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He B, Kram V, Furusawa T, Duverger O, Chu E, Nanduri R, Ishikawa M, Zhang P, Amendt B, Lee J, Bustin M. Epigenetic Regulation of Ameloblast Differentiation by HMGN Proteins. J Dent Res 2024; 103:51-61. [PMID: 37950483 PMCID: PMC10850876 DOI: 10.1177/00220345231202468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Dental enamel formation is coordinated by ameloblast differentiation, production of enamel matrix proteins, and crystal growth. The factors regulating ameloblast differentiation are not fully understood. Here we show that the high mobility group N (HMGN) nucleosomal binding proteins modulate the rate of ameloblast differentiation and enamel formation. We found that HMGN1 and HMGN2 proteins are downregulated during mouse ameloblast differentiation. Genetically altered mice lacking HMGN1 and HMGN2 proteins show faster ameloblast differentiation and a higher rate of enamel deposition in mice molars and incisors. In vitro differentiation of induced pluripotent stem cells to dental epithelium cells showed that HMGN proteins modulate the expression and chromatin accessibility of ameloblast-specific genes and affect the binding of transcription factors epiprofin and PITX2 to ameloblast-specific genes. Our results suggest that HMGN proteins regulate ameloblast differentiation and enamel mineralization by modulating lineage-specific chromatin accessibility and transcription factor binding to ameloblast regulatory sites.
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Affiliation(s)
- B. He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Craniofacial Anomalies and Regeneration Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - V. Kram
- Molecular Biology of Bones & Teeth Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - T. Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - O. Duverger
- Craniofacial Anomalies and Regeneration Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - E.Y. Chu
- Department of General Dentistry, Operative Division, University of Maryland, School of Dentistry, Baltimore, MD, USA
| | - R. Nanduri
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M. Ishikawa
- Department of Pathology and Laboratory Medicine and Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - P. Zhang
- Molecular Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - B.A. Amendt
- Department of Anatomy and Cell Biology, and the Craniofacial Anomalies Research Center, Carver College of Medicine, the University of Iowa, Iowa City, IA, USA
| | - J.S. Lee
- Craniofacial Anomalies and Regeneration Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - M. Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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2
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Nanduri R, Furusawa T, Lobanov A, He B, Xie C, Dadkhah K, Kelly MC, Gavrilova O, Gonzalez FJ, Bustin M. Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins. Nat Commun 2022; 13:7303. [PMID: 36435799 PMCID: PMC9701217 DOI: 10.1038/s41467-022-34964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022] Open
Abstract
White adipose tissue browning is a key metabolic process controlled by epigenetic factors that facilitate changes in gene expression leading to altered cell identity. We find that male mice lacking the nucleosome binding proteins HMGN1 and HMGN2 (DKO mice), show decreased body weight and inguinal WAT mass, but elevated food intake, WAT browning and energy expenditure. DKO white preadipocytes show reduced chromatin accessibility and lower FRA2 and JUN binding at Pparγ and Pparα promoters. White preadipocytes and mouse embryonic fibroblasts from DKO mice show enhanced rate of differentiation into brown-like adipocytes. Differentiating DKO adipocytes show reduced H3K27ac levels at white adipocyte-specific enhancers but elevated H3K27ac levels at brown adipocyte-specific enhancers, suggesting a faster rate of change in cell identity, from white to brown-like adipocytes. Thus, HMGN proteins function as epigenetic factors that stabilize white adipocyte cell identity, thereby modulating the rate of white adipose tissue browning and affecting energy metabolism in mice.
