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MYC, mitochondrial metabolism and O-GlcNAcylation converge to modulate the activity and subcellular localization of DNA and RNA demethylases. Leukemia 2022; 36:1150-1159. [PMID: 34997181 PMCID: PMC8983447 DOI: 10.1038/s41375-021-01489-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 12/31/2022]
Abstract
Mitochondria can function as signaling organelles, and part of this output leads to epigenetic remodeling. The full extent of this far-reaching interplay remains undefined. Here, we show that MYC transcriptionally activates IDH2 and increases alpha-ketoglutarate (αKG) levels. This regulatory step induces the activity of αKG-dependent DNA hydroxylases and RNA demethylases, thus reducing global DNA and RNA methylation. MYC, in a IDH2-dependent manner, also promotes the nuclear accumulation of TET1-TET2-TET3, FTO and ALKBH5. Notably, this subcellular movement correlated with the ability of MYC, in an IDH2-dependent manner, and, unexpectedly, of αKG to directly induce O-GlcNAcylation. Concordantly, modulation of the activity of OGT and OGA, enzymes that control the cycling of this non-canonical mono-glycosylation, largely recapitulated the effects of the MYC-IDH2-αKG axis on the subcellular movement of DNA and RNA demethylases. Together, we uncovered a hitherto unsuspected crosstalk between MYC, αKG and O-GlcNAcylation which could influence the epigenome and epitranscriptome homeostasis.
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2
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Hong F, Wan L, Liu J, Huang K, Xiao Z, Zhang Y, Shi C. Histone methylation regulates Hif-1 signaling cascade in activation of hepatic stellate cells. FEBS Open Bio 2018; 8:406-415. [PMID: 29511617 PMCID: PMC5832973 DOI: 10.1002/2211-5463.12379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 11/28/2017] [Accepted: 12/31/2017] [Indexed: 12/16/2022] Open
Abstract
Liver fibrosis is characterized by deposition of excessive extracellular matrix (ECM). The major source of ECM is activated hepatic stellate cells (HSCs). Previously, we reported that hypoxia-inducible factor-1 (Hif-1) regulates activation of HSCs through autophagy. In current work, human HSC cell line LX-2 was used as cell model. It was determined that trimethylation of H3 histone on lysine 4 (H3K4me3) occurred in the Hif-1 transcriptional complex. Inhibition of modifications of histone methylation suppressed Hif-1 nuclear transport, autophagosome formation, and activation of LX-2 cells. These data suggest that histone methylation modification plays an important role in the Hif-1 signaling cascade regulating HSC activation.
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Affiliation(s)
- Fei Hong
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
| | - Lu Wan
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
| | - Jie Liu
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
| | - Ke Huang
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
| | - Zhenmeng Xiao
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
| | - Yingjing Zhang
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
| | - Chunwei Shi
- Department of Pathogen Biology School of Basic Medicine Huazhong University of Science and Technology Wuhan China
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3
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Zhang W, Xia W, Wang Q, Towers AJ, Chen J, Gao R, Zhang Y, Yen CA, Lee AY, Li Y, Zhou C, Liu K, Zhang J, Gu TP, Chen X, Chang Z, Leung D, Gao S, Jiang YH, Xie W. Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development. Mol Cell 2016; 64:1062-1073. [PMID: 27916660 DOI: 10.1016/j.molcel.2016.10.030] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 08/30/2016] [Accepted: 10/21/2016] [Indexed: 11/19/2022]
Abstract
The methylcytosine oxidase TET proteins play important roles in DNA demethylation and development. However, it remains elusive how exactly they target substrates and execute oxidation. Interestingly, we found that, in mice, the full-length TET1 isoform (TET1e) is restricted to early embryos, embryonic stem cells (ESCs), and primordial germ cells (PGCs). By contrast, a short isoform (TET1s) is preferentially expressed in somatic cells, which lacks the N terminus including the CXXC domain, a DNA-binding module that often recognizes CpG islands (CGIs) where TET1 predominantly occupies. Unexpectedly, TET1s can still bind CGIs despite the fact that its global chromatin binding is significantly reduced. Interestingly, global chromatin binding, but not targeted binding at CGIs, is correlated with TET1-mediated demethylation. Finally, mice with exclusive expression of Tet1s failed to erase imprints in PGCs and displayed developmental defects in progeny. These data show that isoform switch of TET1 regulates epigenetic memory erasure and mouse development.
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Affiliation(s)
- Wenhao Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Aaron J Towers
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jiayu Chen
- School of Life Science and Technology, Tongji University, Shanghai 20092, China
| | - Rui Gao
- School of Life Sciences, Tsinghua University, Beijing 100084, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chia-An Yen
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Yuanyuan Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chen Zhou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kaili Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tian-Peng Gu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiuqi Chen
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zai Chang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shaorong Gao
- School of Life Science and Technology, Tongji University, Shanghai 20092, China
| | - Yong-Hui Jiang
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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4
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Lio CW, Zhang J, González-Avalos E, Hogan PG, Chang X, Rao A. Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility. eLife 2016; 5. [PMID: 27869616 PMCID: PMC5142813 DOI: 10.7554/elife.18290] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 11/18/2016] [Indexed: 12/30/2022] Open
Abstract
Ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine, facilitating DNA demethylation and generating new epigenetic marks. Here we show that concomitant loss of Tet2 and Tet3 in mice at early B cell stage blocked the pro- to pre-B cell transition in the bone marrow, decreased Irf4 expression and impaired the germline transcription and rearrangement of the Igκ locus. Tet2/3-deficient pro-B cells showed increased CpG methylation at the Igκ 3' and distal enhancers that was mimicked by depletion of E2A or PU.1, as well as a global decrease in chromatin accessibility at enhancers. Importantly, re-expression of the Tet2 catalytic domain in Tet2/3-deficient B cells resulted in demethylation of the Igκ enhancers and restored their chromatin accessibility. Our data suggest that TET proteins and lineage-specific transcription factors cooperate to influence chromatin accessibility and Igκ enhancer function by modulating the modification status of DNA.
