101
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TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer. Cell Res 2019; 29:248-250. [PMID: 30607016 DOI: 10.1038/s41422-018-0132-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 11/09/2022] Open
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102
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Zachara NE. Critical observations that shaped our understanding of the function(s) of intracellular glycosylation (O-GlcNAc). FEBS Lett 2018; 592:3950-3975. [PMID: 30414174 DOI: 10.1002/1873-3468.13286] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
Abstract
Almost 100 years after the first descriptions of proteins conjugated to carbohydrates (mucins), several studies suggested that glycoproteins were not restricted to the serum, extracellular matrix, cell surface, or endomembrane system. In the 1980s, key data emerged demonstrating that intracellular proteins were modified by monosaccharides of O-linked β-N-acetylglucosamine (O-GlcNAc). Subsequently, this modification was identified on thousands of proteins that regulate cellular processes as diverse as protein aggregation, localization, post-translational modifications, activity, and interactions. In this Review, we will highlight critical discoveries that shaped our understanding of the molecular events underpinning the impact of O-GlcNAc on protein function, the role that O-GlcNAc plays in maintaining cellular homeostasis, and our understanding of the mechanisms that regulate O-GlcNAc-cycling.
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Affiliation(s)
- Natasha E Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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103
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Berthier A, Vinod M, Porez G, Steenackers A, Alexandre J, Yamakawa N, Gheeraert C, Ploton M, Maréchal X, Dubois-Chevalier J, Hovasse A, Schaeffer-Reiss C, Cianférani S, Rolando C, Bray F, Duez H, Eeckhoute J, Lefebvre T, Staels B, Lefebvre P. Combinatorial regulation of hepatic cytoplasmic signaling and nuclear transcriptional events by the OGT/REV-ERBα complex. Proc Natl Acad Sci U S A 2018; 115:E11033-E11042. [PMID: 30397120 PMCID: PMC6255172 DOI: 10.1073/pnas.1805397115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The nuclear receptor REV-ERBα integrates the circadian clock with hepatic glucose and lipid metabolism by nucleating transcriptional comodulators at genomic regulatory regions. An interactomic approach identified O-GlcNAc transferase (OGT) as a REV-ERBα-interacting protein. By shielding cytoplasmic OGT from proteasomal degradation and favoring OGT activity in the nucleus, REV-ERBα cyclically increased O-GlcNAcylation of multiple cytoplasmic and nuclear proteins as a function of its rhythmically regulated expression, while REV-ERBα ligands mostly affected cytoplasmic OGT activity. We illustrate this finding by showing that REV-ERBα controls OGT-dependent activities of the cytoplasmic protein kinase AKT, an essential relay in insulin signaling, and of ten-of-eleven translocation (TET) enzymes in the nucleus. AKT phosphorylation was inversely correlated to REV-ERBα expression. REV-ERBα enhanced TET activity and DNA hydroxymethylated cytosine (5hmC) levels in the vicinity of REV-ERBα genomic binding sites. As an example, we show that the REV-ERBα/OGT complex modulates SREBP-1c gene expression throughout the fasting/feeding periods by first repressing AKT phosphorylation and by epigenomically priming the Srebf1 promoter for a further rapid response to insulin. Conclusion: REV-ERBα regulates cytoplasmic and nuclear OGT-controlled processes that integrate at the hepatic SREBF1 locus to control basal and insulin-induced expression of the temporally and nutritionally regulated lipogenic SREBP-1c transcript.
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Affiliation(s)
- Alexandre Berthier
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Manjula Vinod
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Geoffrey Porez
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Agata Steenackers
- University of Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Villeneuve d'Ascq F-59655, France
| | - Jérémy Alexandre
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Nao Yamakawa
- University of Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Villeneuve d'Ascq F-59655, France
| | - Céline Gheeraert
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Maheul Ploton
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Xavier Maréchal
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Julie Dubois-Chevalier
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, University of Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR 7178, Strasbourg F-67037, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, University of Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR 7178, Strasbourg F-67037, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, University of Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR 7178, Strasbourg F-67037, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique, CNRS, Unité de Service et de Recherche (USR) 3290, University of Lille, Villeneuve d'Ascq F-59655, France
- Fédération de Recherche Biochimie Structurale et Fonctionnelle des Assemblages Biomoléculaires FRABio, FR 3688 CNRS, University of Lille, Villeneuve d'Ascq F-59655, France
- Institut M.-E. Chevreul, CNRS, FR 2638, University of Lille, Villeneuve d'Ascq F-59655, France
| | - Fabrice Bray
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique, CNRS, Unité de Service et de Recherche (USR) 3290, University of Lille, Villeneuve d'Ascq F-59655, France
- Fédération de Recherche Biochimie Structurale et Fonctionnelle des Assemblages Biomoléculaires FRABio, FR 3688 CNRS, University of Lille, Villeneuve d'Ascq F-59655, France
- Institut M.-E. Chevreul, CNRS, FR 2638, University of Lille, Villeneuve d'Ascq F-59655, France
| | - Hélène Duez
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Jérôme Eeckhoute
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Tony Lefebvre
- University of Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Villeneuve d'Ascq F-59655, France
| | - Bart Staels
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Philippe Lefebvre
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France;
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104
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Chen LL, Lin HP, Zhou WJ, He CX, Zhang ZY, Cheng ZL, Song JB, Liu P, Chen XY, Xia YK, Chen XF, Sun RQ, Zhang JY, Sun YP, Song L, Liu BJ, Du RK, Ding C, Lan F, Huang SL, Zhou F, Liu S, Xiong Y, Ye D, Guan KL. SNIP1 Recruits TET2 to Regulate c-MYC Target Genes and Cellular DNA Damage Response. Cell Rep 2018; 25:1485-1500.e4. [PMID: 30404004 PMCID: PMC6317994 DOI: 10.1016/j.celrep.2018.10.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
The TET2 DNA dioxygenase regulates gene expression by catalyzing demethylation of 5-methylcytosine, thus epigenetically modulating the genome. TET2 does not contain a sequence-specific DNA-binding domain, and how it is recruited to specific genomic sites is not fully understood. Here we carried out a mammalian two-hybrid screen and identified multiple transcriptional regulators potentially interacting with TET2. The SMAD nuclear interacting protein 1 (SNIP1) physically interacts with TET2 and bridges TET2 to bind several transcription factors, including c-MYC. SNIP1 recruits TET2 to the promoters of c-MYC target genes, including those involved in DNA damage response and cell viability. TET2 protects cells from DNA damage-induced apoptosis dependending on SNIP1. Our observations uncover a mechanism for targeting TET2 to specific promoters through a ternary interaction with a co-activator and many sequence-specific DNA-binding factors. This study also reveals a TET2-SNIP1-c-MYC pathway in mediating DNA damage response, thereby connecting epigenetic control to maintenance of genome stability.
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Affiliation(s)
- Lei-Lei Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huai-Peng Lin
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Medical College of Xiamen University, Xiamen 361102, China
| | - Wen-Jie Zhou
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chen-Xi He
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhi-Yong Zhang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhou-Li Cheng
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jun-Bin Song
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Peng Liu
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin-Yu Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yu-Kun Xia
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiu-Fei Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ren-Qiang Sun
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jing-Ye Zhang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Ping Sun
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for National Center for Protein Science (The PHOENIX Center), Beijing, China
| | - Bing-Jie Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Rui-Kai Du
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for National Center for Protein Science (The PHOENIX Center), Beijing, China
| | - Fei Lan
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Sheng-Lin Huang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng Zhou
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Suling Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Yue Xiong
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Dan Ye
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Kun-Liang Guan
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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105
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Biwi J, Biot C, Guerardel Y, Vercoutter-Edouart AS, Lefebvre T. The Many Ways by Which O-GlcNAcylation May Orchestrate the Diversity of Complex Glycosylations. Molecules 2018; 23:molecules23112858. [PMID: 30400201 PMCID: PMC6278486 DOI: 10.3390/molecules23112858] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/31/2022] Open
Abstract
Unlike complex glycosylations, O-GlcNAcylation consists of the addition of a single N-acetylglucosamine unit to serine and threonine residues of target proteins, and is confined within the nucleocytoplasmic and mitochondrial compartments. Nevertheless, a number of clues tend to show that O-GlcNAcylation is a pivotal regulatory element of its complex counterparts. In this perspective, we gather the evidence reported to date regarding this connection. We propose different levels of regulation that encompass the competition for the nucleotide sugar UDP-GlcNAc, and that control the wide class of glycosylation enzymes via their expression, catalytic activity, and trafficking. We sought to better envision that nutrient fluxes control the elaboration of glycans, not only at the level of their structure composition, but also through sweet regulating actors.
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Affiliation(s)
- James Biwi
- Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, CNRS, UMR 8576, UGSF, 59000 Lille, France.
| | - Christophe Biot
- Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, CNRS, UMR 8576, UGSF, 59000 Lille, France.
| | - Yann Guerardel
- Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, CNRS, UMR 8576, UGSF, 59000 Lille, France.
| | | | - Tony Lefebvre
- Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, CNRS, UMR 8576, UGSF, 59000 Lille, France.
