1
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Vargas-López V, Prada LF, Alméciga-Díaz CJ. Evidence of epigenetic landscape shifts in mucopolysaccharidosis IIIB and IVA. Sci Rep 2024; 14:3961. [PMID: 38368436 PMCID: PMC10874391 DOI: 10.1038/s41598-024-54626-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/14/2024] [Indexed: 02/19/2024] Open
Abstract
Lysosomal storage diseases (LSDs) are a group of monogenic diseases characterized by mutations in genes coding for proteins associated with the lysosomal function. Despite the monogenic nature, LSDs patients exhibit variable and heterogeneous clinical manifestations, prompting investigations into epigenetic factors underlying this phenotypic diversity. In this study, we focused on the potential role of epigenetic mechanisms in the pathogenesis of mucopolysaccharidosis IIIB (MPS IIIB) and mucopolysaccharidosis IVA (MPS IVA). We analyzed DNA methylation (5mC) and histone modifications (H3K14 acetylation and H3K9 trimethylation) in MPS IIIB and MPS IVA patients' fibroblasts and healthy controls. The findings revealed that global DNA hypomethylation is present in cell lines for both diseases. At the same time, histone acetylation was increased in MPS IIIB and MPS IVA cells in a donor-dependent way, further indicating a shift towards relaxed open chromatin in these MPS. Finally, the constitutive heterochromatin marker, histone H3K9 trimethylation, only showed reduced clustering in MPS IIIB cells, suggesting limited alterations in heterochromatin organization. These findings collectively emphasize the significance of epigenetic mechanisms in modulating the phenotypic variations observed in LSDs. While global DNA hypomethylation could contribute to the MPS pathogenesis, the study also highlights individual-specific epigenetic responses that might contribute to phenotypic heterogeneity. Further research into the specific genes and pathways affected by these epigenetic changes could provide insights into potential therapeutic interventions for these MPS and other LSDs.
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Affiliation(s)
- Viviana Vargas-López
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Cra. 7 No. 43-82 Edificio 54, Laboratorio 305A, Bogotá D.C., 110231, Colombia
| | - Luisa F Prada
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Cra. 7 No. 43-82 Edificio 54, Laboratorio 305A, Bogotá D.C., 110231, Colombia
| | - Carlos J Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Cra. 7 No. 43-82 Edificio 54, Laboratorio 305A, Bogotá D.C., 110231, Colombia.
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2
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Santos DS, Rocha MA, Mello MLS. Epigenetic studies in insects and the valproic acid perspective. BRAZ J BIOL 2024; 84:e256045. [DOI: 10.1590/1519-6984.256045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/10/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Valproic acid in association with sodium valproate (VPA) is an important anticonvulsant drug used for decades to treat neurological disorders. VPA also acts as an epigenetic modulator by inhibiting histone deacetylases, permitting histone acetylation, affecting the DNA and histone methylation status and gene expression, and inducing chromatin remodeling. Insects represent an important animal model for studies in several areas of science. Their high phenotypic plasticity makes them alternative models for epigenetic studies. This brief review emphasizes recent reports on insect epigenetics and the contribution of studies on the VPA action in insects, including effects on epigenetic markers, extending the pharmacological understanding of the potential of this drug, and demonstrating the usefulness of insects as an alternative animal model to drug studies.
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3
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Chen S, Liu W, Xiong L, Tao Z, Zhao D. Tissue-specific silencing of integrated transgenes achieved through endogenous RNA interference in Caenorhabditis elegans. RNA Biol 2024; 21:1-10. [PMID: 38531838 DOI: 10.1080/15476286.2024.2332856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Transgene silencing is a common phenomenon observed in Caenorhabditis elegans, particularly in the germline, but the precise mechanisms underlying this process remain elusive. Through an analysis of the transcription factors profile of C. elegans, we discovered that the expression of several transgenic reporter lines exhibited tissue-specific silencing, specifically in the intestine of C. elegans. Notably, this silencing could be reversed in mutants defective in endogenous RNA interference (RNAi). Further investigation using knock-in strains revealed that these intestine-silent genes were indeed expressed in vivo, indicating that the organism itself regulates the intestine-specific silencing. This tissue-specific silencing appears to be mediated through the endo-RNAi pathway, with the main factors of this pathway, mut-2 and mut-16, are significantly enriched in the intestine. Additionally, histone modification factors, such as met-2, are involved in this silencing mechanism. Given the crucial role of the intestine in reproduction alongside the germline, the transgene silencing observed in the intestine reflects the self-protective mechanisms employed by the organisms. In summary, our study proposed that compared to other tissues, the transgenic silencing of intestine is specifically regulated by the endo-RNAi pathway.
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Affiliation(s)
- Siyu Chen
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Institute of Sport, Exercise & Health, Tianjin University of Sport, Tianjin, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Weihong Liu
- Intelligent Perception Lab, Hanwang Technology Co. Ltd, Beijing, China
| | - Lei Xiong
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhiju Tao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Di Zhao
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Institute of Sport, Exercise & Health, Tianjin University of Sport, Tianjin, China
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4
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Hou X, Xu M, Zhu C, Gao J, Li M, Chen X, Sun C, Nashan B, Zang J, Zhou Y, Guang S, Feng X. Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans. Nat Commun 2023; 14:1254. [PMID: 36878913 PMCID: PMC9988841 DOI: 10.1038/s41467-023-36898-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
The chromatin organization modifier domain (chromodomain) is an evolutionally conserved motif across eukaryotic species. The chromodomain mainly functions as a histone methyl-lysine reader to modulate gene expression, chromatin spatial conformation and genome stability. Mutations or aberrant expression of chromodomain proteins can result in cancer and other human diseases. Here, we systematically tag chromodomain proteins with green fluorescent protein (GFP) using CRISPR/Cas9 technology in C. elegans. By combining ChIP-seq analysis and imaging, we delineate a comprehensive expression and functional map of chromodomain proteins. We then conduct a candidate-based RNAi screening and identify factors that regulate the expression and subcellular localization of the chromodomain proteins. Specifically, we reveal an H3K9me1/2 reader, CEC-5, both by in vitro biochemistry and in vivo ChIP assays. MET-2, an H3K9me1/2 writer, is required for CEC-5 association with heterochromatin. Both MET-2 and CEC-5 are required for the normal lifespan of C. elegans. Furthermore, a forward genetic screening identifies a conserved Arginine124 of CEC-5's chromodomain, which is essential for CEC-5's association with chromatin and life span regulation. Thus, our work will serve as a reference to explore chromodomain functions and regulation in C. elegans and allow potential applications in aging-related human diseases.
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Affiliation(s)
- Xinhao Hou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Mingjing Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Jianing Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Meili Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Cheng Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Björn Nashan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Jianye Zang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 230027, Hefei, Anhui, P. R. China.
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
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5
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Lam-Ubol A, Phattarataratip E. Distinct histone H3 modification profiles correlate with aggressive characteristics of salivary gland neoplasms. Sci Rep 2022; 12:15063. [PMID: 36064736 PMCID: PMC9445049 DOI: 10.1038/s41598-022-19174-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
Post-translational modification of histones is the crucial event that affect many tumor-specific traits. A diverse type of histone modifications had been reported in different cancers with prognostic implications. This study aimed to examine the degree of histone H3 modifications in salivary gland neoplasms and their associations with tumor pathologic characteristics and proliferative activity. The expression of H3K9Ac, H3K18Ac, H3K9Me3 and Ki-67 in 70 specimens of salivary gland neoplasms, consisting of 30 mucoepidermoid carcinoma (MEC), 20 adenoid cystic carcinoma (ACC) and 20 pleomorphic adenoma (PA), were investigated immunohistochemically. The immunohistochemical scoring of 3 histone modification types and Ki-67 labeling index were determined. Overall, MEC demonstrated elevated H3K9Ac level compared with benign PA. Increased H3K9Me3 in MEC was positively correlated with small nest invasion at tumor front, advanced pathologic grade, and elevated proliferative index. In addition, the significant upregulation of all 3 types of histone H3 modification was noted in solid subtype of ACC and associated with increased cell proliferation. This study indicates that salivary gland neoplasms differentially acquire distinct patterns of histone H3 modification, which impact prognostically relevant cancer phenotypes. The hyperacetylation and methylation of histone H3 could be underpinning the prognostically worsen solid type of ACC, and the trimethylation of H3K9 may be involved in aggressive characteristics of MEC.
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Affiliation(s)
- Aroonwan Lam-Ubol
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, Srinakharinwirot University, 114 Sukhumvit 23 Wattana, Bangkok, 10110, Thailand
| | - Ekarat Phattarataratip
- Department of Oral Pathology, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, Bangkok, 10330, Thailand.