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Affiliation(s)
- Chan-Wang Lio
- Division of Signaling and Gene Expression, San Diego, United States
| | - Jiayuan Zhang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Patrick G Hogan
- Division of Signaling and Gene Expression, San Diego, United States
| | - Xing Chang
- Division of Signaling and Gene Expression, San Diego, United States.,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Sanford Consortium for Regenerative Medicine, San Diego, United States
| | - Anjana Rao
- Division of Signaling and Gene Expression, San Diego, United States.,Sanford Consortium for Regenerative Medicine, San Diego, United States.,Department of Pharmacology, University of California, San Diego, San Diego, United States.,Moores Cancer Center, University of California, San Diego, San Diego, United States
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5
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Ferrer CM, Sodi VL, Reginato MJ. O-GlcNAcylation in Cancer Biology: Linking Metabolism and Signaling. J Mol Biol 2016; 428:3282-3294. [PMID: 27343361 DOI: 10.1016/j.jmb.2016.05.028] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/30/2016] [Indexed: 12/11/2022]
Abstract
The hexosamine biosynthetic pathway (HBP) is highly dependent on multiple metabolic nutrients including glucose, glutamine, and acetyl-CoA. Increased flux through HBP leads to elevated post-translational addition of β-D-N-acetylglucosamine sugars to nuclear and cytoplasmic proteins. Increased total O-GlcNAcylation is emerging as a general characteristic of cancer cells, and recent studies suggest that O-GlcNAcylation is a central communicator of nutritional status to control key signaling and metabolic pathways that regulate multiple cancer cell phenotypes. This review summarizes our current understanding of changes of O-GlcNAc cycling enzymes in cancer, the role of O-GlcNAcylation in tumorigenesis, and the current challenges in targeting this pathway therapeutically.
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Affiliation(s)
- Christina M Ferrer
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Valerie L Sodi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Mauricio J Reginato
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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6
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Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A. Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. Cell Rep 2016; 14:1246-1257. [PMID: 26832418 DOI: 10.1016/j.celrep.2016.01.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/20/2015] [Accepted: 12/29/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC) is the most-influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC co-localizes with specific interactors shows that each interaction points to chromatin remodeling, stemness, differentiation, or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs.
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Affiliation(s)
- David Juan
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center - CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Juliane Perner
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Enrique Carrillo de Santa Pau
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center - CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Simone Marsili
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center - CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - David Ochoa
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ho-Ryun Chung
- Otto-Warburg-Laboratories Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Martin Vingron
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Daniel Rico
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center - CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain.
| | - Alfonso Valencia
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center - CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain.
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7
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Affiliation(s)
- Karen Chiang
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Edward H. Koo
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093; ,
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8
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Abstract
Resetting DNA methylation and reactivation of pluripotency genes are late events in the formation of iPSCs. Recent work by Costa et al. (2013) and Gao et al. (2013) has examined the role of Tet proteins in the hydroxymethylation of pluripotency genes, with the latter replacing Oct4 with Tet1 for reprogramming.
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Affiliation(s)
- Steven A Jackson
- Department of Cell and Regenerative Biology, Wisconsin Institute for Discovery, Epigenetics Theme, University of Wisconsin-Madison, Madison, WI 53706, USA
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9
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TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol 2013; 14:341-56. [PMID: 23698584 DOI: 10.1038/nrm3589] [Citation(s) in RCA: 654] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In many organisms, the methylation of cytosine in DNA has a key role in silencing 'parasitic' DNA elements, regulating transcription and establishing cellular identity. The recent discovery that ten-eleven translocation (TET) proteins are 5-methylcytosine oxidases has provided several chemically plausible pathways for the reversal of DNA methylation, thus triggering a paradigm shift in our understanding of how changes in DNA methylation are coupled to cell differentiation, embryonic development and cancer.
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10
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The dynamics of HCF-1 modulation of herpes simplex virus chromatin during initiation of infection. Viruses 2013; 5:1272-91. [PMID: 23698399 PMCID: PMC3712308 DOI: 10.3390/v5051272] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 12/30/2022] Open
Abstract
Successful infection of herpes simplex virus is dependent upon chromatin modulation by the cellular coactivator host cell factor-1 (HCF-1). This review focuses on the multiple chromatin modulation components associated with HCF-1 and the chromatin-related dynamics mediated by this coactivator that lead to the initiation of herpes simplex virus (HSV) immediate early gene expression.
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