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106
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Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. eLife 2018; 7:34870. [PMID: 30325306 PMCID: PMC6214653 DOI: 10.7554/elife.34870] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 10/15/2018] [Indexed: 12/11/2022] Open
Abstract
TET enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine and higher oxidized derivatives. TETs stably associate with and are post-translationally modified by the nutrient-sensing enzyme OGT, suggesting a connection between metabolism and the epigenome. Here, we show for the first time that modification by OGT enhances TET1 activity in vitro. We identify a TET1 domain that is necessary and sufficient for binding to OGT and report a point mutation that disrupts the TET1-OGT interaction. We show that this interaction is necessary for TET1 to rescue hematopoetic stem cell production in tet mutant zebrafish embryos, suggesting that OGT promotes TET1’s function during development. Finally, we show that disrupting the TET1-OGT interaction in mouse embryonic stem cells changes the abundance of TET2 and 5-methylcytosine, which is accompanied by alterations in gene expression. These results link metabolism and epigenetic control, which may be relevant to the developmental and disease processes regulated by these two enzymes.
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Affiliation(s)
- Joel Hrit
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Leeanne Goodrich
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Cheng Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology (BCMB Allied program), Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Bang-An Wang
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Ji Nie
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Xiaolong Cui
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Elizabeth Allene Martin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Eric Simental
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Jenna Fernandez
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Monica Yun Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Rosa Castanon
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Rahul M Kohli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Chuan He
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Mary Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Barbara Panning
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States
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107
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Tran KA, Dillingham CM, Sridharan R. The role of α-ketoglutarate-dependent proteins in pluripotency acquisition and maintenance. J Biol Chem 2018; 294:5408-5419. [PMID: 30181211 DOI: 10.1074/jbc.tm118.000831] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
α-Ketoglutarate is an important metabolic intermediate that acts as a cofactor for several chromatin-modifying enzymes, including histone demethylases and the Tet family of enzymes that are involved in DNA demethylation. In this review, we focus on the function and genomic localization of these α-ketoglutarate-dependent enzymes in the maintenance of pluripotency during cellular reprogramming to induced pluripotent stem cells and in disruption of pluripotency during in vitro differentiation. The enzymatic function of many of these α-ketoglutarate-dependent proteins is required for pluripotency acquisition and maintenance. A better understanding of their specific function will be essential in furthering our knowledge of pluripotency.
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Affiliation(s)
- Khoa A Tran
- From the Wisconsin Institute for Discovery.,Molecular and Cellular Pharmacology Program, and
| | - Caleb M Dillingham
- From the Wisconsin Institute for Discovery.,Cellular and Molecular Pathology Program, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Rupa Sridharan
- From the Wisconsin Institute for Discovery, .,Department of Cell and Regenerative Biology
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108
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Xing L, Liu Y, Xu S, Xiao J, Wang B, Deng H, Lu Z, Xu Y, Chong K. Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate flowering. EMBO J 2018; 37:embj.201798115. [PMID: 30150325 PMCID: PMC6166131 DOI: 10.15252/embj.201798115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 07/21/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023] Open
Abstract
Post‐translational modification of proteins by O‐linked β‐N‐acetylglucosamine (O‐GlcNAc) is catalyzed by O‐GlcNAc transferases (OGTs). O‐GlcNAc modification of proteins regulates multiple important biological processes in metazoans. However, whether protein O‐GlcNAcylation is involved in epigenetic processes during plant development is largely unknown. Here, we show that loss of function of SECRET AGENT (SEC), an OGT in Arabidopsis, leads to an early flowering phenotype. This results from reduced histone H3 lysine 4 trimethylation (H3K4me3) of FLOWERING LOCUS C (FLC) locus, which encodes a key negative regulator of flowering. SEC activates ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), a histone lysine methyltransferase (HKMT), through O‐GlcNAc modification to augment ATX1‐mediated H3K4me3 histone modification at FLC locus. SEC transfers an O‐GlcNAc group on Ser947 of ATX1, which resides in the SET domain, thereby activating ATX1. Taken together, these results uncover a novel post‐translational O‐GlcNAc modification‐mediated mechanism for regulation of HKMT activity and establish the function of O‐GlcNAc signaling in epigenetic processes in plants.
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Affiliation(s)
- Lijing Xing
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Shujuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hanwen Deng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhuang Lu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China.,National Center for Plant Gene Research, Beijing, China
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109
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Schwann cell O-GlcNAcylation promotes peripheral nerve remyelination via attenuation of the AP-1 transcription factor JUN. Proc Natl Acad Sci U S A 2018; 115:8019-8024. [PMID: 30012597 DOI: 10.1073/pnas.1805538115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Schwann cells (SCs), the glia of the peripheral nervous system, play an essential role in nerve regeneration. Upon nerve injury, SCs are reprogrammed into unique "repair SCs," and these cells remove degenerating axons/myelin debris, promote axonal regrowth, and ultimately remyelinate regenerating axons. The AP-1 transcription factor JUN is promptly induced in SCs upon nerve injury and potently mediates this injury-induced SC plasticity; however, the regulation of these JUN-dependent SC injury responses is unclear. Previously, we produced mice with a SC-specific deletion of O-GlcNAc transferase (OGT). This enzyme catalyzes O-GlcNAcylation, a posttranslational modification that is influenced by the cellular metabolic state. Mice lacking OGT in SCs develop a progressive demyelinating peripheral neuropathy. Here, we investigated the nerve repair process in OGT-SCKO mutant mice and found that the remyelination of regenerating axons is severely impaired. Gene expression profiling of OGT-SCKO SCs revealed that the JUN-dependent SC injury program was elevated in the absence of injury and failed to shut down at the appropriate time after injury. This aberrant JUN activity results in abnormalities in repair SC function and redifferentiation and prevents the timely remyelination. This aberrant nerve injury response is normalized in OGT-SCKO mice with reduced Jun gene dosage in SCs. Mechanistically, OGT O-GlcNAcylates JUN at multiple sites, which then leads to an attenuation of AP-1 transcriptional activity. Together, these results highlight the metabolic oversight of the nerve injury response via the regulation of JUN activity by O-GlcNAcylation, a pathway that could be important in the neuropathy associated with diabetes and aging.
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110
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Sen S, Maulik U. Recent advancement toward significant association between disordered transcripts and virus-infected diseases: a survey. Brief Funct Genomics 2018; 17:458-470. [DOI: 10.1093/bfgp/ely021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sagnik Sen
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, India
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, India
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111
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Abstract
Chromatin is a mighty consumer of cellular energy generated by metabolism. Metabolic status is efficiently coordinated with transcription and translation, which also feed back to regulate metabolism. Conversely, suppression of energy utilization by chromatin processes may serve to preserve energy resources for cell survival. Most of the reactions involved in chromatin modification require metabolites as their cofactors or coenzymes. Therefore, the metabolic status of the cell can influence the spectra of posttranslational histone modifications and the structure, density and location of nucleosomes, impacting epigenetic processes. Thus, transcription, translation, and DNA/RNA biogenesis adapt to cellular metabolism. In addition to dysfunctions of metabolic enzymes, imbalances between metabolism and chromatin activities trigger metabolic disease and life span alteration. Here, we review the synthesis of the metabolites and the relationships between metabolism and chromatin function. Furthermore, we discuss how the chromatin response feeds back to metabolic regulation in biological processes.
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;,
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;,
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112
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Chu Y, Zhao Z, Sant DW, Zhu G, Greenblatt SM, Liu L, Wang J, Cao Z, Tho JC, Chen S, Liu X, Zhang P, Maciejewski JP, Nimer S, Wang G, Yuan W, Yang FC, Xu M. Tet2 Regulates Osteoclast Differentiation by Interacting with Runx1 and Maintaining Genomic 5-Hydroxymethylcytosine (5hmC). GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:172-186. [PMID: 29908294 PMCID: PMC6076382 DOI: 10.1016/j.gpb.2018.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/29/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
As a dioxygenase, Ten-Eleven Translocation 2 (TET2) catalyzes subsequent steps of 5-methylcytosine (5mC) oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hematopoietic stem cells, but its impact on mature hematopoietic cells is not well-characterized. Here we show that Tet2 plays an essential role in osteoclastogenesis. Deletion of Tet2 impairs the differentiation of osteoclast precursor cells (macrophages) and their maturation into bone-resorbing osteoclasts in vitro. Furthermore, Tet2-/- mice exhibit mild osteopetrosis, accompanied by decreased number of osteoclasts in vivo. Tet2 loss in macrophages results in the altered expression of a set of genes implicated in osteoclast differentiation, such as Cebpa, Mafb, and Nfkbiz. Tet2 deletion also leads to a genome-wide alteration in the level of 5-hydroxymethylcytosine (5hmC) and altered expression of a specific subset of macrophage genes associated with osteoclast differentiation. Furthermore, Tet2 interacts with Runx1 and negatively modulates its transcriptional activity. Our studies demonstrate a novel molecular mechanism controlling osteoclast differentiation and function by Tet2, that is, through interactions with Runx1 and the maintenance of genomic 5hmC. Targeting Tet2 and its pathway could be a potential therapeutic strategy for the prevention and treatment of abnormal bone mass caused by the deregulation of osteoclast activities.