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6
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Epigenetic Alterations under Oxidative Stress in Stem Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6439097. [PMID: 36071870 PMCID: PMC9444469 DOI: 10.1155/2022/6439097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022]
Abstract
Epigenetic regulation of gene expression, including DNA methylation and histone modifications, provides finely tuned responses for cells that undergo cellular environment changes. Abundant evidences have demonstrated the detrimental role of oxidative stress in various human pathogenesis since oxidative stress results from the imbalance between reactive oxygen species (ROS) accumulation and antioxidant defense system. Stem cells can self-renew themselves and meanwhile have the potential to differentiate into many other cell types. As some studies have described the effects of oxidative stress on homeostasis and cell fate decision of stem cells, epigenetic alterations have emerged crucial for mediating the stem cell behaviours under oxidative stress. Here, we review recent findings on the oxidative effects on DNA and histone modifications in stem cells. We propose that epigenetic alterations and oxidative stress may influence each other in stem cells.
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7
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Ng GYQ, Sheng DPLK, Bae HG, Kang SW, Fann DYW, Park J, Kim J, Alli-Shaik A, Lee J, Kim E, Park S, Han JW, Karamyan V, Okun E, Dheen T, Hande MP, Vemuganti R, Mallilankaraman K, Lim LHK, Kennedy BK, Drummond GR, Sobey CG, Gunaratne J, Mattson MP, Foo RSY, Jo DG, Arumugam TV. Integrative epigenomic and transcriptomic analyses reveal metabolic switching by intermittent fasting in brain. GeroScience 2022; 44:2171-2194. [PMID: 35357643 DOI: 10.1007/s11357-022-00537-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/21/2022] [Indexed: 11/04/2022] Open
Abstract
Intermittent fasting (IF) remains the most effective intervention to achieve robust anti-aging effects and attenuation of age-related diseases in various species. Epigenetic modifications mediate the biological effects of several environmental factors on gene expression; however, no information is available on the effects of IF on the epigenome. Here, we first found that IF for 3 months caused modulation of H3K9 trimethylation (H3K9me3) in the cerebellum, which in turn orchestrated a plethora of transcriptomic changes involved in robust metabolic switching processes commonly observed during IF. Second, a portion of both the epigenomic and transcriptomic modulations induced by IF was remarkably preserved for at least 3 months post-IF refeeding, indicating that memory of IF-induced epigenetic changes was maintained. Notably, though, we found that termination of IF resulted in a loss of H3K9me3 regulation of the transcriptome. Collectively, our study characterizes the novel effects of IF on the epigenetic-transcriptomic axis, which controls myriad metabolic processes. The comprehensive analyses undertaken in this study reveal a molecular framework for understanding how IF impacts the metabolo-epigenetic axis of the brain and will serve as a valuable resource for future research.
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Affiliation(s)
- Gavin Yong-Quan Ng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Han-Gyu Bae
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sung Wook Kang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David Yang-Wei Fann
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinsu Park
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Joonki Kim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, Gangwon-do, Republic of Korea
| | - Asfa Alli-Shaik
- Translational Biomedical Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jeongmi Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Eunae Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sunyoung Park
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Vardan Karamyan
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Science Center, Amarillo, TX, USA
| | - Eitan Okun
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-IIan University, Ramat Gan, Israel
| | - Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Karthik Mallilankaraman
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lina H K Lim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Brian K Kennedy
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School Medicine, National University of Singapore, Singapore, Singapore.,Buck Institute for Research On Aging, Novato, USA
| | - Grant R Drummond
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Christopher G Sobey
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Jayantha Gunaratne
- Translational Biomedical Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mark P Mattson
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roger Sik-Yin Foo
- Genome Institute of Singapore, Singapore, Singapore. .,Centre for Translational Medicine, Cardiovascular Research Institute, National University Health Systems, National University of Singapore, Singapore, Singapore.
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
| | - Thiruma V Arumugam
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea. .,Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia.
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8
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Positioning of nucleosomes containing γ-H2AX precedes active DNA demethylation and transcription initiation. Nat Commun 2021; 12:1072. [PMID: 33594057 PMCID: PMC7886895 DOI: 10.1038/s41467-021-21227-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 01/12/2021] [Indexed: 01/09/2023] Open
Abstract
In addition to nucleosomes, chromatin contains non-histone chromatin-associated proteins, of which the high-mobility group proteins are the most abundant. Chromatin-mediated regulation of transcription involves DNA methylation and histone modifications. However, the order of events and the precise function of high-mobility group proteins during transcription initiation remain unclear. Here we show that high-mobility group AT-hook 2 protein (HMGA2) induces DNA nicks at the transcription start site, which are required by the histone chaperone FACT complex to incorporate nucleosomes containing the histone variant H2A.X. Further, phosphorylation of H2A.X at S139 (γ-H2AX) is required for repair-mediated DNA demethylation and transcription activation. The relevance of these findings is demonstrated within the context of TGFB1 signaling and idiopathic pulmonary fibrosis, suggesting therapies against this lethal disease. Our data support the concept that chromatin opening during transcriptional initiation involves intermediates with DNA breaks that subsequently require DNA repair mechanisms to ensure genome integrity. The order of DNA methylation and histone modifications during transcription remained unclear. Here the authors show that HMGA2 induces DNA nicks at TGFB1-responsive genes, promoting nucleosome incorporation containing γ-H2AX, which is required for repair-mediated DNA demethylation and transcription.
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9
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Abstract
An unusual feature of papillomaviruses is that their genomes are packaged into virions along with host histones. Viral minichromosomes were visualized as “beads on a string” by electron microscopy in the 1970s but, to date, little is known about the posttranslational modifications of these histones. To investigate this, we analyzed the histone modifications in HPV16/18 quasivirions, wart-derived bovine papillomavirus (BPV1), and wart-derived human papillomavirus type 1 (HPV1) using quantitative mass spectrometry. The chromatin from all three virion samples had abundant posttranslational modifications (acetylation, methylation, and phosphorylation). These histone modifications were verified by acid urea polyacrylamide electrophoresis and immunoblot analysis. Compared to matched host cell controls, the virion minichromosome was enriched in histone modifications associated with active chromatin and depleted for those commonly found in repressed chromatin. We propose that the viral minichromosome acquires specific histone modifications late in infection that are coupled to the mechanisms of viral replication, late gene expression, and encapsidation. We predict that, in turn, these same modifications benefit early stages of infection by helping to evade detection, promoting localization of the viral chromosome to beneficial regions of the nucleus, and promoting early transcription and replication.
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10
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Connor MG, Camarasa TMN, Patey E, Rasid O, Barrio L, Weight CM, Miller DP, Heyderman RS, Lamont RJ, Enninga J, Hamon MA. The histone demethylase KDM6B fine-tunes the host response to Streptococcus pneumoniae. Nat Microbiol 2020; 6:257-269. [PMID: 33349663 DOI: 10.1038/s41564-020-00805-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/28/2020] [Indexed: 01/08/2023]
Abstract
Streptococcus pneumoniae is a natural colonizer of the human respiratory tract and an opportunistic pathogen. Although epithelial cells are among the first to encounter pneumococci, the cellular processes and contribution of epithelial cells to the host response are poorly understood. Here, we show that a S. pneumoniae serotype 6B ST90 strain, which does not cause disease in a murine infection model, induces a unique NF-κB signature response distinct from an invasive-disease-causing isolate of serotype 4 (TIGR4). This signature is characterized by activation of p65 and requires a histone demethylase KDM6B. We show, molecularly, that the interaction of the 6B strain with epithelial cells leads to chromatin remodelling within the IL-11 promoter in a KDM6B-dependent manner, where KDM6B specifically demethylates histone H3 lysine 27 dimethyl. Remodelling of the IL-11 locus facilitates p65 access to three NF-κB sites that are otherwise inaccessible when stimulated by IL-1β or TIGR4. Finally, we demonstrate through chemical inhibition of KDM6B with GSK-J4 inhibitor and through exogenous addition of IL-11 that the host responses to the 6B ST90 and TIGR4 strains can be interchanged both in vitro and in a murine model of infection in vivo. Our studies therefore reveal how a chromatin modifier governs cellular responses during infection.
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Affiliation(s)
| | - Tiphaine M N Camarasa
- G5 Chromatin and Infection, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Emma Patey
- G5 Chromatin and Infection, Institut Pasteur, Paris, France.,University of Glasgow, Scotland, UK
| | - Orhan Rasid
- G5 Chromatin and Infection, Institut Pasteur, Paris, France
| | - Laura Barrio
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,UMR CNRS, Paris, France
| | - Caroline M Weight
- Division of Infection and Immunity, University College London, London, UK
| | - Daniel P Miller
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
| | - Jost Enninga
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,UMR CNRS, Paris, France
| | - Melanie A Hamon
- G5 Chromatin and Infection, Institut Pasteur, Paris, France.