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Affiliation(s)
- Ravikanth Nanduri
- grid.94365.3d0000 0001 2297 5165Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Takashi Furusawa
- grid.94365.3d0000 0001 2297 5165Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Alexei Lobanov
- grid.94365.3d0000 0001 2297 5165CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Bing He
- grid.94365.3d0000 0001 2297 5165Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Carol Xie
- grid.94365.3d0000 0001 2297 5165Nucleic Acid Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kimia Dadkhah
- grid.418021.e0000 0004 0535 8394CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892 USA
| | - Michael C. Kelly
- grid.418021.e0000 0004 0535 8394CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892 USA
| | - Oksana Gavrilova
- grid.94365.3d0000 0001 2297 5165Mouse Metabolism Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Frank J. Gonzalez
- grid.94365.3d0000 0001 2297 5165Nucleic Acid Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Michael Bustin
- grid.94365.3d0000 0001 2297 5165Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
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3
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Eliason S, Su D, Pinho F, Sun Z, Zhang Z, Li X, Sweat M, Venugopalan SR, He B, Bustin M, Amendt BA. HMGN2 represses gene transcription via interaction with transcription factors Lef-1 and Pitx2 during amelogenesis. J Biol Chem 2022; 298:102295. [PMID: 35872015 PMCID: PMC9418915 DOI: 10.1016/j.jbc.2022.102295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/06/2022] Open
Abstract
The chromatin-associated high mobility group protein N2 (HMGN2) cofactor regulates transcription factor activity through both chromatin and protein interactions. Hmgn2 expression is known to be developmentally regulated, but the post-transcriptional mechanisms that regulate Hmgn2 expression and its precise roles in tooth development remain unclear. Here, we demonstrate that HMGN2 inhibits the activity of multiple transcription factors as a general mechanism to regulate early development. Bimolecular fluorescence complementation, pull-down, and coimmunoprecipitation assays show that HMGN2 interacts with the transcription factor Lef-1 through its HMG-box domain as well as with other early development transcription factors, Dlx2, FoxJ1, and Pitx2. Furthermore, EMSAs demonstrate that HMGN2 binding to Lef-1 inhibits its DNA-binding activity. We found that Pitx2 and Hmgn2 associate with H4K5ac and H3K4me2 chromatin marks in the proximal Dlx2 promoter, demonstrating Hmgn2 association with open chromatin. In addition, we demonstrate that microRNAs (miRs) mir-23a and miR-23b directly target Hmgn2, promoting transcriptional activation at several gene promoters, including the amelogenin promoter. In vivo, we found that decreased Hmgn2 expression correlates with increased miR-23 expression in craniofacial tissues as the murine embryo develops. Finally, we show that ablation of Hmgn2 in mice results in increased amelogenin expression because of increased Pitx2, Dlx2, Lef-1, and FoxJ1 transcriptional activity. Taken together, our results demonstrate both post-transcriptional regulation of Hmgn2 by miR-23a/b and post-translational regulation of gene expression by Hmgn2–transcription factor interactions. We conclude that HMGN2 regulates tooth development through its interaction with multiple transcription factors.
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Affiliation(s)
- Steven Eliason
- Department of Anatomy and Cell Biology, and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA
| | - Dan Su
- Department of Anatomy and Cell Biology, and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA
| | | | - Zhao Sun
- Washington University St. Louis, St. Louis, MO
| | | | - Xiao Li
- Texas Heart Institute, Houston, TX
| | | | | | - Bing He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brad A Amendt
- Department of Anatomy and Cell Biology, and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA; Department of Orthodontics, The University of Iowa, Iowa City, IA.
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4
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He B, Zhu I, Postnikov Y, Furusawa T, Jenkins L, Nanduri R, Bustin M, Landsman D. Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin. Epigenetics Chromatin 2022; 15:23. [PMID: 35761366 PMCID: PMC9235084 DOI: 10.1186/s13072-022-00457-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/05/2022] [Indexed: 08/30/2023] Open
Abstract
Background Nucleosomal binding proteins, HMGN, is a family of chromatin architectural proteins that are expressed in all vertebrate nuclei. Although previous studies have discovered that HMGN proteins have important roles in gene regulation and chromatin accessibility, whether and how HMGN proteins affect higher order chromatin status remains unknown. Results We examined the roles that HMGN1 and HMGN2 proteins play in higher order chromatin structures in three different cell types. We interrogated data generated in situ, using several techniques, including Hi–C, Promoter Capture Hi–C, ChIP-seq, and ChIP–MS. Our results show that HMGN proteins occupy the A compartment in the 3D nucleus space. In particular, HMGN proteins occupy genomic regions involved in cell-type-specific long-range promoter–enhancer interactions. Interestingly, depletion of HMGN proteins in the three different cell types does not cause structural changes in higher order chromatin, i.e., in topologically associated domains (TADs) and in A/B compartment scores. Using ChIP-seq combined with mass spectrometry, we discovered protein partners that are directly associated with or neighbors of HMGNs on nucleosomes. Conclusions We determined how HMGN chromatin architectural proteins are positioned within a 3D nucleus space, including the identification of their binding partners in mononucleosomes. Our research indicates that HMGN proteins localize to active chromatin compartments but do not have major effects on 3D higher order chromatin structure and that their binding to chromatin is not dependent on specific protein partners. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00457-4.