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Affiliation(s)
- Yajing Chu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Zhigang Zhao
- Department of Hematology and Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China.
| | - David Wayne Sant
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ganqian Zhu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sarah M Greenblatt
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lin Liu
- Department of Hematology and Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Jinhuan Wang
- Department of Oncology, The Second Affiliated Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Zeng Cao
- Department of Hematology and Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Jeanette Cheng Tho
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Shi Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xiaochen Liu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Peng Zhang
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stephen Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Gaofeng Wang
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Feng-Chun Yang
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Mingjiang Xu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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113
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Liu Y, Peng W, Qu K, Lin X, Zeng Z, Chen J, Wei D, Wang Z. TET2: A Novel Epigenetic Regulator and Potential Intervention Target for Atherosclerosis. DNA Cell Biol 2018; 37:517-523. [PMID: 29653065 DOI: 10.1089/dna.2017.4118] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Atherosclerosis is the underlying cause of cardio-cerebrovascular disease. However, the mechanisms of atherosclerosis are still unclear. The modification of DNA methylation has an important role in atherosclerosis development. As a member of the Ten-eleven translocation (TET) family, TET methylcytosine dioxygenase 2 (TET2) can modify DNA methylation by catalyzing 5-methylcytosine to 5-hydroxymethylcytosine and mediate DNA demethylation. Recent findings suggest that TET2 is related to the phenotype transformation of vascular smooth muscle cells, endothelial dysfunction, and inflammation of macrophage, the key factors of atherosclerosis. Therefore, TET2 may be a potential target for atherosclerosis treatment. This review will elaborate the recent findings that suggest the role of TET2 in atherosclerosis.
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Affiliation(s)
- Yami Liu
- 1 Key Laboratory for Atherosclerology of Hunan Province, Institute of Cardiovascular Disease, University of South China , Hengyang, China
| | - Wen Peng
- 2 Department of Spine Surgery, The First Affiliated Hospital, University of South China , Hengyang, China
| | - Kai Qu
- 3 College of Bioengineering, Chongqing University , Chongqing, China
| | - Xiaolong Lin
- 4 Department of Pathology, The Third People's Hospital of Huizhou , Huizhou, China
| | - Zhaolin Zeng
- 1 Key Laboratory for Atherosclerology of Hunan Province, Institute of Cardiovascular Disease, University of South China , Hengyang, China
| | - Jiaojiao Chen
- 1 Key Laboratory for Atherosclerology of Hunan Province, Institute of Cardiovascular Disease, University of South China , Hengyang, China
| | - Dangheng Wei
- 1 Key Laboratory for Atherosclerology of Hunan Province, Institute of Cardiovascular Disease, University of South China , Hengyang, China
| | - Zuo Wang
- 1 Key Laboratory for Atherosclerology of Hunan Province, Institute of Cardiovascular Disease, University of South China , Hengyang, China
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114
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SanMiguel JM, Abramowitz LK, Bartolomei MS. Imprinted gene dysregulation in a Tet1 null mouse model is stochastic and variable in the germline and offspring. Development 2018; 145:dev160622. [PMID: 29530881 PMCID: PMC5963867 DOI: 10.1242/dev.160622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/04/2018] [Indexed: 12/15/2022]
Abstract
Imprinted genes are expressed from one parental allele and regulated by differential DNA methylation at imprinting control regions (ICRs). ICRs are reprogrammed in the germline through erasure and re-establishment of DNA methylation. Although much is known about DNA methylation establishment, DNA demethylation is less well understood. Recently, the Ten-Eleven Translocation proteins (TET1-3) have been shown to initiate DNA demethylation, with Tet1-/- mice exhibiting aberrant levels of imprinted gene expression and ICR methylation. Nevertheless, the role of TET1 in demethylating ICRs in the female germline and in controlling allele-specific expression remains unknown. Here, we examined ICR-specific DNA methylation in Tet1-/- germ cells and ascertained whether abnormal ICR methylation impacted imprinted gene expression in F1 hybrid somatic tissues derived from Tet1-/- eggs or sperm. We show that Tet1 deficiency is associated with hypermethylation of a subset of ICRs in germ cells. Moreover, ICRs with defective germline reprogramming exhibit aberrant DNA methylation and biallelic expression of linked imprinted genes in somatic tissues. Thus, we define a discrete set of genomic regions that require TET1 for germline reprogramming and discuss mechanisms for stochastic imprinting defects.
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Affiliation(s)
- Jennifer M SanMiguel
- University of Pennsylvania, Perelman School of Medicine, Department of Cell and Developmental Biology, SCTR 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Lara K Abramowitz
- University of Pennsylvania, Perelman School of Medicine, Department of Cell and Developmental Biology, SCTR 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marisa S Bartolomei
- University of Pennsylvania, Perelman School of Medicine, Department of Cell and Developmental Biology, SCTR 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
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115
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Zhu Q, Stöger R, Alberio R. A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline. Front Cell Dev Biol 2018; 6:24. [PMID: 29637072 PMCID: PMC5880922 DOI: 10.3389/fcell.2018.00024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine (5mC) on CpG dinucleotides has been viewed as the major epigenetic modification in eukaryotes for a long time. Apart from 5mC, additional DNA modifications have been discovered in eukaryotic genomes. Many of these modifications are thought to be solely associated with DNA damage. However, growing evidence indicates that some base modifications, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC), and N6-methadenine (6mA), may be of biological relevance, particularly during early stages of embryo development. Although abundance of these DNA modifications in eukaryotic genomes can be low, there are suggestions that they cooperate with other epigenetic markers to affect DNA-protein interactions, gene expression, defense of genome stability and epigenetic inheritance. Little is still known about their distribution in different tissues and their functions during key stages of the animal lifecycle. This review discusses current knowledge and future perspectives of these novel DNA modifications in the mammalian genome with a focus on their dynamic distribution during early embryonic development and their potential function in epigenetic inheritance through the germ line.
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Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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116
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Mariappa D, Ferenbach AT, van Aalten DMF. Effects of hypo- O-GlcNAcylation on Drosophila development. J Biol Chem 2018; 293:7209-7221. [PMID: 29588363 PMCID: PMC5950000 DOI: 10.1074/jbc.ra118.002580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/21/2018] [Indexed: 01/12/2023] Open
Abstract
Post-translational modification of serine/threonine residues in nucleocytoplasmic proteins with GlcNAc (O-GlcNAcylation) is an essential regulatory mechanism in many cellular processes. In Drosophila, null mutants of the Polycomb gene O-GlcNAc transferase (OGT; also known as super sex combs (sxc)) display homeotic phenotypes. To dissect the requirement for O-GlcNAc signaling in Drosophila development, we used CRISPR/Cas9 gene editing to generate rationally designed sxc catalytically hypomorphic or null point mutants. Of the fertile males derived from embryos injected with the CRISPR/Cas9 reagents, 25% produced progeny carrying precise point mutations with no detectable off-target effects. One of these mutants, the catalytically inactive sxcK872M, was recessive lethal, whereas a second mutant, the hypomorphic sxcH537A, was homozygous viable. We observed that reduced total protein O-GlcNAcylation in the sxcH537A mutant is associated with a wing vein phenotype and temperature-dependent lethality. Genetic interaction between sxcH537A and a null allele of Drosophila host cell factor (dHcf), encoding an extensively O-GlcNAcylated transcriptional coactivator, resulted in abnormal scutellar bristle numbers. A similar phenotype was also observed in sxcH537A flies lacking a copy of skuld (skd), a Mediator complex gene known to affect scutellar bristle formation. Interestingly, this phenotype was independent of OGT Polycomb function or dHcf downstream targets. In conclusion, the generation of the endogenous OGT hypomorphic mutant sxcH537A enabled us to identify pleiotropic effects of globally reduced protein O-GlcNAc during Drosophila development. The mutants generated and phenotypes observed in this study provide a platform for discovery of OGT substrates that are critical for Drosophila development.
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Affiliation(s)
- Daniel Mariappa
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
| | - Andrew T Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
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117
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Draime A, Bridoux L, Belpaire M, Pringels T, Degand H, Morsomme P, Rezsohazy R. The O-GlcNAc transferase OGT interacts with and post-translationally modifies the transcription factor HOXA1. FEBS Lett 2018; 592:1185-1201. [PMID: 29465778 DOI: 10.1002/1873-3468.13015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/26/2018] [Accepted: 02/13/2018] [Indexed: 11/06/2022]
Abstract
HOXA1 belongs to the HOX family of transcription factors which are key regulators of animal development. Little is known about the molecular pathways controlling HOXA1. Recent data from our group revealed distinct partner proteins interacting with HOXA1. Among them, OGT is an O-linked N-acetylglucosamine (O-GlcNAc) transferase modifying a variety of proteins involved in different cellular processes including transcription. Here, we confirm OGT as a HOXA1 interactor, we characterise which domains of HOXA1 and OGT are required for the interaction, and we provide evidence that OGT post-translationally modifies HOXA1. Mass spectrometry experiments indeed reveal that HOXA1 can be phosphorylated on the AGGTVGSPQYIHHSY peptide and that upon OGT expression, the phosphate adduct is replaced by an O-GlcNAc group.
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Affiliation(s)
- Amandine Draime
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Magali Belpaire
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Molecular Physiology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Molecular Physiology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
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118
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Abstract
Gametes are highly specialized cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mice, germ cells are first specified in the developing embryo around embryonic day (E) 6.25 as primordial germ cells (PGCs). Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming around E10.5-E11.5, including genome-wide loss of 5-methylcytosine. The underlying molecular mechanisms of this process have remained unclear, leading to our inability to recapitulate this step of germline development in vitro. Here we show, using an integrative approach, that this complex reprogramming process involves coordinated interplay among promoter sequence characteristics, DNA (de)methylation, the polycomb (PRC1) complex and both DNA demethylation-dependent and -independent functions of TET1 to enable the activation of a critical set of germline reprogramming-responsive genes involved in gamete generation and meiosis. Our results also reveal an unexpected role for TET1 in maintaining but not driving DNA demethylation in gonadal PGCs. Collectively, our work uncovers a fundamental biological role for gonadal germline reprogramming and identifies the epigenetic principles of the PGC-to-gonocyte transition that will help to guide attempts to recapitulate complete gametogenesis in vitro.
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119
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Inoue D, Fujino T, Sheridan P, Zhang YZ, Nagase R, Horikawa S, Li Z, Matsui H, Kanai A, Saika M, Yamaguchi R, Kozuka-Hata H, Kawabata KC, Yokoyama A, Goyama S, Inaba T, Imoto S, Miyano S, Xu M, Yang FC, Oyama M, Kitamura T. A novel ASXL1-OGT axis plays roles in H3K4 methylation and tumor suppression in myeloid malignancies. Leukemia 2018; 32:1327-1337. [PMID: 29556021 DOI: 10.1038/s41375-018-0083-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 01/05/2018] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
ASXL1 plays key roles in epigenetic regulation of gene expression through methylation of histone H3K27, and disruption of ASXL1 drives myeloid malignancies, at least in part, via derepression of posterior HOXA loci. However, little is known about the identity of proteins that interact with ASXL1 and about the functions of ASXL1 in modulation of the active histone mark, such as H3K4 methylation. In this study, we demonstrate that ASXL1 is a part of a protein complex containing HCFC1 and OGT; OGT directly stabilizes ASXL1 by O-GlcNAcylation. Disruption of this novel axis inhibited myeloid differentiation and H3K4 methylation as well as H2B glycosylation and impaired transcription of genes involved in myeloid differentiation, splicing, and ribosomal functions; this has implications for myelodysplastic syndrome (MDS) pathogenesis, as each of these processes are perturbed in the disease. This axis is responsible for tumor suppression in the myeloid compartment, as reactivation of OGT induced myeloid differentiation and reduced leukemogenecity both in vivo and in vitro. Our data also suggest that MLL5, a known HCFC1/OGT-interacting protein, is responsible for gene activation by the ASXL1-OGT axis. These data shed light on the novel roles of the ASXL1-OGT axis in H3K4 methylation and activation of transcription.
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Affiliation(s)
- Daichi Inoue
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan.
| | - Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Paul Sheridan
- Laboratory of Genome Data Base, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Yao-Zhong Zhang
- Laboratory of Genome Data Base, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Reina Nagase
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Sayuri Horikawa
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Zaomin Li
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 8608556, Japan
| | - Akinori Kanai
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 7348553, Japan
| | - Makoto Saika
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Rui Yamaguchi
- Laboratory of Genome Data Base, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Kimihito Cojin Kawabata
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan
| | - Susumu Goyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 7348553, Japan
| | - Seiya Imoto
- Laboratory of Genome Data Base, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Satoru Miyano
- Laboratory of Genome Data Base, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Mingjiang Xu
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Feng-Chun Yang
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 1088639, Japan.
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120
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Coluccio A, Ecco G, Duc J, Offner S, Turelli P, Trono D. Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells. Epigenetics Chromatin 2018; 11:7. [PMID: 29482634 PMCID: PMC6389204 DOI: 10.1186/s13072-018-0177-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/16/2018] [Indexed: 01/18/2023] Open
Abstract
Background The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in repressing transposable elements (TEs) and maintaining parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of genome-wide reprogramming that precedes implantation. In naïve murine embryonic stem cells (mESCs), the genome is maintained highly hypomethylated by a combination of TET-mediated active demethylation and lack of de novo methylation, yet KAP1 is tethered by sequence-specific KZFPs to ICRs and TEs where it recruits histone and DNA methyltransferases to impose heterochromatin formation and DNA methylation. Results Here, upon removing either KAP1 or the cognate KZFP, we observed rapid TET2-dependent accumulation of 5hmC at both ICRs and TEs. In the absence of the KZFP/KAP1 complex, ICRs lost heterochromatic histone marks and underwent both active and passive DNA demethylation. For KAP1-bound TEs, 5mC hydroxylation correlated with transcriptional reactivation. Using RNA-seq, we further compared the expression profiles of TEs upon Kap1 removal in wild-type, Dnmt and Tet triple knockout mESCs. While we found that KAP1 represents the main effector of TEs repression in all three settings, we could additionally identify specific groups of TEs further controlled by DNA methylation. Furthermore, we observed that in the absence of TET proteins, activation upon Kap1 depletion was blunted for some TE integrants and increased for others. Conclusions Our results indicate that the KZFP/KAP1 complex maintains heterochromatin and DNA methylation at ICRs and TEs in naïve embryonic stem cells partly by protecting these loci from TET-mediated demethylation. Our study further unveils an unsuspected level of complexity in the transcriptional control of the endovirome by demonstrating often integrant-specific differential influences of histone-based heterochromatin modifications, DNA methylation and 5mC oxidation in regulating TEs expression. Electronic supplementary material The online version of this article (10.1186/s13072-018-0177-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
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121
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Guallar D, Bi X, Pardavila JA, Huang X, Saenz C, Shi X, Zhou H, Faiola F, Ding J, Haruehanroengra P, Yang F, Li D, Sanchez-Priego C, Saunders A, Pan F, Valdes VJ, Kelley K, Blanco MG, Chen L, Wang H, Sheng J, Xu M, Fidalgo M, Shen X, Wang J. RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells. Nat Genet 2018; 50:443-451. [PMID: 29483655 PMCID: PMC5862756 DOI: 10.1038/s41588-018-0060-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 01/16/2018] [Indexed: 12/13/2022]
Abstract
Ten-eleven translocation (TET) proteins play key roles in the regulation of DNA-methylation status by oxidizing 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), which can both serve as a stable epigenetic mark and participate in active demethylation. Unlike the other members of the TET family, TET2 does not contain a DNA-binding domain, and it remains unclear how it is recruited to chromatin. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We found that PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation.
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Affiliation(s)
- Diana Guallar
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Xianju Bi
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jose Angel Pardavila
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Xin Huang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Saenz
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xianle Shi
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Hongwei Zhou
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Faiola
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Junjun Ding
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Fan Yang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Dan Li
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Sanchez-Priego
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arven Saunders
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Feng Pan
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, USA
| | - Victor Julian Valdes
- Department of Cell Biology and Development, Instituto de Fisiologia Celular, UNAM, Mexico City, Mexico
| | - Kevin Kelley
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miguel G Blanco
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Lingyi Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Huayan Wang
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Mingjiang Xu
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, USA
| | - Miguel Fidalgo
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jianlong Wang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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122
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Dahan P, Lu V, Nguyen RMT, Kennedy SAL, Teitell MA. Metabolism in pluripotency: Both driver and passenger? J Biol Chem 2018; 294:5420-5429. [PMID: 29463682 DOI: 10.1074/jbc.tm117.000832] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pluripotent stem cells (PSCs) are highly proliferative cells characterized by robust metabolic demands to power rapid division. For many years considered a passive component or "passenger" of cell-fate determination, cell metabolism is now starting to take center stage as a driver of cell fate outcomes. This review provides an update and analysis of our current understanding of PSC metabolism and its role in self-renewal, differentiation, and somatic cell reprogramming to pluripotency. Moreover, we present evidence on the active roles metabolism plays in shaping the epigenome to influence patterns of gene expression that may model key features of early embryonic development.
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Affiliation(s)
- Perrine Dahan
- From the Departments of Pathology and Laboratory Medicine and
| | - Vivian Lu
- Molecular and Medical Pharmacology and
| | | | - Stephanie A L Kennedy
- From the Departments of Pathology and Laboratory Medicine and.,the Department of Biology, California State University at Northridge, Northridge, California 91330
| | - Michael A Teitell
- From the Departments of Pathology and Laboratory Medicine and .,the California NanoSystems Institute.,Department of Bioengineering, and.,Molecular Biology Institute, UCLA, Los Angeles, California 90095, and.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, California 90095.,the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095
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123
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Burr S, Caldwell A, Chong M, Beretta M, Metcalf S, Hancock M, Arno M, Balu S, Kropf VL, Mistry RK, Shah AM, Mann GE, Brewer AC. Oxygen gradients can determine epigenetic asymmetry and cellular differentiation via differential regulation of Tet activity in embryonic stem cells. Nucleic Acids Res 2018; 46:1210-1226. [PMID: 29186571 PMCID: PMC5814828 DOI: 10.1093/nar/gkx1197] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
Graded levels of molecular oxygen (O2) exist within developing mammalian embryos and can differentially regulate cellular specification pathways. During differentiation, cells acquire distinct epigenetic landscapes, which determine their function, however the mechanisms which regulate this are poorly understood. The demethylation of 5-methylcytosine (5mC) is achieved via successive oxidation reactions catalysed by the Ten-Eleven-Translocation (Tet) enzymes, yielding the 5-hydroxymethylcytosine (5hmC) intermediate. These require O2 as a co-factor, and hence may link epigenetic processes directly to O2 gradients during development. We demonstrate that the activities of Tet enzymes display distinct patterns of [O2]-dependency, and that Tet1 activity, specifically, is subject to differential regulation within a range of O2 which is physiologically relevant in embryogenesis. Further, differentiating embryonic stem cells displayed a transient burst of 5hmC, which was both dependent upon Tet1 and inhibited by low (1%) [O2]. A GC-rich promoter region within the Tet3 locus was identified as a significant target of this 5mC-hydroxylation. Further, this region was shown to associate with Tet1, and display the histone epigenetic marks, H3K4me3 and H3K27me3, which are characteristic of a bivalent, developmentally 'poised' promoter. We conclude that Tet1 activity, determined by [O2] may play a critical role in regulating cellular differentiation and fate in embryogenesis.
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Affiliation(s)
- Simon Burr
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Anna Caldwell
- King's Centre of Excellence for Mass Spectrometry, King's College London, London SE1 9NH, UK
| | - Mei Chong
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Matteo Beretta
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Stephen Metcalf
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Matthew Hancock
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Matthew Arno
- King's Genomic Centre, King's College London, London SE1 9NH, UK
| | - Sucharitha Balu
- King's Genomic Centre, King's College London, London SE1 9NH, UK
| | - Valeria Leon Kropf
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Rajesh K Mistry
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Ajay M Shah
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Giovanni E Mann
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Alison C Brewer
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
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124
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Smeets E, Lynch AG, Prekovic S, Van den Broeck T, Moris L, Helsen C, Joniau S, Claessens F, Massie CE. The role of TET-mediated DNA hydroxymethylation in prostate cancer. Mol Cell Endocrinol 2018; 462:41-55. [PMID: 28870782 DOI: 10.1016/j.mce.2017.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/30/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Ten-eleven translocation (TET) proteins are recently characterized dioxygenases that regulate demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine and further derivatives. The recent finding that 5hmC is also a stable and independent epigenetic modification indicates that these proteins play an important role in diverse physiological and pathological processes such as neural and tumor development. Both the genomic distribution of (hydroxy)methylation and the expression and activity of TET proteins are dysregulated in a wide range of cancers including prostate cancer. Up to now it is still unknown how changes in TET and 5(h)mC profiles are related to the pathogenesis of prostate cancer. In this review, we explore recent advances in the current understanding of how TET expression and function are regulated in development and cancer. Furthermore, we look at the impact on 5hmC in prostate cancer and the potential underlying mechanisms. Finally, we tried to summarize the latest techniques for detecting and quantifying global and locus-specific 5hmC levels of genomic DNA.
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Affiliation(s)
- E Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - A G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - S Prekovic
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - T Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - L Moris
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - C Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - S Joniau
- Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - F Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - C E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
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125
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Deniz Ö, de la Rica L, Cheng KCL, Spensberger D, Branco MR. SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells. Genome Biol 2018; 19:6. [PMID: 29351814 PMCID: PMC5775534 DOI: 10.1186/s13059-017-1376-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/07/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role. It has been suggested that SETDB1 protects ERVs from TET-dependent DNA demethylation, but the relevance of this mechanism for ERV expression remains unclear. Moreover, previous studies have been performed in primed ESCs, which are not epigenetically or transcriptionally representative of preimplantation embryos. RESULTS We use naïve ESCs to investigate the role of SETDB1 in ERV regulation and its relationship with TET-mediated DNA demethylation. Naïve ESCs show an increased dependency on SETDB1 for ERV silencing when compared to primed ESCs, including at the highly mutagenic intracisternal A particles (IAPs). We find that in the absence of SETDB1, TET2 activates IAP elements in a catalytic-dependent manner. Surprisingly, TET2 does not drive changes in DNA methylation levels at IAPs, suggesting that it regulates these retrotransposons indirectly. Instead, SETDB1 depletion leads to a TET2-dependent loss of H4R3me2s, which is indispensable for IAP silencing during epigenetic reprogramming. CONCLUSIONS Our results demonstrate a novel and unexpected role for SETDB1 in protecting IAPs from TET2-dependent histone arginine demethylation.
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Affiliation(s)
- Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Lorenzo de la Rica
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK.,Present address: The Royal Society, 6-9 Carlton House Terrace, London, SW1Y 5AG, UK
| | - Kevin C L Cheng
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Dominik Spensberger
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.,Present address: Gene Targeting Facility, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK.
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126
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Kang KA, Piao MJ, Ryu YS, Kang HK, Chang WY, Keum YS, Hyun JW. Interaction of DNA demethylase and histone methyltransferase upregulates Nrf2 in 5-fluorouracil-resistant colon cancer cells. Oncotarget 2018; 7:40594-40620. [PMID: 27259240 PMCID: PMC5130030 DOI: 10.18632/oncotarget.9745] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/09/2016] [Indexed: 01/05/2023] Open
Abstract
We recently reported that DNA demethylase ten-eleven translocation 1 (TET1) upregulates nuclear factor erythroid 2-related factor 2 (Nrf2) in 5-fluorouracil-resistant colon cancer cells (SNUC5/5-FUR). In the present study, we examined the effect of histone modifications on Nrf2 transcriptional activation. Histone deacetylase (HDAC) and histone acetyltransferase (HAT) were respectively decreased and increased in SNUC5/5-FUR cells as compared to non-resistant parent cells. Mixed-lineage leukemia (MLL), a histone methyltransferase, was upregulated, leading to increased trimethylation of histone H3 lysine 4, while G9a was downregulated, leading to decreased dimethylation of histone H3 lysine 9. siRNA-mediated MLL knockdown decreased levels of Nrf2 and HO-1 to a greater extent than did silencing HAT1. Host cell factor 1 (HCF1) was upregulated in SNUC5/5-FUR cells, and we observed interaction between HCF1 and MLL. Upregulation of O-GlcNAc transferase (OGT), an activator of HCF1, was also associated with HCF1-MLL interaction. In SNUC5/5-FUR cells, a larger fraction of OGT was bound to TET1, which recruits OGT to the Nrf2 promoter region, than in SNUC5 cells. These findings indicate that SNUC5/5-FUR cells are under oxidative stress, which induces expression of histone methylation-related proteins as well as DNA demethylase, leading to upregulation of Nrf2 and 5-FU resistance.
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Affiliation(s)
- Kyoung Ah Kang
- School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
| | - Mei Jing Piao
- School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
| | - Yea Seong Ryu
- School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
| | - Hee Kyoung Kang
- School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
| | - Weon Young Chang
- School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
| | - Young Sam Keum
- Department of Biochemistry, College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea
| | - Jin Won Hyun
- School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
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127
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Very N, Lefebvre T, El Yazidi-Belkoura I. Drug resistance related to aberrant glycosylation in colorectal cancer. Oncotarget 2018; 9:1380-1402. [PMID: 29416702 PMCID: PMC5787446 DOI: 10.18632/oncotarget.22377] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/04/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the fourth leading cause of cancer-related deaths in the world. Drug resistance of tumour cells remains the main challenge toward curative treatments efficiency. Several epidemiologic studies link emergence and recurrence of this cancer to metabolic disorders. Glycosylation that modifies more than 80% of human proteins is one of the most widepread nutrient-sensitive post-translational modifications. Aberrant glycosylation participates in the development and progression of cancer. Thus, some of these glycan changes like carbohydrate antigen CA 19-9 (sialyl Lewis a, sLea) or those found on carcinoembryonic antigen (CEA) are already used as clinical biomarkers to detect and monitor CRC. The current review highlights emerging evidences accumulated mainly during the last decade that establish the role played by altered glycosylations in CRC drug resistance mechanisms that induce resistance to apoptosis and activation of signaling pathways, alter drug absorption and metabolism, and led to stemness acquisition. Knowledge in this field of investigation could aid to the development of better therapeutic approaches with new predictive biomarkers and targets tied in with adapted diet.
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Affiliation(s)
- Ninon Very
- Unité de Glycobiologie Structurale et Fonctionnelle, UGSF-UMR 8576 CNRS, Université de Lille, Lille 59000, France
| | - Tony Lefebvre
- Unité de Glycobiologie Structurale et Fonctionnelle, UGSF-UMR 8576 CNRS, Université de Lille, Lille 59000, France
| | - Ikram El Yazidi-Belkoura
- Unité de Glycobiologie Structurale et Fonctionnelle, UGSF-UMR 8576 CNRS, Université de Lille, Lille 59000, France
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128
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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129
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Impact of DNA methylation programming on normal and pre-leukemic hematopoiesis. Semin Cancer Biol 2017; 51:89-100. [PMID: 28964938 DOI: 10.1016/j.semcancer.2017.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/30/2022]
Abstract
Epigenome regulation is a critical mechanism that governs cell identity, lineage specification and developmental cell fates. With the advent of low-input and single-cell technologies as well as sophisticated cell labeling techniques, our understanding of transcriptional and epigenetic regulation of hematopoiesis is currently undergoing dramatic changes. Increasingly, evidence suggests that the epigenome conformation acts as a critical decision-making mechanism that instructs self-renewal, differentiation and developmental fates of hematopoietic progenitor cells. When dysregulated, this leads to the evolution of disease states such as leukemia. Indeed, aberrations in DNA methylation, histone modifications and genome architecture are characteristic features of many hematopoietic neoplasms in which epigenetic enzymes are frequently mutated. Sequencing studies and characterization of the epigenetic landscape in lymphomas, leukemias and in aged healthy individuals with clonal hematopoiesis have been indispensible to identify epigenetic regulators that play a role in transformation or pre-disposition to hematopoietic malignancies. In this review, we outline the current view of the hematopoietic system and the epigenetic mechanisms regulating hematopoiesis under homeostatic conditions, with a particular focus on the role of DNA methylation in this process. We will also summarize the current knowledge on the mechanisms underlying dysregulated DNA methylation in hematologic malignancies and how this contributes to our understanding of the physiological functions of epigenetic regulators in hematopoiesis.
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130
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Abstract
The physiological identity of every cell is maintained by highly specific transcriptional networks that establish a coherent molecular program that is in tune with nutritional conditions. The regulation of cell-specific transcriptional networks is accomplished by an epigenetic program via chromatin-modifying enzymes, whose activity is directly dependent on metabolites such as acetyl-coenzyme A, S-adenosylmethionine, and NAD+, among others. Therefore, these nuclear activities are directly influenced by the nutritional status of the cell. In addition to nutritional availability, this highly collaborative program between epigenetic dynamics and metabolism is further interconnected with other environmental cues provided by the day-night cycles imposed by circadian rhythms. Herein, we review molecular pathways and their metabolites associated with epigenetic adaptations modulated by histone- and DNA-modifying enzymes and their responsiveness to the environment in the context of health and disease.
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131
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Zhang P, Rausch C, Hastert FD, Boneva B, Filatova A, Patil SJ, Nuber UA, Gao Y, Zhao X, Cardoso MC. Methyl-CpG binding domain protein 1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner. Nucleic Acids Res 2017; 45:7118-7136. [PMID: 28449087 PMCID: PMC5499542 DOI: 10.1093/nar/gkx281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022] Open
Abstract
Cytosine modifications diversify and structure the genome thereby controlling proper development and differentiation. Here, we focus on the interplay of the 5-methylcytosine reader Mbd1 and modifier Tet1 by analyzing their dynamic subcellular localization and the formation of the Tet oxidation product 5-hydroxymethylcytosine in mammalian cells. Our results demonstrate that Mbd1 enhances Tet1-mediated 5-methylcytosine oxidation. We show that this is due to enhancing the localization of Tet1, but not of Tet2 and Tet3 at heterochromatic DNA. We find that the recruitment of Tet1 and concomitantly its catalytic activity eventually leads to the displacement of Mbd1 from methylated DNA. Finally, we demonstrate that increased Tet1 heterochromatin localization and 5-methylcytosine oxidation are dependent on the CXXC3 domain of Mbd1, which recognizes unmethylated CpG dinucleotides. The Mbd1 CXXC3 domain deletion isoform, which retains only binding to methylated CpGs, on the other hand, blocks Tet1-mediated 5-methylcytosine to 5-hydroxymethylcytosine conversion, indicating opposite biological effects of Mbd1 isoforms. Our study provides new insights on how cytosine modifications, their modifiers and readers cross-regulate themselves.
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Affiliation(s)
- Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Boyana Boneva
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Alina Filatova
- Stem Cell and Developmental Biology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sujit J. Patil
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Yu Gao
- Waisman Center & Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xinyu Zhao
- Waisman Center & Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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132
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Abstract
O-GlcNAcylation - the attachment of O-linked N-acetylglucosamine (O-GlcNAc) moieties to cytoplasmic, nuclear and mitochondrial proteins - is a post-translational modification that regulates fundamental cellular processes in metazoans. A single pair of enzymes - O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) - controls the dynamic cycling of this protein modification in a nutrient- and stress-responsive manner. Recent years have seen remarkable advances in our understanding of O-GlcNAcylation at levels that range from structural and molecular biology to cell signalling and gene regulation to physiology and disease. New mechanisms and functions of O-GlcNAcylation that are emerging from these recent developments enable us to begin constructing a unified conceptual framework through which the significance of this modification in cellular and organismal physiology can be understood.
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Affiliation(s)
- Xiaoyong Yang
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Kevin Qian
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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133
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Yin X, Xu Y. Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 945:275-302. [PMID: 27826843 DOI: 10.1007/978-3-319-43624-1_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mammalian DNA methylation mainly occurs at the carbon-C5 position of cytosine (5mC). TET enzymes were discovered to successively oxidize 5mC to 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). TET enzymes and oxidized 5mC derivatives play important roles in various biological and pathological processes, including regulation of DNA demethylation, gene transcription, embryonic development, and oncogenesis. In this chapter, we will discuss the discovery of TET-mediated 5mC oxidation and the structure, function, and regulation of TET enzymes.
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Affiliation(s)
- Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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134
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Abstract
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation. Additionally, many regulatory mechanisms of this process have been identified. Technological advances in mapping and tracing the oxidized forms of 5mC allow further dissection of their functions. Furthermore, the biological functions of active DNA demethylation in various biological contexts have also been revealed. In this Review, we summarize the recent advances and highlight key unanswered questions.
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135
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a‐Hdac complex in embryonic stem cells required for self‐renewal. EMBO J 2017. [DOI: https://doi.org/10.15252/embj.201696307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology British Columbia Cancer Research Center Vancouver BC Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Diego Pasini
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
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136
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal. EMBO J 2017; 36:2216-2232. [PMID: 28554894 DOI: 10.15252/embj.201696307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022] Open
Abstract
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, which also contains Ogt and Tet1. Fam60a binds on H3K4me3-positive promoters in ES cells, together with Ogt, Tet1 and Sin3a, and is essential to maintain the complex on chromatin. Finally, we show that depletion of Fam60a phenocopies the loss of Sin3a, leading to reduced proliferation, an extended G1-phase and the deregulation of lineage genes. Taken together, Fam60a is an essential core subunit of a variant Sin3a complex in ES cells that is required to promote rapid proliferation and prevent unscheduled differentiation.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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137
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Epigenetic dysregulation of hematopoietic stem cells and preleukemic state. Int J Hematol 2017; 106:34-44. [PMID: 28555413 DOI: 10.1007/s12185-017-2257-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/16/2017] [Indexed: 12/31/2022]
Abstract
Recent genetic analyses have revealed that premalignant somatic mutations in hematopoietic cells are common in older people without an evidence of hematologic malignancies, leading to clonal hematopoietic expansion. This phenomenon has been termed clonal hematopoiesis of indeterminate potential (CHIP). Frequency of such clonal somatic mutations increases with age: in 5-10% of people older than 70 years and around 20% of people older than 90 years. The most commonly mutated genes found in individuals with CHIP were epigenetic regulators, including DNA methyltransferase 3A (DNMT3A), Ten-eleven-translocation 2 (TET2), and Additional sex combs-like 1 (ASXL1), which are also recurrently mutated in myeloid malignancies. Recent functional studies have uncovered pleiotropic effect of mutations in DNMT3A, TET2, and ASXL1 in hematopoietic stem cell regulation and leukemic transformation. Of note, CHIP is associated with an increased risk of hematologic malignancy and all-cause mortality, albeit the annual risk of leukemic transformation was relatively low (0.5-1%). These findings suggest that clonal hematopoiesis per se may not be sufficient to engender preleukemic state. Further studies are required to decipher the exact mechanism by which preleukemic stem cells originate and transform into a full-blown leukemic state.
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138
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Levine ZG, Walker S. The Biochemistry of O-GlcNAc Transferase: Which Functions Make It Essential in Mammalian Cells? Annu Rev Biochem 2017; 85:631-57. [PMID: 27294441 DOI: 10.1146/annurev-biochem-060713-035344] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O-linked N-acetylglucosamine transferase (OGT) is found in all metazoans and plays an important role in development but at the single-cell level is only essential in dividing mammalian cells. Postmitotic mammalian cells and cells of invertebrates such as Caenorhabditis elegans and Drosophila can survive without copies of OGT. Why OGT is required in dividing mammalian cells but not in other cells remains unknown. OGT has multiple biochemical activities. Beyond its well-known role in adding β-O-GlcNAc to serine and threonine residues of nuclear and cytoplasmic proteins, OGT also acts as a protease in the maturation of the cell cycle regulator host cell factor 1 (HCF-1) and serves as an integral member of several protein complexes, many of them linked to gene expression. In this review, we summarize current understanding of the mechanisms underlying OGT's biochemical activities and address whether known functions of OGT could be related to its essential role in dividing mammalian cells.
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Affiliation(s)
- Zebulon G Levine
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115; ,
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139
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Protein O-GlcNAcylation: emerging mechanisms and functions. Nat Rev Mol Cell Biol 2017. [PMID: 28488703 DOI: 10.1038/nrm.2017.22,+10.1038/nrn.2017.89,+10.1038/nrn.2017.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
O-GlcNAcylation - the attachment of O-linked N-acetylglucosamine (O-GlcNAc) moieties to cytoplasmic, nuclear and mitochondrial proteins - is a post-translational modification that regulates fundamental cellular processes in metazoans. A single pair of enzymes - O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) - controls the dynamic cycling of this protein modification in a nutrient- and stress-responsive manner. Recent years have seen remarkable advances in our understanding of O-GlcNAcylation at levels that range from structural and molecular biology to cell signalling and gene regulation to physiology and disease. New mechanisms and functions of O-GlcNAcylation that are emerging from these recent developments enable us to begin constructing a unified conceptual framework through which the significance of this modification in cellular and organismal physiology can be understood.
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140
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Abstract
O-GlcNAcylation - the attachment of O-linked N-acetylglucosamine (O-GlcNAc) moieties to cytoplasmic, nuclear and mitochondrial proteins - is a post-translational modification that regulates fundamental cellular processes in metazoans. A single pair of enzymes - O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) - controls the dynamic cycling of this protein modification in a nutrient- and stress-responsive manner. Recent years have seen remarkable advances in our understanding of O-GlcNAcylation at levels that range from structural and molecular biology to cell signalling and gene regulation to physiology and disease. New mechanisms and functions of O-GlcNAcylation that are emerging from these recent developments enable us to begin constructing a unified conceptual framework through which the significance of this modification in cellular and organismal physiology can be understood.
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141
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Potential coordination role between O-GlcNAcylation and epigenetics. Protein Cell 2017; 8:713-723. [PMID: 28488246 PMCID: PMC5636747 DOI: 10.1007/s13238-017-0416-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 11/25/2022] Open
Abstract
Dynamic changes of the post-translational O-GlcNAc modification (O-GlcNAcylation) are controlled by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and the glycoside hydrolase O-GlcNAcase (OGA) in cells. O-GlcNAcylation often occurs on serine (Ser) and threonine (Thr) residues of the specific substrate proteins via the addition of O-GlcNAc group by OGT. It has been known that O-GlcNAcylation is not only involved in many fundamental cellular processes, but also plays an important role in cancer development through various mechanisms. Recently, accumulating data reveal that O-GlcNAcylation at histones or non-histone proteins can lead to the start of the subsequent biological processes, suggesting that O-GlcNAcylation as ‘protein code’ or ‘histone code’ may provide recognition platforms or executive instructions for subsequent recruitment of proteins to carry out the specific functions. In this review, we summarize the interaction of O-GlcNAcylation and epigenetic changes, introduce recent research findings that link crosstalk between O-GlcNAcylation and epigenetic changes, and speculate on the potential coordination role of O-GlcNAcylation with epigenetic changes in intracellular biological processes.
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142
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O-GlcNAcylation and chromatin remodeling in mammals: an up-to-date overview. Biochem Soc Trans 2017; 45:323-338. [PMID: 28408473 DOI: 10.1042/bst20160388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
Abstract
Post-translational modifications of histones and the dynamic DNA methylation cycle are finely regulated by a myriad of chromatin-binding factors and chromatin-modifying enzymes. Epigenetic modifications ensure local changes in the architecture of chromatin, thus controlling in fine the accessibility of the machinery of transcription, replication or DNA repair to the chromatin. Over the past decade, the nutrient-sensor enzyme O-GlcNAc transferase (OGT) has emerged as a modulator of chromatin remodeling. In mammals, OGT acts either directly through dynamic and reversible O-GlcNAcylation of histones and chromatin effectors, or in an indirect manner through its recruitment into chromatin-bound multiprotein complexes. In particular, there is an increasing amount of evidence of a cross-talk between OGT and the DNA dioxygenase ten-eleven translocation proteins that catalyze active DNA demethylation. Conversely, the stability of OGT itself can be controlled by the histone lysine-specific demethylase 2 (LSD2). Finally, a few studies have explored the role of O-GlcNAcase (OGA) in chromatin remodeling. In this review, we summarize the recent findings on the link between OGT, OGA and chromatin regulators in mammalian cellular models, and discuss their relevance in physiological and pathological conditions.
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143
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Wu D, Zhao L, Feng Z, Yu C, Ding J, Wang L, Wang F, Liu D, Zhu H, Xing F, Conaway JW, Conaway RC, Cai Y, Jin J. O-Linked N-acetylglucosamine transferase 1 regulates global histone H4 acetylation via stabilization of the nonspecific lethal protein NSL3. J Biol Chem 2017; 292:10014-10025. [PMID: 28450392 DOI: 10.1074/jbc.m117.781401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/25/2017] [Indexed: 01/16/2023] Open
Abstract
The human males absent on the first (MOF)-containing histone acetyltransferase nonspecific lethal (NSL) complex comprises nine subunits including the O-linked N-acetylglucosamine (O-GlcNAc) transferase, isoform 1 (OGT1). However, whether the O-GlcNAc transferase activity of OGT1 controls histone acetyltransferase activity of the NSL complex and whether OGT1 physically interacts with the other NSL complex subunits remain unclear. Here, we demonstrate that OGT1 regulates the activity of the NSL complex by mainly acetylating histone H4 Lys-16, Lys-5, and Lys-8 via O-GlcNAcylation and stabilization of the NSL complex subunit NSL3. Knocking down or overexpressing OGT1 in human cells remarkably affected the global acetylation of histone H4 residues Lys-16, Lys-5, and Lys-8. Because OGT1 is a subunit of the NSL complex, we also investigated the function of OGT1 in this complex. Co-transfection/co-immunoprecipitation experiments combined with in vitro O-GlcNAc transferase assays confirmed that OGT1 specifically binds to and O-GlcNAcylates NSL3. In addition, wheat germ agglutinin affinity purification verified the occurrence of O-GlcNAc modification on NSL3 in cells. Moreover, O-GlcNAcylation of NSL3 by wild-type OGT1 (OGT1-WT) stabilized NSL3. This stabilization was lost after co-transfection of NSL3 with an OGT1 mutant, OGT1C964A, that lacks O-GlcNAc transferase activity. Furthermore, stabilization of NSL3 by OGT1-WT significantly increased the global acetylation levels of H4 Lys-5, Lys-8, and Lys-16 in cells. These results suggest that OGT1 regulates the activity of the NSL complex by stabilizing NSL3.
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Affiliation(s)
| | | | | | - Chao Yu
- From the School of Life Sciences
| | | | | | - Fei Wang
- From the School of Life Sciences
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | | | | | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Lawrence, Kansas 66045
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Lawrence, Kansas 66045
| | - Yong Cai
- From the School of Life Sciences, .,National Engineering Laboratory for AIDS Vaccine, and.,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun 130012, China
| | - Jingji Jin
- From the School of Life Sciences, .,National Engineering Laboratory for AIDS Vaccine, and.,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun 130012, China
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144
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Tie G, Yan J, Khair L, Messina JA, Deng A, Kang J, Fazzio T, Messina LM. Hypercholesterolemia Increases Colorectal Cancer Incidence by Reducing Production of NKT and γδ T Cells from Hematopoietic Stem Cells. Cancer Res 2017; 77:2351-2362. [PMID: 28249902 DOI: 10.1158/0008-5472.can-16-1916] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 10/31/2016] [Accepted: 02/24/2017] [Indexed: 12/12/2022]
Abstract
Obesity will soon surpass smoking as the most preventable cause of cancer. Hypercholesterolemia, a common comorbidity of obesity, has been shown to increase cancer risk, especially colorectal cancer. However, the mechanism by which hypercholesterolemia or any metabolic disorder increases cancer risk remains unknown. In this study, we show that hypercholesterolemia increases the incidence and pathologic severity of colorectal neoplasia in two independent mouse models. Hypocholesterolemia induced an oxidant stress-dependent increase in miR101c, which downregulated Tet1 in hematopoietic stem cells (HSC), resulting in reduced expression of genes critical to natural killer T cell (NKT) and γδ T-cell differentiation. These effects reduced the number and function of terminally differentiated NKT and γδ T cells in the thymus, the colon submucosa, and during early tumorigenesis. These results suggest a novel mechanism by which a metabolic disorder induces epigenetic changes to reduce lineage priming of HSC toward immune cells, thereby compromising immunosurveillance against cancer. Cancer Res; 77(9); 2351-62. ©2017 AACR.
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Affiliation(s)
- Guodong Tie
- Diabetes Center of Excellence and Division of Vascular and Endovascular Surgery, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jinglian Yan
- Diabetes Center of Excellence and Division of Vascular and Endovascular Surgery, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lyne Khair
- Diabetes Center of Excellence and Division of Vascular and Endovascular Surgery, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Julia A Messina
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina
| | - April Deng
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Joonsoo Kang
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Thomas Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Louis M Messina
- Diabetes Center of Excellence and Division of Vascular and Endovascular Surgery, University of Massachusetts Medical School, Worcester, Massachusetts.
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145
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Chen R, Zhang Q, Duan X, York P, Chen GD, Yin P, Zhu H, Xu M, Chen P, Wu Q, Li D, Samarut J, Xu G, Zhang P, Cao X, Li J, Wong J. The 5-Hydroxymethylcytosine (5hmC) Reader UHRF2 Is Required for Normal Levels of 5hmC in Mouse Adult Brain and Spatial Learning and Memory. J Biol Chem 2017; 292:4533-4543. [PMID: 28115522 DOI: 10.1074/jbc.m116.754580] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/27/2016] [Indexed: 12/21/2022] Open
Abstract
UHRF2 has been implicated as a novel regulator for both DNA methylation (5mC) and hydroxymethylation (5hmC), but its physiological function and role in DNA methylation/hydroxymethylation are unknown. Here we show that in mice, UHRF2 is more abundantly expressed in the brain and a few other tissues. Uhrf2 knock-out mice are viable and fertile and exhibit no gross defect. Although there is no significant change of DNA methylation, the Uhrf2 null mice exhibit a reduction of 5hmC in the brain, including the cortex and hippocampus. Furthermore, the Uhrf2 null mice exhibit a partial impairment in spatial memory acquisition and retention. Consistent with the phenotype, gene expression profiling uncovers a role for UHRF2 in regulating neuron-related gene expression. Finally, we provide evidence that UHRF2 binds 5hmC in cells but does not appear to affect the TET1 enzymatic activity. Together, our study supports UHRF2 as a bona fide 5hmC reader and further demonstrates a role for 5hmC in neuronal function.
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Affiliation(s)
- Ruoyu Chen
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qiao Zhang
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaoya Duan
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Philippe York
- the Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030
| | - Guo-Dong Chen
- the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengcheng Yin
- the Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China
| | - Haijun Zhu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Meichen Xu
- the Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China
| | - Peilin Chen
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qihan Wu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dali Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jacques Samarut
- the Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon 69007, France, and
| | - Guoliang Xu
- the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Pumin Zhang
- the Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030
| | - Xiaohua Cao
- the Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China
| | - Jiwen Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China,
| | - Jiemin Wong
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China, .,the Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
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146
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Guo H, Zhang B, Nairn AV, Nagy T, Moremen KW, Buckhaults P, Pierce M. O-Linked N-Acetylglucosamine ( O-GlcNAc) Expression Levels Epigenetically Regulate Colon Cancer Tumorigenesis by Affecting the Cancer Stem Cell Compartment via Modulating Expression of Transcriptional Factor MYBL1. J Biol Chem 2017; 292:4123-4137. [PMID: 28096468 DOI: 10.1074/jbc.m116.763201] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/15/2017] [Indexed: 12/19/2022] Open
Abstract
To study the regulation of colorectal adenocarcinoma progression by O-GlcNAc, we have focused on the O-GlcNAc-mediated epigenetic regulation of human colon cancer stem cells (CCSC). Xenograft tumors from colon tumor cells with O-linked N-acetylglucosamine transferase (OGT) knockdown grew significantly slower than those formed from control cells, indicating a reduced proliferation of tumor cells due to inhibition of OGT expression. Significant reduction of the CCSC population was observed in the tumor cells after OGT knockdown, whereas tumor cells treated with the O-GlcNAcase inhibitor showed an increased CCSC population, indicating that O-GlcNAc levels regulated the CCSC compartment. When grown in suspension, tumor cells with OGT knockdown showed a reduced ability to form tumorspheres, indicating a reduced self-renewal of CCSC due to reduced levels of O-GlcNAc. ChIP-sequencing experiments using an anti-O-GlcNAc antibody revealed significant chromatin enrichment of O-GlcNAc-modified proteins at the promoter of the transcription factor MYBL1, which was also characterized by the presence of H3K27me3. RNA-sequencing analysis showed an increased expression of MYBL1 in tumor cells with OGT knockdown. Forced overexpression of MYBL1 led to a reduced population of CCSC and tumor growth in vivo, similar to the effects of OGT silencing. Moreover, two CpG islands near the transcription start site of MYBL1 were identified, and O-GlcNAc levels regulated their methylation status. These results strongly argue that O-GlcNAc epigenetically regulates MYBL1, functioning similarly to H3K27me3. The aberrant CCSC compartment observed after modulating O-GlcNAc levels is therefore likely to result, at least in part, from the epigenetic regulation of MYBL1 expression by O-GlcNAc, thereby significantly affecting tumor progression.
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Affiliation(s)
- Huabei Guo
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, and
| | - Bing Zhang
- the Boston Children's Hospital, Harvard University, Boston, Massachusetts 02115, and
| | - Alison V Nairn
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, and
| | - Tamas Nagy
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602
| | - Kelley W Moremen
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, and
| | - Phillip Buckhaults
- the South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208
| | - Michael Pierce
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, and
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147
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Ryall JG, Cliff T, Dalton S, Sartorelli V. Metabolic Reprogramming of Stem Cell Epigenetics. Cell Stem Cell 2017; 17:651-662. [PMID: 26637942 DOI: 10.1016/j.stem.2015.11.012] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
For many years, stem cell metabolism was viewed as a byproduct of cell fate status rather than an active regulatory mechanism; however, there is now a growing appreciation that metabolic pathways influence epigenetic changes associated with lineage commitment, specification, and self-renewal. Here we review how metabolites generated during glycolytic and oxidative processes are utilized in enzymatic reactions leading to epigenetic modifications and transcriptional regulation. We discuss how "metabolic reprogramming" contributes to global epigenetic changes in the context of naive and primed pluripotent states, somatic reprogramming, and hematopoietic and skeletal muscle tissue stem cells, and we discuss the implications for regenerative medicine.
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Affiliation(s)
- James G Ryall
- Stem Cell Metabolism and Regenerative Medicine Group, Basic & Clinical Myology Laboratory, Department of Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Tim Cliff
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, Athens, GA 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, Athens, GA 30602, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20829, USA.
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148
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Long-Term Effects of the Periconception Period on Embryo Epigenetic Profile and Phenotype: The Role of Stress and How This Effect Is Mediated. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1014:117-135. [PMID: 28864988 DOI: 10.1007/978-3-319-62414-3_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Stress represents an unavoidable aspect of human life, and pathologies associated with dysregulation of stress mechanisms - particularly psychiatric disorders - represent a significant global health problem. While it has long been observed that levels of stress experienced in the periconception period may greatly affect the offspring's risk of psychiatric disorders, the mechanisms underlying these associations are not yet comprehensively understood. In order to address this question, this chapter will take a 'top-down' approach, by first defining stress and associated concepts, before exploring the mechanistic basis of the stress response in the form of the hypothalamic-pituitary-adrenal (HPA) axis, and how dysregulation of the HPA axis can impede our mental and physical health, primarily via imbalances in glucocorticoids (GCs) and their corresponding receptors (GRs) in the brain. The current extent of knowledge pertaining to the impact of stress on developmental programming and epigenetic inheritance is then extensively discussed, including the role of chromatin remodelling associated with specific HPA axis-related genes and the possible role of regulatory RNAs as messengers of environmental stress both in the intrauterine environment and across the germ line. Furthering our understanding of the role of stress on embryonic development is crucial if we are to increase our predictive power of disease risk and devise-effective treatments and intervention strategies.
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149
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Cimmino L, Aifantis I. Alternative roles for oxidized mCs and TETs. Curr Opin Genet Dev 2016; 42:1-7. [PMID: 27939598 DOI: 10.1016/j.gde.2016.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/09/2023]
Abstract
Ten-eleven-translocation (TET) proteins oxidize 5-methylcytosine (5mC) to form stable or transient modifications (oxi-mCs) in the mammalian genome. Genome-wide mapping and protein interaction studies have shown that 5mC and oxi-mCs have unique distribution patterns and alternative roles in gene expression. In addition, oxi-mCs may interact with specific chromatin regulators, transcription factors and DNA repair proteins to maintain genomic integrity or alter DNA replication and transcriptional elongation rates. In this review we will discuss recent advances in our understanding of how TETs and 5hmC exert their epigenetic function as tumor suppressors by playing alternative roles in transcriptional regulation and genomic stability.
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Affiliation(s)
- Luisa Cimmino
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
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150
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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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