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11
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Hauck AK, Zhou T, Upadhyay A, Sun Y, O’Connor MB, Chen Y, Bernlohr DA. Histone Carbonylation Is a Redox-Regulated Epigenomic Mark That Accumulates with Obesity and Aging. Antioxidants (Basel) 2020; 9:antiox9121210. [PMID: 33271806 PMCID: PMC7761391 DOI: 10.3390/antiox9121210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023] Open
Abstract
Oxidative stress is a hallmark of metabolic disease, though the mechanisms that define this link are not fully understood. Irreversible modification of proteins by reactive lipid aldehydes (protein carbonylation) is a major consequence of oxidative stress in adipose tissue and the substrates and specificity of this modification are largely unexplored. Here we show that histones are avidly modified by 4-hydroxynonenal (4-HNE) in vitro and in vivo. Carbonylation of histones by 4-HNE increased with age in male flies and visceral fat depots of mice and was potentiated in genetic (ob/ob) and high-fat feeding models of obesity. Proteomic evaluation of in vitro 4-HNE- modified histones led to the identification of both Michael and Schiff base adducts. In contrast, mapping of sites in vivo from obese mice exclusively revealed Michael adducts. In total, we identified 11 sites of 4-hydroxy hexenal (4-HHE) and 10 sites of 4-HNE histone modification in visceral adipose tissue. In summary, these results characterize adipose histone carbonylation as a redox-linked epigenomic mark associated with metabolic disease and aging.
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Affiliation(s)
- Amy K. Hauck
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.K.H.); (T.Z.); (Y.C.)
| | - Tong Zhou
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.K.H.); (T.Z.); (Y.C.)
| | - Ambuj Upadhyay
- Department of Molecular Biology, Cell Biology, Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN 55455, USA; (A.U.); (M.B.O.)
| | - Yuxiang Sun
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA;
| | - Michael B. O’Connor
- Department of Molecular Biology, Cell Biology, Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN 55455, USA; (A.U.); (M.B.O.)
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.K.H.); (T.Z.); (Y.C.)
| | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.K.H.); (T.Z.); (Y.C.)
- Correspondence:
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13
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Szabó B, Németh K, Mészáros K, Szücs N, Czirják S, Reiniger L, Rajnai H, Krencz I, Karászi K, Krokker L, Patócs A, Butz H. Demethylation Status of Somatic DNA Extracted From Pituitary Neuroendocrine Tumors Indicates Proliferative Behavior. J Clin Endocrinol Metab 2020; 105:5813957. [PMID: 32232382 DOI: 10.1210/clinem/dgaa156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/27/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND Cytosine intermediaries 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), epigenetic hallmarks, have never been investigated in pituitary neuroendocrine tumors (PitNET). OBJECTIVE To examine methylation-demethylation status of global deoxyribonucleic acid (DNA) in PitNET tissues and to assess its correlation with clinical and biological parameters. MATERIALS AND METHODS Altogether, 57 PitNET and 25 corresponding plasma samples were collected. 5mC and 5hmC were investigated using liquid chromatography-tandem mass spectrometry. Expression of DNA methyltransferase 1 (DNMT1); tet methylcytosine dioxygenase 1 through 3 (TET1-3); and ubiquitin-like, containing PHD and RING finger domains 1 and 2 (UHRF1-2) were measured by reverse transcription-polymerase chain reaction. Levels of 5hmC and UHRF1-2 were explored by immunohistochemistry. Effect of demethylating agent decitabine was tested on pituitary cell lines. RESULTS 5hmC/5mC ratio was higher in less differentiated PitNET samples. A negative correlation between Ki-67 proliferation index and 5hmC, 5hmC to 5mC ratio were revealed. Higher 5mC was observed in SF-1 + gonadotroph adenomas with a higher Ki-67 index. Expressions of TET2 and TET3 were significantly higher in adenomas with higher proliferation rate. UHRF1 showed gradually increased expression in higher proliferative adenoma samples, and a significant positive correlation was detected between UHRF2 expression and 5hmC level. Decitabine treatment significantly decreased 5mC and increased 5hmC levels in both cell lines, accompanied with decreased cell viability and proliferation. CONCLUSION The demethylation process negatively correlated with proliferation rate and the ratio of 5hmC to 5mC was higher in less differentiated adenomas. Therefore, epigenetic markers can be potential biomarkers for PitNET behavior. Altering the epigenome in adenoma cells by decitabine decreased proliferation, suggesting that this treatment might be a novel medical treatment for PitNET.
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Affiliation(s)
- Borbála Szabó
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Kinga Németh
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Katalin Mészáros
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Nikolette Szücs
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Sándor Czirják
- National Institute of Clinical Neurosciences, Budapest, Hungary
| | - Lilla Reiniger
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Hajnalka Rajnai
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ildikó Krencz
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Karászi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Lilla Krokker
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology
| | - Henriett Butz
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology
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Liu M, Saha N, Gajan A, Saadat N, Gupta SV, Pile LA. A complex interplay between SAM synthetase and the epigenetic regulator SIN3 controls metabolism and transcription. J Biol Chem 2019; 295:375-389. [PMID: 31776190 DOI: 10.1074/jbc.ra119.010032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/25/2019] [Indexed: 12/30/2022] Open
Abstract
The SIN3 histone-modifying complex regulates the expression of multiple methionine catabolic genes, including SAM synthetase (Sam-S), as well as SAM levels. To further dissect the relationship between methionine catabolism and epigenetic regulation by SIN3, we sought to identify genes and metabolic pathways controlled by SIN3 and SAM synthetase (SAM-S) in Drosophila melanogaster Using several approaches, including RNAi-mediated gene silencing, RNA-Seq- and quantitative RT-PCR-based transcriptomics, and ultra-high-performance LC-MS/MS- and GC/MS-based metabolomics, we found that, as a global transcriptional regulator, SIN3 impacted a wide range of genes and pathways. In contrast, SAM-S affected only a narrow range of genes and pathways. The expression and levels of additional genes and metabolites, however, were altered in Sin3A+Sam-S dual knockdown cells. This analysis revealed that SIN3 and SAM-S regulate overlapping pathways, many of which involve one-carbon and central carbon metabolisms. In some cases, the factors acted independently; in some others, redundantly; and for a third set, in opposition. Together, these results, obtained from experiments with the chromatin regulator SIN3 and the metabolic enzyme SAM-S, uncover a complex relationship between metabolism and epigenetic regulation.
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Affiliation(s)
- Mengying Liu
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202; Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109
| | - Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Detroit, Michigan 48201
| | - Nadia Saadat
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202; College of Engineering and Science, University of Detroit Mercy, Detroit, Michigan 48221
| | - Smiti V Gupta
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
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Zhang C, Huang C, Sui X, Zhong X, Yang W, Hu X, Li Y. Association between gene methylation and HBV infection in hepatocellular carcinoma: A meta-analysis. J Cancer 2019; 10:6457-6465. [PMID: 31772678 PMCID: PMC6856736 DOI: 10.7150/jca.33005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
Gene methylation is an epigenetic alteration in hepatocellular carcinoma (HCC), and hepatitis B virus (HBV) plays a crucial role in carcinogenesis of HCC. However, the association between gene methylation and HBV infection in HCC remains unclear. In our study, we conducted a comprehensive meta-analysis to evaluate the association. A total of 1,148 studies were initially retrieved from some literature database. After a four-step filtration, we obtained 69 case-control studies in this meta-analysis. Our results showed six genes (p16, RASSF1A, GSTP1, APC, p15 and SFRP1) in HBV-positive carcinoma tissues, one gene (GSTP1) in HBV-positive adjacent tissues and two gene (p16 and APC) in HBV-positive carcinoma serums, which were significantly hypermethylated. Subgroup meta-analysis by geographical populations revealed that GSTP1 methylation was significantly higher in HBV-positive carcinoma tissues in China and Japan. In addition, p16 and RASSF1A methylation was significantly higher in China but not in Japan. Our study indicated that HBV infection could induce DNA methylation in HCC and DNA methylation could lead to the development of HBV-related HCC.
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Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Changxin Huang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xinbing Sui
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xueqing Zhong
- Department of Gastroenterology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Wenjun Yang
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xiangrong Hu
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yongqiang Li
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang, China
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16
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Sánchez O, Mendonca A, Min A, Liu J, Yuan C. Monitoring Histone Methylation (H3K9me3) Changes in Live Cells. ACS OMEGA 2019; 4:13250-13259. [PMID: 31460452 PMCID: PMC6705211 DOI: 10.1021/acsomega.9b01413] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/19/2019] [Indexed: 05/16/2023]
Abstract
H3K9me3 (methylation of lysine 9 of histone H3) is an epigenetic modification that acts as a repressor mark. Several diseases, including cancers and neurological disorders, have been associated with aberrant changes in H3K9me3 levels. Different tools have been developed to enable detection and quantification of H3K9me3 levels in cells. Most techniques, however, lack live cell compatibility. To address this concern, we have engineered recombinant protein sensors for probing H3K9me3 in situ. A heterodimeric sensor containing a chromodomain and chromo shadow domain from HP1a was found to be optimal in recognizing H3K9me3 and exhibited similar spatial resolution to commercial antibodies. Our sensor offers similar quantitative accuracy in characterizing changes in H3K9me3 compared to antibodies but claims single cell resolution. The sensor was applied to evaluate changes in H3K9me3 responding to environmental chemical atrazine (ATZ). ATZ was found to result in significant reductions in H3K9me3 levels after 24 h of exposure. Its impact on the distribution of H3K9me3 among cell populations was also assessed and found to be distinctive. We foresee the application of our sensors in multiple toxicity and drug-screening applications.