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Affiliation(s)
- Bing He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, Intramural Research Program, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ravikanth Nanduri
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, Intramural Research Program, National Library of Medicine, Bethesda, MD, 20894, USA.
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5
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Zhang S, Postnikov Y, Lobanov A, Furusawa T, Deng T, Bustin M. H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors. Commun Biol 2022; 5:159. [PMID: 35197580 PMCID: PMC8866397 DOI: 10.1038/s42003-022-03099-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes containing acetylated H3K27 are a major epigenetic mark of active chromatin and identify cell-type specific chromatin regulatory regions which serve as binding sites for transcription factors. Here we show that the ubiquitous nucleosome binding proteins HMGN1 and HMGN2 bind preferentially to H3K27ac nucleosomes at cell-type specific chromatin regulatory regions. HMGNs bind directly to the acetylated nucleosome; the H3K27ac residue and linker DNA facilitate the preferential binding of HMGNs to the modified nucleosomes. Loss of HMGNs increases the levels of H3K27me3 and the histone H1 occupancy at enhancers and promoters and alters the interaction of transcription factors with chromatin. These experiments indicate that the H3K27ac epigenetic mark enhances the interaction of architectural protein with chromatin regulatory sites and identify determinants that facilitate the localization of HMGN proteins at regulatory sites to modulate cell-type specific gene expression. The nucleosome-binding proteins HMGN1 and HMGN2 prefer acetylated nucleosomes at H3K27ac and the loss of this interaction alters binding of transcription factors to chromatin.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Maryland, MD, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA.,Cell Translation Laboratory, NCATS, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA.
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6
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Wu Q, Sun L, Hu X, Wang X, Xu F, Chen B, Liang X, Xia J, Wang P, Aibara D, Zhang S, Zeng G, Yun C, Yan Y, Zhu Y, Bustin M, Zhang S, Gonzalez FJ, Jiang C. Suppressing the intestinal farnesoid X receptor/sphingomyelin phosphodiesterase 3 axis decreases atherosclerosis. J Clin Invest 2021; 131:142865. [PMID: 33938457 DOI: 10.1172/jci142865] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Intestinal farnesoid X receptor (FXR) signaling is involved in the development of obesity, fatty liver disease, and type 2 diabetes. However, the role of intestinal FXR in atherosclerosis and its potential as a target for clinical treatment have not been explored. The serum levels of fibroblast growth factor 19 (FGF19), which is encoded by an FXR target gene, were much higher in patients with hypercholesterolemia than in control subjects and were positively related to circulating ceramide levels, indicating a link between intestinal FXR, ceramide metabolism, and atherosclerosis. Among ApoE-/- mice fed a high-cholesterol diet (HCD), intestinal FXR deficiency (in FxrΔIE ApoE-/- mice) or direct FXR inhibition (via treatment with the FXR antagonist glycoursodeoxycholic acid [GUDCA]) decreased atherosclerosis and reduced the levels of circulating ceramides and cholesterol. Sphingomyelin phosphodiesterase 3 (SMPD3), which is involved in ceramide synthesis in the intestine, was identified as an FXR target gene. SMPD3 overexpression or C16:0 ceramide supplementation eliminated the improvements in atherosclerosis in FxrΔIE ApoE-/- mice. Administration of GUDCA or GW4869, an SMPD3 inhibitor, elicited therapeutic effects on established atherosclerosis in ApoE-/- mice by decreasing circulating ceramide levels. This study identified an intestinal FXR/SMPD3 axis that is a potential target for atherosclerosis therapy.
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Affiliation(s)
- Qing Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Xiaomin Hu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xuemei Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Feng Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Bo Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xianyi Liang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jialin Xia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Pengcheng Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Daisuke Aibara
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Shaofei Zhang
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chuyu Yun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yu Yan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yicheng Zhu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Michael Bustin
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Shuyang Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China
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7
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Sung M, Babagana M, Oh KS, Chakraborty S, Pacholewska A, Furusawa T, Bustin M. Functional macrophage chromatin landscapes depend on HMGN1/HMGN2. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.69.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The High Mobility Group (HMG) proteins are ubiquitously present in the nuclei of all vertebrate cells. HMG proteins bind dynamically to chromatin without DNA sequence specificity, and they affect DNA-dependent functions such as replication, repair, and transcription, but only in the context of chromatin. HMGs are also suggested to play an important role in the immune system. Both HMGB1 and HMGN1 can act as alarmins. HMGN proteins also affect the response of B lymphocytes to bacterial LPS stimulation. HMGN proteins are typically enriched at regulatory sites such as enhancers and promoters, and have been shown to affect the chromatin landscape, suggesting a role in epigenetic regulatory processes. In LPS-stimulated bone marrow-derived macrophages (BMDMs), most HMG genes are downregulated in response to LPS (Oh KS et al, 2017 Immunity, PMID: 28801231. To understand the role of HMG proteins in the regulation of macrophage chromatin, we performed RNA-seq and ATAC-seq on BMDMs and two tissue-resident macrophage populations from mice lacking both HMGN1 and HMGN2. We identified several hundred differentially expressed genes in BMDMs with a large gene cluster showing female-specific downregulation in the double knockout. In peritoneal macrophages, the largest differentially expressed gene cluster was from the female-specific upregulated genes. The most dramatic transcriptome-wide changes were observed in microglia. Interestingly, MHC genes were commonly upregulated in macrophages from mutant mice. Together with alterations in chromatin, this raises the possibility that HMGNs maintain functional macrophage enhancers with specificity for the resident tissue.
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8
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Morales Torres C, Wu MY, Hobor S, Wainwright EN, Martin MJ, Patel H, Grey W, Grönroos E, Howell S, Carvalho J, Snijders AP, Bustin M, Bonnet D, Smith PD, Swanton C, Howell M, Scaffidi P. Selective inhibition of cancer cell self-renewal through a Quisinostat-histone H1.0 axis. Nat Commun 2020; 11:1792. [PMID: 32286289 PMCID: PMC7156485 DOI: 10.1038/s41467-020-15615-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 03/19/2020] [Indexed: 12/24/2022] Open
Abstract
Continuous cancer growth is driven by subsets of self-renewing malignant cells. Targeting of uncontrolled self-renewal through inhibition of stem cell-related signaling pathways has proven challenging. Here, we show that cancer cells can be selectively deprived of self-renewal ability by interfering with their epigenetic state. Re-expression of histone H1.0, a tumor-suppressive factor that inhibits cancer cell self-renewal in many cancer types, can be broadly induced by the clinically well-tolerated compound Quisinostat. Through H1.0, Quisinostat inhibits cancer cell self-renewal and halts tumor maintenance without affecting normal stem cell function. Quisinostat also hinders expansion of cells surviving targeted therapy, independently of the cancer types and the resistance mechanism, and inhibits disease relapse in mouse models of lung cancer. Our results identify H1.0 as a major mediator of Quisinostat's antitumor effect and suggest that sequential administration of targeted therapy and Quisinostat may be a broadly applicable strategy to induce a prolonged response in patients.
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Affiliation(s)
| | - Mary Y Wu
- High-Throughput Screening, Francis Crick Institute, London, NW1 1AT, UK
| | - Sebastijan Hobor
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | | | | | - Harshil Patel
- Bioinformatics and Biostatistics, Francis Crick Institute, London, NW1 1AT, UK
| | - William Grey
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | - Steven Howell
- Proteomics, Francis Crick Institute, London, NW1 1AT, UK
| | - Joana Carvalho
- Experimental Histopathology, Francis Crick Institute, London, NW1 1AT, UK
| | | | - Michael Bustin
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | - Paul D Smith
- Oncology R&D, AstraZeneca, Cambridge, CB2 0RE, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Michael Howell
- High-Throughput Screening, Francis Crick Institute, London, NW1 1AT, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, Francis Crick Institute, London, NW1 1AT, UK.
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
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9
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Cabal-Hierro L, van Galen P, Prado MA, Higby KJ, Togami K, Mowery CT, Paulo JA, Xie Y, Cejas P, Furusawa T, Bustin M, Long HW, Sykes DB, Gygi SP, Finley D, Bernstein BE, Lane AA. Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun 2020; 11:1406. [PMID: 32179749 PMCID: PMC7076002 DOI: 10.1038/s41467-020-15221-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/27/2020] [Indexed: 01/26/2023] Open
Abstract
Chromatin organization is a highly orchestrated process that influences gene expression, in part by modulating access of regulatory factors to DNA and nucleosomes. Here, we report that the chromatin accessibility regulator HMGN1, a target of recurrent DNA copy gains in leukemia, controls myeloid differentiation. HMGN1 amplification is associated with increased accessibility, expression, and histone H3K27 acetylation of loci important for hematopoietic stem cells (HSCs) and leukemia, such as HoxA cluster genes. In vivo, HMGN1 overexpression is linked to decreased quiescence and increased HSC activity in bone marrow transplantation. HMGN1 overexpression also cooperates with the AML-ETO9a fusion oncoprotein to impair myeloid differentiation and enhance leukemia stem cell (LSC) activity. Inhibition of histone acetyltransferases CBP/p300 relieves the HMGN1-associated differentiation block. These data nominate factors that modulate chromatin accessibility as regulators of HSCs and LSCs, and suggest that targeting HMGN1 or its downstream effects on histone acetylation could be therapeutically active in AML.
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Affiliation(s)
- Lucia Cabal-Hierro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peter van Galen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kelly J Higby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Katsuhiro Togami
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Cody T Mowery
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Takashi Furusawa
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Bradley E Bernstein
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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10
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Mowery CT, Reyes JM, Cabal-Hierro L, Higby KJ, Karlin KL, Wang JH, Kimmerling RJ, Cejas P, Lim K, Li H, Furusawa T, Long HW, Pellman D, Chapuy B, Bustin M, Manalis SR, Westbrook TF, Lin CY, Lane AA. Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression. Cell Rep 2019; 25:1898-1911.e5. [PMID: 30428356 PMCID: PMC6321629 DOI: 10.1016/j.celrep.2018.10.061] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/21/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute normalization unmasks global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulates transcriptional changes seen with triplication of a Down syndrome critical region on distal chromosome 21, and HMGN1 is necessary for B cell phenotypes in DS models. Absolute exogenous-normalized chromatin immunoprecipitation sequencing (ChIP-Rx) also reveals a global increase in histone H3K27 acetylation caused by HMGN1. Transcriptional amplification downstream of HMGN1 is enriched for stage-specific programs of B cells and B cell acute lymphoblastic leukemia, dependent on the developmental cellular context. These data offer a mechanistic explanation for DS transcriptional patterns and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted. How trisomy 21 contributes to Down syndrome phenotypes, including increased leukemia risk, is not well understood. Mowery et al. use per-cell normalization approaches to reveal global transcriptional amplification in Down syndrome models. HMGN1 overexpression is sufficient to induce these alterations and promotes lineage-associated transcriptional programs, signaling, and B cell progenitor phenotypes.
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Affiliation(s)
- Cody T Mowery
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jaime M Reyes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lucia Cabal-Hierro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly J Higby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kristen L Karlin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Jarey H Wang
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert J Kimmerling
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hubo Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Takashi Furusawa
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Department of Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Scott R Manalis
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas F Westbrook
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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11
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Zhang S, Deng T, Tang W, He B, Furusawa T, Ambs S, Bustin M. Epigenetic regulation of REX1 expression and chromatin binding specificity by HMGNs. Nucleic Acids Res 2019; 47:4449-4461. [PMID: 30838422 DOI: 10.1093/nar/gkz161] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 12/16/2022] Open
Abstract
HMGN proteins localize to chromatin regulatory sites and modulate the cell-type specific transcription profile; however, the molecular mechanism whereby these ubiquitous nucleosome binding proteins affect gene expression is not fully understood. Here, we show that HMGNs regulate the expression of Rex1, one of the most highly transcribed genes in mouse embryonic stem cells (ESCs), by recruiting the transcription factors NANOG, OCT4 and SOX2 to an ESC-specific super enhancer located in the 5' region of Rex1. HMGNs facilitate the establishment of an epigenetic landscape characteristic of active chromatin and enhancer promoter interactions, as seen by chromatin conformation capture. Loss of HMGNs alters the local epigenetic profile, increases histone H1 occupancy, decreases transcription factors binding and reduces enhancer promoter interactions, thereby downregulating, but not abolishing Rex1 expression. ChIP-seq analyses show high colocalization of HMGNs and of REX1, a zinc finger protein, at promoters and enhancers. Loss of HMGNs preferentially reduces the specific binding of REX1 to these chromatin regulatory sites. Thus, HMGNs affects both the expression and the chromatin binding specificity of REX1. We suggest that HMGNs affect cell-type specific gene expression by modulating the binding specificity of transcription factors to chromatin.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Bing He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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He B, Deng T, Zhu I, Furusawa T, Zhang S, Tang W, Postnikov Y, Ambs S, Li CC, Livak F, Landsman D, Bustin M. Binding of HMGN proteins to cell specific enhancers stabilizes cell identity. Nat Commun 2018; 9:5240. [PMID: 30532006 PMCID: PMC6286339 DOI: 10.1038/s41467-018-07687-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/15/2018] [Indexed: 01/10/2023] Open
Abstract
The dynamic nature of the chromatin epigenetic landscape plays a key role in the establishment and maintenance of cell identity, yet the factors that affect the dynamics of the epigenome are not fully known. Here we find that the ubiquitous nucleosome binding proteins HMGN1 and HMGN2 preferentially colocalize with epigenetic marks of active chromatin, and with cell-type specific enhancers. Loss of HMGNs enhances the rate of OSKM induced reprogramming of mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs), and the ASCL1 induced conversion of fibroblast into neurons. During transcription factor induced reprogramming to pluripotency, loss of HMGNs accelerates the erasure of the MEF-specific epigenetic landscape and the establishment of an iPSCs-specific chromatin landscape, without affecting the pluripotency potential and the differentiation potential of the reprogrammed cells. Thus, HMGN proteins modulate the plasticity of the chromatin epigenetic landscape thereby stabilizing, rather than determining cell identity. HMGN1 and HMGN2 are ubiquitous nucleosome binding proteins. Here the authors provide evidence that HMGN proteins preferentially localize to chromatin regulatory sites to modulate the plasticity of the epigenetic landscape, proposing that HGMNs stabilize, rather than determine, cell identity.
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Affiliation(s)
- Bing He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Caiyi Cherry Li
- Laboratory of Genomic Integrity, Center for Cancer Research National Cancer Institute National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ferenc Livak
- Laboratory of Genomic Integrity, Center for Cancer Research National Cancer Institute National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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13
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Mishra P, Tang W, Putluri V, Dorsey TH, Jin F, Wang F, Zhu D, Amable L, Deng T, Zhang S, Killian JK, Wang Y, Minas TZ, Yfantis HG, Lee DH, Sreekumar A, Bustin M, Liu W, Putluri N, Ambs S. ADHFE1 is a breast cancer oncogene and induces metabolic reprogramming. J Clin Invest 2017; 128:323-340. [PMID: 29202474 DOI: 10.1172/jci93815] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/17/2017] [Indexed: 12/12/2022] Open
Abstract
Metabolic reprogramming in breast tumors is linked to increases in putative oncogenic metabolites that may contribute to malignant transformation. We previously showed that accumulation of the oncometabolite, 2-hydroxyglutarate (2HG), in breast tumors was associated with MYC signaling, but not with isocitrate dehydrogenase (IDH) mutations, suggesting a distinct mechanism for increased 2HG in breast cancer. Here, we determined that D-2HG is the predominant enantiomer in human breast tumors and show that the D-2HG-producing mitochondrial enzyme, alcohol dehydrogenase, iron-containing protein 1 (ADHFE1), is a breast cancer oncogene that decreases patient survival. We found that MYC upregulates ADHFE1 through changes in iron metabolism while coexpression of both ADHFE1 and MYC strongly enhanced orthotopic tumor growth in MCF7 cells. Moreover, ADHFE1 promoted metabolic reprogramming with increased formation of D-2HG and reactive oxygen, a reductive glutamine metabolism, and modifications of the epigenetic landscape, leading to cellular dedifferentiation, enhanced mesenchymal transition, and phenocopying alterations that occur with high D-2HG levels in cancer cells with IDH mutations. Together, our data support the hypothesis that ADHFE1 and MYC signaling contribute to D-2HG accumulation in breast tumors and show that D-2HG is an oncogenic metabolite and potential driver of disease progression.
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Affiliation(s)
- Prachi Mishra
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Vasanta Putluri
- Department of Molecular and Cell Biology, Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, and.,Advanced Technology Core, Baylor College of Medicine, Houston, Texas, USA
| | - Tiffany H Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Feng Jin
- Department of Molecular and Cell Biology, Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, and.,Advanced Technology Core, Baylor College of Medicine, Houston, Texas, USA
| | - Fang Wang
- Agios Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Donewei Zhu
- Agios Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Lauren Amable
- National Institute of Minority Health and Health Disparities
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, CCR, NCI, and
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, CCR, NCI, and
| | - J Keith Killian
- Genetics Branch, CCR, and Clinical Molecular Profiling Core, NCI, NIH, Bethesda, Maryland, USA
| | - Yonghong Wang
- Genetics Branch, CCR, and Clinical Molecular Profiling Core, NCI, NIH, Bethesda, Maryland, USA
| | - Tsion Z Minas
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Harry G Yfantis
- Pathology and Laboratory Medicine, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA
| | - Dong H Lee
- Pathology and Laboratory Medicine, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA
| | - Arun Sreekumar
- Department of Molecular and Cell Biology, Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, and
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, CCR, NCI, and
| | - Wei Liu
- Agios Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Nagireddy Putluri
- Department of Molecular and Cell Biology, Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, and.,Advanced Technology Core, Baylor College of Medicine, Houston, Texas, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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14
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Murphy KJ, Cutter AR, Fang H, Postnikov YV, Bustin M, Hayes JJ. HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic Acids Res 2017; 45:9917-9930. [PMID: 28973435 PMCID: PMC5622319 DOI: 10.1093/nar/gkx579] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/28/2017] [Indexed: 01/23/2023] Open
Abstract
The structure of the nucleosome, the basic building block of the chromatin fiber, plays a key role in epigenetic regulatory processes that affect DNA-dependent processes in the context of chromatin. Members of the HMGN family of proteins bind specifically to nucleosomes and affect chromatin structure and function, including transcription and DNA repair. To better understand the mechanisms by which HMGN 1 and 2 alter chromatin, we analyzed their effect on the organization of histone tails and linker histone H1 in nucleosomes. We find that HMGNs counteract linker histone (H1)-dependent stabilization of higher order ‘tertiary’ chromatin structures but do not alter the intrinsic ability of nucleosome arrays to undergo salt-induced compaction and self-association. Surprisingly, HMGNs do not displace H1s from nucleosomes; rather these proteins bind nucleosomes simultaneously with H1s without disturbing specific contacts between the H1 globular domain and nucleosomal DNA. However, HMGNs do alter the nucleosome-dependent condensation of the linker histone C-terminal domain, which is critical for stabilizing higher-order chromatin structures. Moreover, HMGNs affect the interactions of the core histone tail domains with nucleosomal DNA, redirecting the tails to more interior positions within the nucleosome. Our studies provide new insights into the molecular mechanisms whereby HMGNs affect chromatin structure.
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Affiliation(s)
- Kevin J Murphy
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Amber R Cutter
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - He Fang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Yuri V Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
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15
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Deng T, Postnikov Y, Zhang S, Garrett L, Becker L, Rácz I, Hölter SM, Wurst W, Fuchs H, Gailus-Durner V, de Angelis MH, Bustin M. Interplay between H1 and HMGN epigenetically regulates OLIG1&2 expression and oligodendrocyte differentiation. Nucleic Acids Res 2017; 45:3031-3045. [PMID: 27923998 PMCID: PMC5389484 DOI: 10.1093/nar/gkw1222] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/22/2016] [Indexed: 01/22/2023] Open
Abstract
An interplay between the nucleosome binding proteins H1 and HMGN is known to affect chromatin dynamics, but the biological significance of this interplay is still not clear. We find that during embryonic stem cell differentiation loss of HMGNs leads to down regulation of genes involved in neural differentiation, and that the transcription factor OLIG2 is a central node in the affected pathway. Loss of HMGNs affects the expression of OLIG2 as well as that of OLIG1, two transcription factors that are crucial for oligodendrocyte lineage specification and nerve myelination. Loss of HMGNs increases the chromatin binding of histone H1, thereby recruiting the histone methyltransferase EZH2 and elevating H3K27me3 levels, thus conferring a repressive epigenetic signature at Olig1&2 sites. Embryonic stem cells lacking HMGNs show reduced ability to differentiate towards the oligodendrocyte lineage, and mice lacking HMGNs show reduced oligodendrocyte count and decreased spinal cord myelination, and display related neurological phenotypes. Thus, the presence of HMGN proteins is required for proper expression of neural differentiation genes during embryonic stem cell differentiation. Specifically, we demonstrate that the dynamic interplay between HMGNs and H1 in chromatin epigenetically regulates the expression of OLIG1&2, thereby affecting oligodendrocyte development and myelination, and mouse behavior.
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Affiliation(s)
- Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lillian Garrett
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ildikó Rácz
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Molecular Psychiatry, University of Bonn, 53125 Bonn, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Technische Universität München-Weihenstephan, Chair of Developmental Genetics c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE) Site Munich, Munich Germany.,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, 85354 Freising, Germany.,German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Kugler J, Postnikov YV, Furusawa T, Kimura S, Bustin M. Elevated HMGN4 expression potentiates thyroid tumorigenesis. Carcinogenesis 2017; 38:391-401. [PMID: 28186538 DOI: 10.1093/carcin/bgx015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022] Open
Abstract
Thyroid cancer originates from genetic and epigenetic changes that alter gene expression and cellular signaling pathways. Here, we report that altered expression of the nucleosome-binding protein HMGN4 potentiates thyroid tumorigenesis. Bioinformatics analyses reveal increased HMGN4 expression in thyroid cancer. We find that upregulation of HMGN4 expression in mouse and human cells, and in the thyroid of transgenic mice, alters the cellular transcription profile, downregulates the expression of the tumor suppressors Atm, Atrx and Brca2, and elevates the levels of the DNA damage marker γH2AX. Mouse and human cells overexpressing HMGN4 show increased tumorigenicity as measured by colony formation, by tumor generation in nude mice, and by the formation of preneoplastic lesions in the thyroid of transgenic mice. Our study identifies a novel epigenetic factor that potentiates thyroid oncogenesis and raises the possibility that HMGN4 may serve as an additional diagnostic marker, or therapeutic target in certain thyroid cancers.
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Affiliation(s)
- Jamie Kugler
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
| | - Yuri V Postnikov
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
| | - Takashi Furusawa
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
| | - Shioko Kimura
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
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17
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Abstract
The primary function of the genome is to store, propagate, and express the genetic information that gives rise to a cell's architectural and functional machinery. However, the genome is also a major structural component of the cell. Besides its genetic roles, the genome affects cellular functions by nongenetic means through its physical and structural properties, particularly by exerting mechanical forces and by serving as a scaffold for binding of cellular components. Major cellular processes affected by nongenetic functions of the genome include establishment of nuclear structure, signal transduction, mechanoresponses, cell migration, and vision in nocturnal animals. We discuss the concept, mechanisms, and implications of nongenetic functions of the genome.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, MD 20892, USA
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18
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Conlon T, Merthan L, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Furusawa T, Bustin M, Eickelberg O, Yildirim AÖ. Emphysema susceptibility is modulated by the epigenetic regulator HMGN5. Pneumologie 2016. [DOI: 10.1055/s-0036-1583492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M. HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res 2016; 44:7144-58. [PMID: 27112571 PMCID: PMC5009722 DOI: 10.1093/nar/gkw323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/14/2016] [Indexed: 12/18/2022] