many post-translational modifications, which alter its activity, localization and stability, thus ultimately modulating its response to various forms of genotoxic stress. In this review, we focus on the role of recently discovered lysine-specific modifications of p53, methylation and acetylation in particular, and their effects on p53 activity in damaged cells. We also discuss a possibility of mutual influence of covalent modifications in the p53 and histone proteins located in the vicinity of p53 binding sites in chromatin and propose important ramifications stemming from this hypothesis.
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Concerted activities of distinct H4K20 methyltransferases at DNA double-strand breaks regulate 53BP1 nucleation and NHEJ-directed repair. Cell Rep 2014; 8:430-8. [PMID: 25001286 DOI: 10.1016/j.celrep.2014.06.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 12/28/2022] Open
Abstract
Although selective binding of 53BP1 to dimethylated histone H4 lysine 20 (H4K20me2) at DNA double-strand breaks (DSBs) is a necessary and pivotal determinant of nonhomologous end joining (NHEJ)-directed repair, the enzymes that generate H4K20me2 at DSBs were unclear. Here, we determined that the PR-Set7 monomethyltransferase (H4K20me1) regulates de novo H4K20 methylation at DSBs. Rapid recruitment of PR-Set7 to DSBs was dependent on the NHEJ Ku70 protein and necessary for NHEJ-directed repair. PR-Set7 monomethyltransferase activity was required, but insufficient, for H4K20me2 and 53BP1 nucleation at DSBs. We determined that PR-Set7-mediated H4K20me1 facilitates Suv4-20 methyltransferase recruitment and catalysis to generate H4K20me2 necessary for 53BP1 binding. The orchestrated and concerted activities of PR-Set7 and Suv4-20 were required for proficient 53BP1 nucleation and DSB repair. This report identifies PR-Set7 as an essential component of NHEJ and implicates PR-Set7 as a central determinant of NHEJ-directed repair early in mammalian DSB repair pathway choice.
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Kapoor-Vazirani P, Vertino PM. A dual role for the histone methyltransferase PR-SET7/SETD8 and histone H4 lysine 20 monomethylation in the local regulation of RNA polymerase II pausing. J Biol Chem 2014; 289:7425-37. [PMID: 24459145 DOI: 10.1074/jbc.m113.520783] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase II (Pol II) promoter-proximal pausing plays a critical role in postinitiation transcriptional regulation at many metazoan genes. We showed recently that histone H4 lysine 16 acetylation (H4K16Ac), mediated by the MSL complex, facilitates the release of paused Pol II. In contrast, H4 lysine 20 trimethylation (H4K20me3), mediated by SUV420H2, enforces Pol II pausing by inhibiting MSL recruitment. However, how the balance between H4K16Ac and H4K20me3 is locally regulated remains unclear. Here, we demonstrate that PR-SET7/SETD8, which monomethylates histone H4 lysine 20 (H4K20me1), controls both H4K16Ac and H4K20me3 and in doing so, regulates Pol II pausing dynamics. We find that PR-SET7-mediated H4K20me1 is necessary for the recruitment of the MSL complex, subsequent H4K16Ac, and release of Pol II into active elongation. Although dispensable for SUV420H2 recruitment, PR-SET7-mediated H4K20me1 is required for H4K20me3. Although depletion of SUV420H2 is sufficient to deplete H4K20me3 and relieve an H4K20me3-induced pause, pausing is maintained in the absence of PR-SET7 despite H4K20me3 depletion because of an inability to recruit the MSL complex in the absence of H4K20me1. These findings highlight the requirement for PR-SET7 and H4K20me1 in establishing both the H4K16Ac and H4K20me3 marks and point to a dual role in the local regulation of Pol II pausing.
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Affiliation(s)
- Priya Kapoor-Vazirani
- From the Department of Radiation Oncology and the Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia 30322
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34
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Congdon LM, Sims JK, Tuzon CT, Rice JC. The PR-Set7 binding domain of Riz1 is required for the H4K20me1-H3K9me1 trans-tail 'histone code' and Riz1 tumor suppressor function. Nucleic Acids Res 2014; 42:3580-9. [PMID: 24423864 PMCID: PMC3973283 DOI: 10.1093/nar/gkt1377] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
PR-Set7/Set8/KMT5a is the sole histone H4 lysine 20 monomethyltransferase (H4K20me1) in metazoans and is essential for proper cell division and genomic stability. We unexpectedly discovered that normal cellular levels of monomethylated histone H3 lysine 9 (H3K9me1) were also dependent on PR-Set7, but independent of its catalytic activity. This observation suggested that PR-Set7 interacts with an H3K9 monomethyltransferase to establish the previously reported H4K20me1-H3K9me1 trans-tail ‘histone code’. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. The PR-Set7 binding domain was required for Riz1 nuclear localization and maintenance of the H4K20me1-H3K9me1 trans-tail ‘histone code’. Although Riz1 can function as a repressor, Riz1/H3K9me1 was dispensable for the repression of genes regulated by PR-Set7/H4K20me1. Frameshift mutations resulting in a truncated Riz1 incapable of binding PR-Set7 occur frequently in various aggressive cancers. In these cancer cells, expression of wild-type Riz1 restored tumor suppression by decreasing proliferation and increasing apoptosis. These phenotypes were not observed in cells expressing either the Riz1 PR/SET domain or PR-Set7 binding domain indicating that Riz1 methyltransferase activity and PR-Set7 binding domain are both essential for Riz1 tumor suppressor function.
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Affiliation(s)
- Lauren M Congdon
- Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Harlyne J. Norris Cancer Research Tower, Los Angeles, CA 90033, USA
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Herz HM, Garruss A, Shilatifard A. SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem Sci 2013; 38:621-39. [PMID: 24148750 DOI: 10.1016/j.tibs.2013.09.004] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/06/2013] [Accepted: 09/12/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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Genetic variation in a microRNA-502 minding site in SET8 gene confers clinical outcome of non-small cell lung cancer in a Chinese population. PLoS One 2013; 8:e77024. [PMID: 24146953 PMCID: PMC3795636 DOI: 10.1371/journal.pone.0077024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/27/2013] [Indexed: 12/28/2022] Open
Abstract
Background Genetic variants may influence microRNA-target interaction through modulate their binding affinity, creating or destroying miRNA-binding sites. SET8, a member of the SET domain-containing methyltransferase, has been implicated in a variety array of biological processes. Methods Using Taqman assay, we genotyped a polymorphism rs16917496 T>C within the miR-502 binding site in the 3′-untranslated region of the SET8 gene in 576 non-small cell lung cancer (NSCLC) patients. Functions of rs16917496 were investigated using luciferase activity assay and validated by immunostaining. Results Log-rank test and cox regression indicated that the CC genotype was associated with a longer survival and a reduced risk of death for NSCLC [58.0 vs. 41.0 months, P = 0.031; hazard ratio = 0.44, 95% confidential interval: 0.26–0.74]. Further stepwise regression analysis suggested rs16917496 was an independently favorable factor for prognosis and the protective effect more prominent in never smokers, patients without diabetes and patients who received chemotherapy. A significant interaction was observed between rs16917496 and smoking status in relation to NSCLC survival (P<0.001). Luciferase activity assay showed a lower expression level for C allele as compared with T allele, and the miR-502 had an effect on modulation of SET8 gene in vitro. The CC genotype was associated with reduced SET8 protein expression based on immunostaining of 192 NSCLC tissue sample (P = 0.007). Lower levels of SET8 were associated with a non-significantly longer survival (55.0 vs. 43.1 months). Conclusion Our data suggested that the rs16917496 T>C located at miR-502 binding site contributes to NSCLC survival by altering SET8 expression through modulating miRNA-target interaction.
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Yu N, Huangyang P, Yang X, Han X, Yan R, Jia H, Shang Y, Sun L. microRNA-7 suppresses the invasive potential of breast cancer cells and sensitizes cells to DNA damages by targeting histone methyltransferase SET8. J Biol Chem 2013; 288:19633-42. [PMID: 23720754 DOI: 10.1074/jbc.m113.475657] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
SET8 (SET domain containing 8) is a histone H4 lysine 20 (H4K20)-specific monomethyltransferase in higher eukaryotes that exerts diverse functions in transcription regulation, DNA repair, tumor metastasis, and genome integrity. The activity of SET8 is tightly controlled during cell cycle through post-translational modifications, including ubiquitination, phosphorylation, and sumoylation. However, how the expression of SET8 is regulated is not fully understood. Here, we report that microRNA-7 is a negative regulator of SET8. We demonstrated that microRNA-7 inhibits H4K20 monomethylation and suppresses epithelial-mesenchymal transition and the invasive potential of breast cancer cells. We showed that microRNA-7 promotes spontaneous DNA damages and sensitizes cells to induced DNA damages. Our experiments provide a molecular mechanism for the regulation of SET8 and extend the biological function of microRNA-7 to DNA damage response, supporting the pursuit of microRNA-7 as a potential target for breast cancer intervention.
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Affiliation(s)
- Na Yu
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
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Vavouri T, Lehner B. Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol 2012. [PMID: 23186133 PMCID: PMC3580500 DOI: 10.1186/gb-2012-13-11-r110] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications. Results Here we report that genes with CpG island promoters have a characteristic transcription-associated chromatin organization. This signature includes high levels of the transcription elongation-associated histone modifications H4K20me1, H2BK5me1 and H3K79me1/2/3 in the 5' end of the gene, depletion of the activation marks H2AK5ac, H3K14ac and H3K23ac immediately downstream of the transcription start site (TSS), and characteristic epigenetic asymmetries around the TSS. The chromosome organization factor CTCF may be bound upstream of RNA polymerase in most active CpG island promoters, and an unstable nucleosome at the TSS may be specifically marked by H4K20me3, the first example of such a modification. H3K36 monomethylation is only detected as enriched in the bodies of active genes that have CpG island promoters. Finally, as expression levels increase, peak modification levels of the histone methylations H3K9me1, H3K4me1, H3K4me2 and H3K27me1 shift further away from the TSS into the gene body. Conclusions These results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS. The identity, positioning, shape and relative ordering of transcription-associated histone modifications differ between genes with and without CpG island promoters. This supports a model where chromatin organization reflects not only transcription activity but also the type of promoter in which transcription initiates.
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Koturbash I, Simpson NE, Beland FA, Pogribny IP. Alterations in histone H4 lysine 20 methylation: implications for cancer detection and prevention. Antioxid Redox Signal 2012; 17:365-74. [PMID: 22035019 DOI: 10.1089/ars.2011.4370] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
SIGNIFICANCE Cancer development and progression are associated with numerous genetic, epigenetic, and metabolic changes. RECENT ADVANCES A number of epigenetic aberrations have been characterized in cancer, including DNA methylation and various histone modification changes. One of the most unique and enigmatic epigenetic marks that is noticeably altered in several major human cancers is methylation of histone H4 lysine 20; however, there is insufficient knowledge of the underlying molecular mechanisms associated with this abberation. CRITICAL ISSUES This review presents current evidence of the role of histone H4 lysine 20 methylation in normal and cancer cells and during tumorigenesis induced by genotoxic and nongenotoxic carcinogens. Additionally, it describes molecular mechanisms that may cause this alteration and highlights the significance of this epigenetic mark as an early indicator of carcinogenesis. FUTURE DIRECTIONS Accumulating evidence suggests that dietary components may be significant regulators of the cellular epigenome, including histone methylation, by providing and maintaining the adequate levels of S-adenosyl-L-methionine, flavin adenine dinucleotide, α-ketoglutarate, and iron. Future research should elucidate the potential for modifying cellular metabolism through dietary intervention for timely regulation of the epigenome as means for the prevention of cancer development.
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Affiliation(s)
- Igor Koturbash
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
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Abstract
The reversible and dynamic methylation of proteins on lysine residues can greatly increase the signaling potential of the modified factor. In addition to histones, several other nuclear factors such as the tumor suppressor and transcription factor p53 undergo lysine methylation, suggesting that this modification may be a common mechanism for modulating protein–protein interactions and key cellular signaling pathways. This article focuses on how lysine methylation events on the C-terminal tail of p53 are generated, sensed and transduced to modulate p53 functions.
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Affiliation(s)
- Lisandra E West
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription. Genes Dev 2012; 26:325-37. [PMID: 22345514 DOI: 10.1101/gad.177444.111] [Citation(s) in RCA: 235] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Histone post-translational modifications impact many aspects of chromatin and nuclear function. Histone H4 Lys 20 methylation (H4K20me) has been implicated in regulating diverse processes ranging from the DNA damage response, mitotic condensation, and DNA replication to gene regulation. PR-Set7/Set8/KMT5a is the sole enzyme that catalyzes monomethylation of H4K20 (H4K20me1). It is required for maintenance of all levels of H4K20me, and, importantly, loss of PR-Set7 is catastrophic for the earliest stages of mouse embryonic development. These findings have placed PR-Set7, H4K20me, and proteins that recognize this modification as central nodes of many important pathways. In this review, we discuss the mechanisms required for regulation of PR-Set7 and H4K20me1 levels and attempt to unravel the many functions attributed to these proteins.
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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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Zhou H, Ning Z, E. Starr A, Abu-Farha M, Figeys D. Advancements in Top-Down Proteomics. Anal Chem 2011; 84:720-34. [DOI: 10.1021/ac202882y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Zhibing Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
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Edwards CR, Dang W, Berger SL. Histone H4 lysine 20 of Saccharomyces cerevisiae is monomethylated and functions in subtelomeric silencing. Biochemistry 2011; 50:10473-83. [PMID: 21985125 DOI: 10.1021/bi201120q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Histones undergo post-translational modifications that are linked to important biological processes. Previous studies have indicated that lysine methylation correlating with closed or repressive chromatin is absent in the budding yeast Saccharomyces cerevisiae, including at H4 lysine 20 (K20). Here we provide functional evidence for H4 K20 monomethylation (K20me1) in budding yeast. H4 K20me1 is detectable on endogenous H4 by western analysis using methyl-specific antibodies, and the signal is abrogated by H4 K20 substitutions and by competition with H4 K20me1 peptides. Using chromatin immunoprecipitation, we show that H4 K20me1 levels are highest at heterochromatic locations, including subtelomeres, the silent mating type locus, and rDNA repeats, and lowest at centromeres within euchromatin. Further, an H4 K20A substitution strongly reduced heterochromatic reporter silencing at telomeres and the silent mating type locus and led to an increase in subtelomeric endogenous gene expression. The correlation between the location of H4 K20me1 and the effect of the H4 K20A substitution suggests that this modification plays a repressive function. Our findings reveal the first negative regulatory histone methylation in budding yeast and indicate that H4 K20me1 is evolutionarily conserved from simple to complex eukaryotes.
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Affiliation(s)
- Christopher R Edwards
- Department of Cellular and Developmental Biology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Finding a balance: how diverse dosage compensation strategies modify histone h4 to regulate transcription. GENETICS RESEARCH INTERNATIONAL 2011; 2012:795069. [PMID: 22567401 PMCID: PMC3335593 DOI: 10.1155/2012/795069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/08/2011] [Indexed: 01/21/2023]
Abstract
Dosage compensation balances gene expression levels between the sex chromosomes and autosomes and sex-chromosome-linked gene expression levels between the sexes. Different dosage compensation strategies evolved in different lineages, but all involve changes in chromatin. This paper discusses our current understanding of how modifications of the histone H4 tail, particularly changes in levels of H4 lysine 16 acetylation and H4 lysine 20 methylation, can be used in different contexts to either modulate gene expression levels twofold or to completely inhibit transcription.
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SET8 promotes epithelial-mesenchymal transition and confers TWIST dual transcriptional activities. EMBO J 2011; 31:110-23. [PMID: 21983900 DOI: 10.1038/emboj.2011.364] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 09/09/2011] [Indexed: 12/13/2022] Open
Abstract
SET8 is implicated in transcriptional regulation, heterochromatin formation, genomic stability, cell-cycle progression, and development. As such, it is predicted that SET8 might be involved in the development and progression of tumour. However, whether and how SET8 might be implicated in tumourigenesis is currently unknown. Here, we report that SET8 is physically associated with TWIST, a master regulator of epithelial-mesenchymal transition (EMT). We demonstrated that SET8 and TWIST are functionally interdependent in promoting EMT and enhancing the invasive potential of breast cancer cells in vitro and in vivo. We showed that SET8 acts as a dual epigenetic modifier on the promoters of the TWIST target genes E-cadherin and N-cadherin via its H4K20 monomethylation activity. Significantly, in breast carcinoma samples, SET8 expression is positively correlated with metastasis and the expression of TWIST and N-cadherin and negatively correlated with E-cadherin. Together, our experiments revealed a novel role for SET8 in tumour invasion and metastasis and provide a molecular mechanism underlying TWIST-promoted EMT, suggesting SET8 as a potential target for intervention of the metastasis of breast cancer.
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Spektor TM, Congdon LM, Veerappan CS, Rice JC. The UBC9 E2 SUMO conjugating enzyme binds the PR-Set7 histone methyltransferase to facilitate target gene repression. PLoS One 2011; 6:e22785. [PMID: 21829513 PMCID: PMC3146489 DOI: 10.1371/journal.pone.0022785] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 07/07/2011] [Indexed: 01/30/2023] Open
Abstract
PR-Set7/Set8/KMT5a is a chromatin-modifying enzyme that specifically monomethylates lysine 20 of histone H4 (H4K20me1). In this study we attempted to identify PR-Set7-interacting proteins reasoning that these proteins would provide important insights into the role of PR-Set7 in transcriptional regulation. Using an unbiased yeast two-hybrid approach, we discovered that PR-Set7 interacts with the UBC9 E2 SUMO conjugating enzyme. This interaction was confirmed in human cells and we demonstrated that PR-Set7 was preferentially modified with SUMO1 in vivo. Further in vitro studies revealed that UBC9 directly binds PR-Set7 proximal to the catalytic SET domain. Two putative SUMO consensus sites were identified in this region and both were capable of being SUMOylated in vitro. The absence of either or both SUMO sites did not perturb nuclear localization of PR-Set7. By employing whole genome expression arrays, we identified a panel of genes whose expression was significantly altered in the absence of PR-Set7. The vast majority of these genes displayed increased expression strongly suggesting that PR-Set7 predominantly functions as a transcriptional repressor. Importantly, the reduction of UBC9 resulted in the consistent derepression of several of these newly identified genes regulated by PR-Set7. Our findings indicate that direct interaction with UBC9 facilitates the repressive effects of PR-Set7 at specific target genes, most likely by SUMOylating PR-Set7.
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Affiliation(s)
- Tanya M. Spektor
- Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Lauren M. Congdon
- Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Chendhore S. Veerappan
- Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Judd C. Rice
- Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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Foreman KW, Brown M, Park F, Emtage S, Harriss J, Das C, Zhu L, Crew A, Arnold L, Shaaban S, Tucker P. Structural and functional profiling of the human histone methyltransferase SMYD3. PLoS One 2011; 6:e22290. [PMID: 21779408 PMCID: PMC3136521 DOI: 10.1371/journal.pone.0022290] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/21/2011] [Indexed: 12/13/2022] Open
Abstract
The SET and MYND Domain (SMYD) proteins comprise a unique family of multi-domain SET histone methyltransferases that are implicated in human cancer progression. Here we report an analysis of the crystal structure of the full length human SMYD3 in a complex with an analog of the S-adenosyl methionine (SAM) methyl donor cofactor. The structure revealed an overall compact architecture in which the "split-SET" domain adopts a canonical SET domain fold and closely assembles with a Zn-binding MYND domain and a C-terminal superhelical 9 α-helical bundle similar to that observed for the mouse SMYD1 structure. Together, these structurally interlocked domains impose a highly confined binding pocket for histone substrates, suggesting a regulated mechanism for its enzymatic activity. Our mutational and biochemical analyses confirm regulatory roles of the unique structural elements both inside and outside the core SET domain and establish a previously undetected preference for trimethylation of H4K20.
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Affiliation(s)
- Kenneth W Foreman
- OSI Pharmaceuticals, Inc., Farmingdale, New York, United States of America.
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Brustel J, Tardat M, Kirsh O, Grimaud C, Julien E. Coupling mitosis to DNA replication: the emerging role of the histone H4-lysine 20 methyltransferase PR-Set7. Trends Cell Biol 2011; 21:452-60. [PMID: 21632252 DOI: 10.1016/j.tcb.2011.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/19/2011] [Accepted: 04/26/2011] [Indexed: 01/23/2023]
Abstract
To ensure accurate inheritance of genetic information through cell proliferation, chromosomes must be precisely copied only during S phase, and then correctly condensed and segregated during mitosis. Several new findings suggest that this tight coupling between DNA replication and mitosis is in part controlled by cell cycle regulated chromatin modifications, in particular due to the changing activity of lysine methyltransferase PR-Set7/SET8 that is responsible for the monomethylation of histone H4 at lysine 20. Cell cycle oscillation of PR-Set7 is orchestrated by ubiquitin-mediated proteolysis, and interference with this regulatory process leads to unscheduled licensing of replication origins and altered timing of mitotic chromosome compaction. This review provides an overview of how PR-Set7 regulates these two cell cycle events and highlights questions that remain to be addressed.
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Affiliation(s)
- Julien Brustel
- Institut de Génétique Moléculaire de Montpellier (IGMM), Université Montpellier 2 and Université Montpellier 1, Centre National de la Recherche Scientifique (CNRS) Unité Mixte Recherche, France.
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Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 2011; 21:175-86. [PMID: 21342762 DOI: 10.1016/j.gde.2011.01.022] [Citation(s) in RCA: 293] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 01/18/2011] [Indexed: 12/16/2022]
Abstract
Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin to fit inside the nucleus. The dynamics of higher-order chromatin compaction play a crucial role in transcription and other biological processes inherent to DNA. Many factors, including histone variants, histone modifications, DNA methylation, and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. In this review, we focus on the recent progress in elucidating the structure of the 30-nm chromatin fiber. We also discuss the structural plasticity/dynamics and epigenetic inheritance of higher-order chromatin and the roles of chromatin higher-order organization in eukaryotic gene regulation.
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