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Affiliation(s)
- Oscar
F. Sánchez
- Davidson
School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette 47907, Indiana, United States
| | - Agnes Mendonca
- Davidson
School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette 47907, Indiana, United States
| | - Alan Min
- Department
of Computer Science, Purdue University, West Lafayette 47907, Indiana, United States
| | - Jichang Liu
- State
Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chongli Yuan
- Davidson
School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette 47907, Indiana, United States
- Purdue
University Center for Cancer Research, West Lafayette 47907, Indiana, United States
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17
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Rao RA, Ketkar AA, Kedia N, Krishnamoorthy VK, Lakshmanan V, Kumar P, Mohanty A, Kumar SD, Raja SO, Gulyani A, Chaturvedi CP, Brand M, Palakodeti D, Rampalli S. KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation. EMBO Rep 2019; 20:e43260. [PMID: 30858340 PMCID: PMC6501005 DOI: 10.15252/embr.201643260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non-histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non-histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2-marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.
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Affiliation(s)
- Radhika Arasala Rao
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
- Sastra University, Tirumalaisamudram, Thanjavur, Tamilnadu, India
| | - Alhad Ashok Ketkar
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Neelam Kedia
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Vignesh K Krishnamoorthy
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Vairavan Lakshmanan
- Sastra University, Tirumalaisamudram, Thanjavur, Tamilnadu, India
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Pankaj Kumar
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Abhishek Mohanty
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Shilpa Dilip Kumar
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Sufi O Raja
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Akash Gulyani
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Chandra Prakash Chaturvedi
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Marjorie Brand
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Shravanti Rampalli
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
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18
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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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19
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Alvarenga EM, Imperador CH, Bardella VB, Rodrigues VL, Mondin M, Cabral-de-Mello DC, Moraes AS, Mello MLS. Histone acetylation and methylation marks in chromatin of Panstrongylus megistus (Hemiptera, Reduviidae). Acta Histochem 2018; 120:572-577. [PMID: 30005894 DOI: 10.1016/j.acthis.2018.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022]
Abstract
Panstrongylus megistus, a potential vector of Chagas disease, currently occupies a wider geographic distribution in Brazil than Triatoma infestans, another member of the hemipteran Reduviidae family and a vector of the same disease. A small heterochromatic body (chromocenter) formed by the Y chromosome is evident in the somatic cells of P. megistus, differing in size and chromosome type contribution from the well-studied chromocenters present in T. infestans. While the overall distribution of histone epigenetic marks differ when comparing the heterochromatin and euchromatin territories in T. infestans, no similar data have been established for other hemipteran reduviids, including P. megistus. In the present work, histone acetylation and methylation marks were investigated in cells of Malpighian tubules of P. megistus 5th instar nymphs using immunocytochemical assays and compared to previously published data for T. infestans. Although similarities between these species were found regarding absence of acetylated H3K9, H4K8 and H4K16, and H3K9me and H3K9me2 in the chromocenter, presence of these marks in euchromatin, and presence of H3K9me3 in the chromocenter, no intimate association of acetylated H4K8 and 18S rDNA was revealed in the chromocenter of P. megistus. The elevated abundance of H3K9me2 marks at the nuclear periphery in P. megistus cells, differing from data for T. infestans, is suggested to reflect differences in the interaction of lamina-associated chromatin domains with the nuclear lamina, methyl-transferase modulation and/or association with the last DNA endoreplication step in 5th instar nymphs, which is a matter for further investigation.
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20
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Yu X, Chen H, Zuo C, Jin X, Yin Y, Wang H, Jin M, Ozato K, Xu S. Chromatin remodeling: demethylating H3K4me3 of type I IFNs gene by Rbp2 through interacting with Piasy for transcriptional attenuation. FASEB J 2018; 32:552-567. [PMID: 28970247 DOI: 10.1096/fj.201700088rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Type I IFNs (IFNIs) are involved in the course of antiviral and antimicrobial activities; however, robust inductions of these can lead to host immunopathology. We have reported that the Pias (protein inhibitor of activated signal transducer and activator of transcription) family member, Piasy, possesses the ability to suppress IFNI transcriptions in mouse embryonic fibroblasts (MEFs), yet the specific molecular mechanism by which it acts remains elusive. Here, we identify that the H3K4me3 levels, one activation mark of genes, in MEFs that were stimulated by poly(I:C) were impaired by Piasy in the IFN-β gene. Piasy bound to the promoter region of the IFN-β gene in MEFs. Meanwhile, retinoblastoma binding protein 2 (Rbp2) was proven to be the only known and novel H3K4me3 demethylase that interacted with Piasy. Overexpression of Rbp2, but not its enzymatically inactive mutant Rbp2H483G/E485Q, retarded the transcription activities of IFNI, whereas small interfering RNA-mediated or short hairpin RNA-mediated knockdown of Rbp2 enhanced IFNI promoter responses. Above all, coexpression of Piasy and Rbp2 led to statistically less IFNI induction than overexpression of either Piasy or Rbp2 alone. Mechanistically, Piasy bound to the Jmjc domain (451-503 aa) of Rbp2 via its PINIT domain (101-218 aa), which is consistent with the domain required for their attenuation of transcription and H3K4me3 levels of IFNI genes. Our study demonstrates that Piasy may prevent exaggerated transcription of IFNI by Rbp2-mediated demethylation of H3K4me3 of IFNI, avoiding excessive immune responses.-Yu, X., Chen, H., Zuo, C., Jin, X., Yin, Y., Wang, H., Jin, M., Ozato, K., Xu, S. Chromatin remodeling: demethylating H3K4me3 of type I IFNs gene by Rbp2 through interacting with Piasy for transcriptional attenuation.
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Affiliation(s)
- Xiaoli Yu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Hui Chen
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Zuo
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xi Jin
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yibing Yin
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hong Wang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Mei Jin
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Keiko Ozato
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Songxiao Xu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
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Poleshko A, Shah PP, Gupta M, Babu A, Morley MP, Manderfield LJ, Ifkovits JL, Calderon D, Aghajanian H, Sierra-Pagán JE, Sun Z, Wang Q, Li L, Dubois NC, Morrisey EE, Lazar MA, Smith CL, Epstein JA, Jain R. Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction. Cell 2017; 171:573-587.e14. [PMID: 29033129 DOI: 10.1016/j.cell.2017.09.018] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/25/2017] [Accepted: 09/12/2017] [Indexed: 01/15/2023]
Abstract
Progenitor cells differentiate into specialized cell types through coordinated expression of lineage-specific genes and modification of complex chromatin configurations. We demonstrate that a histone deacetylase (Hdac3) organizes heterochromatin at the nuclear lamina during cardiac progenitor lineage restriction. Specification of cardiomyocytes is associated with reorganization of peripheral heterochromatin, and independent of deacetylase activity, Hdac3 tethers peripheral heterochromatin containing lineage-relevant genes to the nuclear lamina. Deletion of Hdac3 in cardiac progenitor cells releases genomic regions from the nuclear periphery, leading to precocious cardiac gene expression and differentiation into cardiomyocytes; in contrast, restricting Hdac3 to the nuclear periphery rescues myogenesis in progenitors otherwise lacking Hdac3. Our results suggest that availability of genomic regions for activation by lineage-specific factors is regulated in part through dynamic chromatin-nuclear lamina interactions and that competence of a progenitor cell to respond to differentiation signals may depend upon coordinated movement of responding gene loci away from the nuclear periphery.
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Affiliation(s)
- Andrey Poleshko
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Parisha P Shah
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mudit Gupta
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apoorva Babu
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael P Morley
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren J Manderfield
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie L Ifkovits
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Damelys Calderon
- Department of Cell, Developmental, and Regenerative Biology, Mindich Child Health and Development Institute, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Haig Aghajanian
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Javier E Sierra-Pagán
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zheng Sun
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and the Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qiaohong Wang
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Li
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole C Dubois
- Department of Cell, Developmental, and Regenerative Biology, Mindich Child Health and Development Institute, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward E Morrisey
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine and the Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl L Smith
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, and the Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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22
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Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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23
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Olszewska M, Barciszewska MZ, Fraczek M, Huleyuk N, Chernykh VB, Zastavna D, Barciszewski J, Kurpisz M. Global methylation status of sperm DNA in carriers of chromosome structural aberrations. Asian J Androl 2017; 19:117-124. [PMID: 26908061 PMCID: PMC5227660 DOI: 10.4103/1008-682x.168684] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Male infertility might be clearly associated with aberrant DNA methylation patterns in human spermatozoa. An association between oxidative stress and the global methylation status of the sperm genome has also been suggested. The aim of the present study was to determine whether the global sperm DNA methylation status was affected in the spermatozoa of carriers of chromosome structural aberrations. The relationships between the 5-methylcytosine (m5C) levels in spermatozoa and chromatin integrity status were evaluated. The study patients comprised male carriers of chromosome structural aberrations with reproductive failure (n = 24), and the controls comprised normozoospermic sperm volunteers (n = 23). The global m5C level was measured using thin-layer chromatography (TLC) and immunofluorescence (IF) techniques. The sperm chromatin integrity was assessed using aniline blue (AB) staining and TUNEL assay. The mean m5C levels were similar between the investigated chromosome structural aberrations carriers (P) and controls (K). However, sperm chromatin integrity tests revealed significantly higher values in chromosomal rearrangement carriers than in controls (P < 0.05). Although the potential relationship between sperm chromatin integrity status and sperm DNA fragmentation and the m5C level juxtaposed in both analyzed groups (P vs K) was represented in a clearly opposite manner, the low chromatin integrity might be associated with the high hypomethylation status of the sperm DNA observed in carriers of chromosome structural aberrations.
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Affiliation(s)
- Marta Olszewska
- Department of Reproductive Biology and Stem Cells, Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Miroslawa Z Barciszewska
- Department of RNA Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Monika Fraczek
- Department of Reproductive Biology and Stem Cells, Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Nataliya Huleyuk
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lysenko Street 31a, 79000 Lviv, Ukraine
| | - Vyacheslav B Chernykh
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, 115478 Moscow, Russian Federation
| | - Danuta Zastavna
- Institute of Hereditary Pathology, Ukrainian Academy of Medical Sciences, Lysenko Street 31a, 79000 Lviv, Ukraine
| | - Jan Barciszewski
- Department of RNA Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Kurpisz
- Department of Reproductive Biology and Stem Cells, Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
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24
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Pradhan RN, Bues JJ, Gardeux V, Schwalie PC, Alpern D, Chen W, Russeil J, Raghav SK, Deplancke B. Dissecting the brown adipogenic regulatory network using integrative genomics. Sci Rep 2017; 7:42130. [PMID: 28181539 PMCID: PMC5299609 DOI: 10.1038/srep42130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022] Open
Abstract
Brown adipocytes regulate energy expenditure via mitochondrial uncoupling, which makes them attractive therapeutic targets to tackle obesity. However, the regulatory mechanisms underlying brown adipogenesis are still poorly understood. To address this, we profiled the transcriptome and chromatin state during mouse brown fat cell differentiation, revealing extensive gene expression changes and chromatin remodeling, especially during the first day post-differentiation. To identify putatively causal regulators, we performed transcription factor binding site overrepresentation analyses in active chromatin regions and prioritized factors based on their expression correlation with the bona-fide brown adipogenic marker Ucp1 across multiple mouse and human datasets. Using loss-of-function assays, we evaluated both the phenotypic effect as well as the transcriptomic impact of several putative regulators on the differentiation process, uncovering ZFP467, HOXA4 and Nuclear Factor I A (NFIA) as novel transcriptional regulators. Of these, NFIA emerged as the regulator yielding the strongest molecular and cellular phenotypes. To examine its regulatory function, we profiled the genomic localization of NFIA, identifying it as a key early regulator of terminal brown fat cell differentiation.
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Affiliation(s)
- Rachana N Pradhan
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Johannes J Bues
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Vincent Gardeux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Petra C Schwalie
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Daniel Alpern
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Wanze Chen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Julie Russeil
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | | | - Bart Deplancke
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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25
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Abstract
Progression of cells through distinct phases of the cell cycle, and transition into out-of-cycling states, such as terminal differentiation and senescence, is accompanied by specific patterns of gene expression. These cell fate decisions are mediated not only by distinct transcription factors, but also chromatin modifiers that establish heritable epigenetic patterns. Lysine methyltransferases (KMTs) that mediate methylation marks on histone and non-histone proteins are now recognized as important regulators of gene expression in cycling and non-cycling cells. Among these, the SUV39 sub-family of KMTs, which includes SUV39H1, SUV39H2, G9a, GLP, SETDB1, and SETDB2, play a prominent role. In this review, we discuss their biochemical properties, sub-cellular localization and function in cell cycle, differentiation programs, and cellular senescence. We also discuss their aberrant expression in cancers, which exhibit de-regulation of cell cycle and differentiation.
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Affiliation(s)
- Vinay Kumar Rao
- a Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Ananya Pal
- a Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- a Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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26
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Wu R, Wang Z, Zhang H, Gan H, Zhang Z. H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication. Nucleic Acids Res 2017; 45:169-180. [PMID: 27679476 PMCID: PMC5224507 DOI: 10.1093/nar/gkw848] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 11/30/2022] Open
Abstract
DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.
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Affiliation(s)
- Rentian Wu
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55902, USA
| | - Zhiquan Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55902, USA
| | - Honglian Zhang
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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27
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Liu M, Pile LA. The Transcriptional Corepressor SIN3 Directly Regulates Genes Involved in Methionine Catabolism and Affects Histone Methylation, Linking Epigenetics and Metabolism. J Biol Chem 2016; 292:1970-1976. [PMID: 28028175 DOI: 10.1074/jbc.m116.749754] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/23/2016] [Indexed: 11/06/2022] Open
Abstract
Chromatin modification and cellular metabolism are tightly connected. Chromatin modifiers regulate the expression of genes involved in metabolism and, in turn, the levels of metabolites. The generated metabolites are utilized by chromatin modifiers to affect epigenetic modification. The mechanism for this cross-talk, however, remains incompletely understood. The corepressor SIN3 controls histone acetylation through association with the histone deacetylase RPD3. The SIN3 complex is known to regulate genes involved in a number of metabolic processes. Here, we find that Drosophila SIN3 binds to the promoter region of genes involved in methionine catabolism and that this binding affects histone modification, which in turn influences gene expression. Specifically, we observe that reduced expression of SIN3 leads to an increase in S-adenosylmethionine (SAM), which is the major cellular donor of methyl groups for protein modification. Additionally, Sin3A knockdown results in an increase in global histone H3K4me3 levels. Furthermore, decreased H3K4me3 caused by knockdown of either SAM synthetase (Sam-S) or the histone methyltransferase Set1 is restored to near normal levels when SIN3 is also reduced. Taken together, these results indicate that knockdown of Sin3A directly alters the expression of methionine metabolic genes to increase SAM, which in turn leads to an increase in global H3K4me3. Our study reveals that SIN3 is an important epigenetic regulator directly connecting methionine metabolism and histone modification.
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Affiliation(s)
- Mengying Liu
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Lori A Pile
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
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28
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Iguchi E, Safgren SL, Marks DL, Olson RL, Fernandez-Zapico ME. Pancreatic Cancer, A Mis-interpreter of the Epigenetic Language. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:575-590. [PMID: 28018146 PMCID: PMC5168833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pancreatic cancer is the third leading cause of cancer mortality in the U.S. with close to 40,000 deaths per year. Pancreatic ductal adenocarcinoma (PDAC) represents approximately 90 percent of all pancreatic cancer cases and is the most lethal form of the disease. Current therapies for PDAC are ineffective and most patients cannot be treated by surgical resection. Most research efforts have primarily focused on how genetic alterations cause, alter progression, contribute to diagnosis, and influence PDAC management. Over the past two decades, a model has been advanced of PDAC initiation and progression as a multi-step process driven by the acquisition of mutations leading to loss of tumor suppressors and activation of oncogenes. The recognition of the essential roles of these genetic alterations in the development of PDAC has revolutionized our knowledge of this disease. However, none of these findings have turned into effective treatment for this dismal malignancy. In recent years, studies in the areas of chromatin modifications, and non-coding RNAs have uncovered mechanisms for regulating gene expression which occur independently of genetic alterations. Chromatin-based mechanisms are interwoven with microRNA-driven regulation of protein translation to create an integrated epigenetic language, which is grossly dysregulated in PDAC. Thus in PDAC, key tumor suppressors that are well established to play a role in PDAC may be repressed, and oncogenes can be upregulated secondary to epigenetic alterations. Unlike mutations, epigenetic changes are potentially reversible. Given this feature of epigenetic mechanisms, it is conceivable that targeting epigenetic-based events promoting and maintaining PDAC could serve as foundation for the development of new therapeutic and diagnostic approaches for this disease.
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Affiliation(s)
- Eriko Iguchi
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - David L. Marks
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Rachel L. Olson
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
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29
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Muramatsu D, Kimura H, Kotoshiba K, Tachibana M, Shinkai Y. Pericentric H3K9me3 Formation by HP1 Interaction-defective Histone Methyltransferase Suv39h1. Cell Struct Funct 2016; 41:145-152. [PMID: 27733730 DOI: 10.1247/csf.16013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pericentric regions form epigenetically organized, silent heterochromatin structures that accumulate histone H3 lysine 9 tri-methylation (H3K9me3) and heterochromatin protein 1 (HP1), a methylated H3K9-binding protein. At pericentric regions, Suv39h is the major enzyme that generates H3K9me3. Suv39h also interacts directly with HP1. However, the importance of HP1 interaction for Suv39h-mediated H3K9me3 formation at the pericentromere is not well characterized. To address this question, we introduced HP1 binding-defective, N-terminally truncated mouse Suv39h1 (ΔN) into Suv39h-deficient cells. Pericentric H3K9me3-positive cells were not detected by endogenous-level expression of ΔN. Notably, ΔN could induce pericentric accumulation of H3K9me3 as wild type Suv39h1 did if it was overexpressed. These findings demonstrate that the N-terminal region of Suv39h1, presumably via HP1-Suv39h1 interaction, is required for Suv39h1-mediated pericentric H3K9me3 formation, but can be overridden if Suv39h1 is overproduced, indicating that Suv39h1-mediated heterochromatin formation is controlled by multiple modules, including HP1.
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30
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Asaka MN, Kawaguchi A, Sakai Y, Mori K, Nagata K. Polycomb repressive complex 2 facilitates the nuclear export of the influenza viral genome through the interaction with M1. Sci Rep 2016; 6:33608. [PMID: 27646999 PMCID: PMC5028886 DOI: 10.1038/srep33608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/30/2016] [Indexed: 12/15/2022] Open
Abstract
The organization of nuclear domains is crucial for biological events including virus infection. Newly synthesized influenza viral genome forms viral ribonucleoprotein (vRNP) complexes and is exported from the nucleus to the cytoplasm through a CRM1-dependent pathway mediated by viral proteins M1 and NS2. However, the spatio-temporal regulation of the progeny vRNP in the nucleus is still unclear. Here we found that polycomb repressive complex 2 (PRC2), which contains a methyltransferase subunit EZH2 and catalyzes histone H3K27me3 for the formation of facultative heterochromatin, is a positive factor for the virus production. Depletion of PRC2 complex showed the nuclear accumulation of vRNP and the reduction of M1-vRNP complex formation. We also found that PRC2 complex directly binds to M1, and facilitates the interaction of M1 with vRNP. In conclusion, we propose that the progeny vRNP could be recruited to facultative heterochromatin and assembled into the export complex mediated by PRC2 complex.
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Affiliation(s)
- Masamitsu N Asaka
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Yuri Sakai
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Kotaro Mori
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
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31
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Wu Q, Guan J, Zhou S. Histone modification patterns in highly differentiation cells. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2015.11.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes in Caenorhabditis Species. Genetics 2016; 203:1641-58. [PMID: 27280692 DOI: 10.1534/genetics.116.191130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/06/2016] [Indexed: 01/19/2023] Open
Abstract
During meiosis in the heterogametic sex in some species, sex chromosomes undergo meiotic sex chromosome inactivation (MSCI), which results in acquisition of repressive chromatin and transcriptional silencing. In Caenorhabditis elegans, MSCI is mediated by MET-2 methyltransferase deposition of histone H3 lysine 9 dimethylation. Here we examined the meiotic chromatin landscape in germ lines of four Caenorhabditis species; C. remanei and C. brenneri represent ancestral gonochorism, while C. briggsae and C. elegans are two lineages that independently evolved hermaphroditism. While MSCI is conserved across all four species, repressive chromatin modifications are distinct and do not correlate with reproductive mode. In contrast to C. elegans and C. remanei germ cells where X chromosomes are enriched for histone H3 lysine 9 dimethylation, X chromosomes in C. briggsae and C. brenneri germ cells are enriched for histone H3 lysine 9 trimethylation. Inactivation of C. briggsae MET-2 resulted in germ-line X chromosome transcription and checkpoint activation. Further, both histone H3 lysine 9 di- and trimethylation were reduced in Cbr-met-2 mutant germ lines, suggesting that in contrast to C. elegans, H3 lysine 9 di- and trimethylation are interdependent. C. briggsae H3 lysine 9 trimethylation was redistributed in the presence of asynapsed chromosomes in a sex-specific manner in the related process of meiotic silencing of unsynapsed chromatin. However, these repressive marks did not influence X chromosome replication timing. Examination of additional Caenorhabditis species revealed diverse H3 lysine 9 methylation patterns on the X, suggesting that the sex chromosome epigenome evolves rapidly.
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33
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Alvarenga EM, Rodrigues VL, Moraes AS, Naves LS, Mondin M, Felisbino MB, Mello MLS. Histone epigenetic marks in heterochromatin and euchromatin of the Chagas' disease vector, Triatoma infestans. Acta Histochem 2016; 118:401-12. [PMID: 27079857 DOI: 10.1016/j.acthis.2016.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 01/23/2023]
Abstract
Triatoma infestans, a vector of Chagas' disease, shows several particular cell biology characteristics, including the presence of conspicuous heterochromatic bodies (chromocenters) where DNA methylation has not been previously detected. Whether histone modifications contribute to the condensed state of these bodies has not yet been studied. Here, we investigated epigenetic modifications of histones H3 and H4 and presence of the non-histone heterochromatin protein (HP1-α) in the chromocenters and euchromatin of T. infestans cell nuclei, using immunocytochemistry. The effect of different concentrations of the histone deacetylase inhibitors valproic acid (VPA) and sodium butyrate (NaBt) on chromocenter condensation was visually examined; in VPA-treated specimens, this effect was also analyzed by image analysis. Trimethylated H3K9 signals, which were revealed in chromocenter and non-chromocenter areas, were strongest in chromocenters, whereas selected acetylated histone marks and mono- and dimethylated H3K9 and H4K20 signals were detected only in euchromatin. Weak trimethylated H4K20 signals and variable distribution of HP1-α were detected in chromocenters of part of the cellular population analyzed. Although specific VPA and NaBt treatment conditions affected the heterochromatin condensation pattern, they did not induce a decrease in survival and molting rates of the T. infestans nymphs. The VPA-induced chromatin remodeling was not accompanied by induction of H3K9 acetylation in chromocenters. Present findings regarding histone modifications and effects following VPA or NaBt treatments did not yet solve the question of which factors are responsible for maintenance of the condensed state of chromocenters in T. infestans. A possibility requiring further investigation remains on histone methylation marks and/or non-histone proteins.
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34
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Black JC, Whetstine JR. Tipping the lysine methylation balance in disease. Biopolymers 2016; 99:127-35. [PMID: 23175387 DOI: 10.1002/bip.22136] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 12/28/2022]
Abstract
Genomic instability is a major contributing factor to the development and onset of diseases such as cancer. Emerging evidence has demonstrated that maintaining the proper balance of histone lysine methylation is critical to preserve genomic integrity. Genome-wide association studies, gene sequencing, and genome-wide mapping approaches have helped identify mutations, copy number changes, and aberrant gene regulation of lysine methyltransferases (KMTs) and demethylases (KDMs) associated with cancer and cognitive disorders. Structural analysis of KMTs and KDMs has demonstrated the drugability of these enzymes and has led to the discovery of small molecule inhibitors. Use of these inhibitors has allowed better understanding of the biochemical properties of KMTs and KDMs and demonstrated potential for therapeutic use. This review will highlight the methyl modifications, KMTs and KDMs associated with cancer and neurological disorders and how KMT and KDM and the potential for treatment of these conditions with small molecule inhibitors.
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Affiliation(s)
- Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13th Street, Charlestown, MA 02129
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35
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Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep 2015; 16:1620-39. [PMID: 26564907 PMCID: PMC4687429 DOI: 10.15252/embr.201541113] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023] Open
Abstract
Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes.
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Affiliation(s)
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
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36
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Disruption of Methionine Metabolism in Drosophila melanogaster Impacts Histone Methylation and Results in Loss of Viability. G3-GENES GENOMES GENETICS 2015; 6:121-32. [PMID: 26546310 PMCID: PMC4704710 DOI: 10.1534/g3.115.024273] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Histone methylation levels, which are determined by the action of both histone demethylases and methyltransferases, impact multiple biological processes by affecting gene expression activity. Methionine metabolism generates the major methyl donor S-adenosylmethionine (SAM) for histone methylation. The functions of methionine metabolic enzymes in regulating biological processes as well as the interaction between the methionine pathway and histone methylation, however, are still not fully understood. Here, we report that reduced levels of some enzymes involved in methionine metabolism and histone demethylases lead to lethality as well as wing development and cell proliferation defects in Drosophila melanogaster. Additionally, disruption of methionine metabolism can directly affect histone methylation levels. Reduction of little imaginal discs (LID) histone demethylase, but not lysine-specific demethylase 2 (KDM2) demethylase, is able to counter the effects on histone methylation due to reduction of SAM synthetase (SAM-S). Taken together, these results reveal an essential role of key enzymes that control methionine metabolism and histone methylation. Additionally, these findings are an indication of a strong connection between metabolism and epigenetics.
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Abdouh M, Hanna R, El Hajjar J, Flamier A, Bernier G. The Polycomb Repressive Complex 1 Protein BMI1 Is Required for Constitutive Heterochromatin Formation and Silencing in Mammalian Somatic Cells. J Biol Chem 2015; 291:182-97. [PMID: 26468281 DOI: 10.1074/jbc.m115.662403] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 01/08/2023] Open
Abstract
The polycomb repressive complex 1 (PRC1), containing the core BMI1 and RING1A/B proteins, mono-ubiquitinylates histone H2A (H2A(ub)) and is associated with silenced developmental genes at facultative heterochromatin. It is, however, assumed that the PRC1 is excluded from constitutive heterochromatin in somatic cells based on work performed on mouse embryonic stem cells and oocytes. We show here that BMI1 is required for constitutive heterochromatin formation and silencing in human and mouse somatic cells. BMI1 was highly enriched at intergenic and pericentric heterochromatin, co-immunoprecipitated with the architectural heterochromatin proteins HP1, DEK1, and ATRx, and was required for their localization. In contrast, BRCA1 localization was BMI1-independent and partially redundant with that of BMI1 for H2A(ub) deposition, constitutive heterochromatin formation, and silencing. These observations suggest a dynamic and developmentally regulated model of PRC1 occupancy at constitutive heterochromatin, and where BMI1 function in somatic cells is to stabilize the repetitive genome.
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Affiliation(s)
- Mohamed Abdouh
- From the Department of Neurosciences, University of Montreal, and The Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montreal H1T 2M4, Canada
| | - Roy Hanna
- From the Department of Neurosciences, University of Montreal, and The Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montreal H1T 2M4, Canada
| | - Jida El Hajjar
- From the Department of Neurosciences, University of Montreal, and The Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montreal H1T 2M4, Canada
| | - Anthony Flamier
- From the Department of Neurosciences, University of Montreal, and The Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montreal H1T 2M4, Canada
| | - Gilbert Bernier
- From the Department of Neurosciences, University of Montreal, and The Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boul. l'Assomption, Montreal H1T 2M4, Canada
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Sonic Hedgehog Signaling Affected by Promoter Hypermethylation Induces Aberrant Gli2 Expression in Spina Bifida. Mol Neurobiol 2015; 53:5413-24. [PMID: 26446020 DOI: 10.1007/s12035-015-9447-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 09/16/2015] [Indexed: 02/06/2023]
Abstract
GLI2 is a key mediator of the sonic hedgehog (Shh) signaling pathway and plays an important role in neural tube development during vertebrate embryogenesis; however, the role of gli2 in human folate-related neural tube defects remains unclear. In this study, we compared methylation status and polymorphisms of gli2 between spina bifida patients and a control group to explore the underlying mechanisms related to folate deficiency in spina bifida. No single nucleotide polymorphism was found to be significantly different between the two groups, although gli2 methylation levels were significantly increased in spina bifida samples, accompanied by aberrant GLI2 expression. Moreover, a prominent negative correlation was found between the folate level in brain tissue and the gli2 methylation status (r = -0.41, P = 0.014), and gli2 hypermethylation increased the risk of spina bifida with an odds ratio of 12.45 (95 % confidence interval: 2.71-57.22, P = 0.001). In addition, we established a cell model to illustrate the effect of gli2 expression and the accessibility of chromatin affected by methylation. High gli2 and gli1 mRNA expression was detected in 5-Aza-treated cells, while gli2 hypermethylation resulted in chromatin inaccessibility and a reduced association with nuclear proteins containing transcriptional factors. More meaningful to the pathway, the effect gene of the Shh pathway, gli1, was found to have a reduced level of expression along with a decreased expression of gli2 in our cell model. Aberrant high methylation resulted in the low expression of gli2 in spina bifida, which was affected by the change in chromatin status and the capacity of transcription factor binding.
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Ozaki Y, Fujiwara K, Ikeda M, Ozaki T, Terui T, Soma M, Inazawa J, Nagase H. The oncogenic role of GASC1 in chemically induced mouse skin cancer. Mamm Genome 2015; 26:591-7. [DOI: 10.1007/s00335-015-9592-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
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Abdolmaleky HM, Zhou JR, Thiagalingam S. An update on the epigenetics of psychotic diseases and autism. Epigenomics 2015; 7:427-49. [DOI: 10.2217/epi.14.85] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The examination of potential roles of epigenetic alterations in the pathogenesis of psychotic diseases have become an essential alternative in recent years as genetic studies alone are yet to uncover major gene(s) for psychosis. Here, we describe the current state of knowledge from the gene-specific and genome-wide studies of postmortem brain and blood cells indicating that aberrant DNA methylation, histone modifications and dysregulation of micro-RNAs are linked to the pathogenesis of mental diseases. There is also strong evidence supporting that all classes of psychiatric drugs modulate diverse features of the epigenome. While comprehensive environmental and genetic/epigenetic studies are uncovering the origins, and the key genes/pathways affected in psychotic diseases, characterizing the epigenetic effects of psychiatric drugs may help to design novel therapies in psychiatry.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Departments of Medicine (Biomedical Genetics Section), Genetics & Genomics, Boston University School of Medicine, Boston, MA 02118, USA
- Nutrition/Metabolism Laboratory at Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory at Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Sam Thiagalingam
- Departments of Medicine (Biomedical Genetics Section), Genetics & Genomics, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
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Abstract
PURPOSE OF REVIEW Gallbladder cancer (GBC) should be considered an orphan disease in oncology and represent a unique carcinogenetic model. This review will analyse some of the current aspects of GBC. RECENT FINDINGS Chile has the highest incidence and mortality of GBC in the world. Most patients are diagnosed in advanced stages with few treatment options. During the last two decades, little progress has been made in early diagnosis and treatment. At the molecular level, recent access to next-generation sequencing and other techniques for detecting the mutations of multiple genes have made advances in this area. SUMMARY The use of therapies targeted according to the detection of specific molecular alterations is in the early stages of evaluation and could represent a significant advance in the treatment of a large number of patients from developing countries.
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Abstract
The lung develops from a very simple outpouching of the foregut into a highly complex, finely structured organ with multiple specialized cell types that are required for its normal physiological function. During both the development of the lung and its remodeling in the context of disease or response to injury, gene expression must be activated and silenced in a coordinated manner to achieve the tremendous phenotypic heterogeneity of cell types required for homeostasis and pathogenesis. Epigenetic mechanisms, consisting of DNA base modifications such as methylation, alteration of histones resulting in chromatin modification, and the action of noncoding RNA, control the regulation of information "beyond the genome" required for both lung modeling and remodeling. Epigenetic regulation is subject to modification by environmental stimuli, such as oxidative stress, infection, and aging, and is thus critically important in chronic remodeling disorders such as idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), bronchopulmonary dysplasia (BPD), and pulmonary hypertension (PH). Technological advances have made it possible to evaluate genome-wide epigenetic changes (epigenomics) in diseases of lung remodeling, clarifying existing pathophysiological paradigms and uncovering novel mechanisms of disease. Many of these represent new therapeutic targets. Advances in epigenomic technology will accelerate our understanding of lung development and remodeling, and lead to novel treatments for chronic lung diseases.
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Affiliation(s)
- James S Hagood
- Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego and Rady Children's Hospital of San Diego, San Diego, California
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Affiliation(s)
- Hannah Landecker
- Institute for Society and Genetics, Department of Sociology, University of California Los Angeles, Box 957221, 1320 Rolfe Hall, Los Angeles, CA 90095-7221, CA, USA.
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Lappé M, Landecker H. How The Genome Got a Life Span. NEW GENETICS AND SOCIETY 2015; 34:152-176. [PMID: 26213491 PMCID: PMC4512745 DOI: 10.1080/14636778.2015.1034851] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 03/03/2015] [Indexed: 05/15/2023]
Abstract
In the space of little more than a decade, ideas of the human genome have shifted significantly, with the emergence of the notion that the genome an individual changes with development, age, disease, environmental inputs, and time. This paper examines the emergence of the genome with a life span, one that experiences drift, instability and mutability, and a host of other temporal changes. We argue that developments in chromatin biology have provided the basis for this genomic embodiment of experience and exposure. We analyze how time has come to matter for the genome through chromatin, providing analysis of examples in which the human life course is being explored as a set of material changes to chromatin. A genome with a lifespan aligns the molecular and the experiential in new ways, shifting ideas of life stages, their interrelation, and the temporality of health and disease.
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Affiliation(s)
- Martine Lappé
- Columbia University Center for Research on Ethical, Legal, and Social Implications of Psychiatric, Neurologic, & Behavioral Genetics, 1051 Riverside Drive New York, NY 10032
| | - Hannah Landecker
- Institute for Society and Genetics And the Department of Sociology, University of California Los Angeles, Box 957221, 1320 Rolfe Hall, Los Angeles, CA 90095-7221 Telephone: 310-825-1517
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Huisman C, van der Wijst MGP, Falahi F, Overkamp J, Karsten G, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Prolonged re-expression of the hypermethylated gene EPB41L3 using artificial transcription factors and epigenetic drugs. Epigenetics 2015; 10:384-96. [PMID: 25830725 DOI: 10.1080/15592294.2015.1034415] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) is considered a significant event in the progression of cancer. For example, EPB41L3, a potential biomarker in cervical cancer, is often silenced by cancer-specific promoter methylation. Artificial transcription factors (ATFs) are unique tools to re-express such silenced TSGs to functional levels; however, the induced effects are considered transient. Here, we aimed to improve the efficiency and sustainability of gene re-expression using engineered zinc fingers fused to VP64 (ZF-ATFs) or DNA methylation modifiers (ZF-Tet2 or ZF-TDG) and/or by co-treatment with epigenetic drugs [5-aza-2'-deoxycytidine or Trichostatin A (TSA)]. The EPB41L3-ZF effectively bound its methylated endogenous locus, as also confirmed by ChIP-seq. ZF-ATFs reactivated the epigenetically silenced target gene EPB41L3 (∼ 10-fold) in breast, ovarian, and cervical cancer cell lines. Prolonged high levels of EPB41L3 (∼ 150-fold) induction could be achieved by short-term co-treatment with epigenetic drugs. Interestingly, for otherwise ineffective ZF-Tet2 or ZF-TDG treatments, TSA facilitated re-expression of EPB41L3 up to twofold. ATF-mediated re-expression demonstrated a tumor suppressive role for EPB41L3 in cervical cancer cell lines. In conclusion, epigenetic reprogramming provides a novel way to improve sustainability of re-expression of epigenetically silenced promoters.
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Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1440-53. [DOI: 10.1016/j.bbagrm.2014.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/22/2023]
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Flowers S, Patel PJ, Gleicher S, Amer K, Himelman E, Goel S, Moran E. p107-Dependent recruitment of SWI/SNF to the alkaline phosphatase promoter during osteoblast differentiation. Bone 2014; 69:47-54. [PMID: 25182511 PMCID: PMC5222550 DOI: 10.1016/j.bone.2014.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/11/2014] [Accepted: 08/16/2014] [Indexed: 12/28/2022]
Abstract
The retinoblastoma protein family is intimately involved in the regulation of tissue specific gene expression during mesenchymal stem cell differentiation. The role of the following proteins, pRB, p107 and p130, is particularly significant in differentiation to the osteoblast lineage, as human germ-line mutations of RB1 greatly increase susceptibility to osteosarcoma. During differentiation, pRB directly targets certain osteogenic genes for activation, including the alkaline phosphatase-encoding gene Alpl. Chromatin immunoprecipitation (ChIP) assays indicate that Alpl is targeted by p107 in differentiating osteoblasts selectively during activation with the same dynamics as pRB, which suggests that p107 helps promote Alpl activation. Mouse models indicate overlapping roles for pRB and p107 in bone and cartilage formation, but very little is known about direct tissue-specific gene targets of p107, or the consequences of targeting by p107. Here, the roles of p107 and pRB were compared using shRNA-mediated knockdown genetics in an osteoblast progenitor model, MC3T3-E1 cells. The results show that p107 has a distinct role along with pRB in induction of Alpl. Deficiency of p107 does not impede recruitment of transcription factors recognized as pRB co-activation partners at the promoter; however, p107 is required for the efficient recruitment of an activating SWI/SNF chromatin-remodeling complex, an essential event in Alpl induction.
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Affiliation(s)
- Stephen Flowers
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Parth J Patel
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Stephanie Gleicher
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Kamal Amer
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Eric Himelman
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Shruti Goel
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Elizabeth Moran
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA.
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Zuchegna C, Aceto F, Bertoni A, Romano A, Perillo B, Laccetti P, Gottesman ME, Avvedimento EV, Porcellini A. Mechanism of retinoic acid-induced transcription: histone code, DNA oxidation and formation of chromatin loops. Nucleic Acids Res 2014; 42:11040-55. [PMID: 25217584 PMCID: PMC4176188 DOI: 10.1093/nar/gku823] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Histone methylation changes and formation of chromatin loops involving enhancers, promoters and 3′ end regions of genes have been variously associated with active transcription in eukaryotes. We have studied the effect of activation of the retinoic A receptor, at the RARE–promoter chromatin of CASP9 and CYP26A1 genes, 15 and 45 min following RA exposure, and we found that histone H3 lysines 4 and 9 are demethylated by the lysine-specific demethylase, LSD1 and by the JMJ-domain containing demethylase, D2A. The action of the oxidase (LSD1) and a dioxygenase (JMJD2A) in the presence of Fe++ elicits an oxidation wave that locally modifies the DNA and recruits the enzymes involved in base and nucleotide excision repair (BER and NER). These events are essential for the formation of chromatin loop(s) that juxtapose the RARE element with the 5′ transcription start site and the 3′ end of the genes. The RARE bound-receptor governs the 5′ and 3′ end selection and directs the productive transcription cycle of RNA polymerase. These data mechanistically link chromatin loops, histone methylation changes and localized DNA repair with transcription.
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Affiliation(s)
- Candida Zuchegna
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
| | - Fabiana Aceto
- Dipartimento di Medicina e di Scienze della Salute, Università del Molise, 86100 Campobasso, Italy
| | - Alessandra Bertoni
- Dipartimento di Medicina Molecolare e Biotecnologie mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy
| | - Antonella Romano
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
| | - Bruno Perillo
- Istituto di Scienze dell'Alimentazione, C.N.R., 83100 Avellino, Italy
| | - Paolo Laccetti
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
| | - Max E Gottesman
- Institute of Cancer Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Enrico V Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy
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Dietz KN, Di Stefano L, Maher RC, Zhu H, Macdonald ME, Gusella JF, Walker JA. The Drosophila Huntington's disease gene ortholog dhtt influences chromatin regulation during development. Hum Mol Genet 2014; 24:330-45. [PMID: 25168387 DOI: 10.1093/hmg/ddu446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Huntington's disease is an autosomal dominant neurodegenerative disorder caused by a CAG expansion mutation in HTT, the gene encoding huntingtin. Evidence from both human genotype-phenotype relationships and mouse model systems suggests that the mutation acts by dysregulating some normal activity of huntingtin. Recent work in the mouse has revealed a role for huntingtin in epigenetic regulation during development. Here, we examine the role of the Drosophila huntingtin ortholog (dhtt) in chromatin regulation in the development of the fly. Although null dhtt mutants display no overt phenotype, we found that dhtt acts as a suppressor of position-effect variegation (PEV), suggesting that it influences chromatin organization. We demonstrate that dhtt affects heterochromatin spreading in a PEV model by modulating histone H3K9 methylation levels at the heterochromatin-euchromatin boundary. To gain mechanistic insights into how dhtt influences chromatin function, we conducted a candidate genetic screen using RNAi lines targeting known PEV modifier genes. We found that dhtt modifies phenotypes caused by knockdown of a number of key epigenetic regulators, including chromatin-associated proteins, histone demethylases (HDMs) and methyltransferases. Notably, dhtt strongly modifies phenotypes resulting from loss of the HDM dLsd1, in both the ovary and wing, and we demonstrate that dhtt appears to act as a facilitator of dLsd1 function in regulating global histone H3K4 methylation levels. These findings suggest that a fundamental aspect of huntingtin function in heterochromatin/euchromatin organization is evolutionarily conserved across phyla.
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Affiliation(s)
- Kevin N Dietz
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Luisa Di Stefano
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, UMR 5088, Université de Toulouse and Centre National de la Recherche Scientifique, 31062 Toulouse, France and
| | - Robert C Maher
- Center for Cancer Research, Massachusetts General Hospital, Building 149, 13th Street, Charlestown, MA 02129, USA
| | - Hui Zhu
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - Marcy E Macdonald
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
| | - James A Walker
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge St., Boston, MA 02114, USA
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Balazs R. Epigenetic mechanisms in Alzheimer's disease. Degener Neurol Neuromuscul Dis 2014; 4:85-102. [PMID: 32669903 PMCID: PMC7337154 DOI: 10.2147/dnnd.s37341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/19/2014] [Indexed: 11/25/2022] Open
Abstract
The worldwide increase in life expectancy is leading to an increase in age-dependent diseases, including nonfamilial, sporadic Alzheimer’s disease (AD), which is the subject of this review. The etiology and pathophysiology of the disease is not fully understood, but present observations suggest that, in addition to genetic risk factors, environmental influences may be involved via epigenetic mechanisms. Currently, there is no effective treatment, but there are indications that lifestyle has an impact on the development of the disease. This view is supported by preclinical studies not only showing that human lifestyle-equivalent interventions have a positive effect on cognitive function in animal models of AD, but also indicating the involvement of underlying epigenetic mechanisms. After a brief overview of the most characteristic chromatin modifications, ie, DNA methylation and histone modifications, epigenetic changes associated with aging are considered, given that aging is the most important risk factor for AD. This is followed by a description of some epigenetic alterations recognized in AD. The impact of environmental factors and lifestyle on the epigenome is then considered. Epigenetic treatments with HDAC inhibitors and RNA-based drugs are considered, which – while still in preclinical stages – are promising for potential benefit. It is concluded that while awaiting results from clinical trials in progress, focusing on lifestyle adjustments with an epigenetic background are the best way to prevent/delay the onset of this devastating disease.
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Affiliation(s)
- Robert Balazs
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
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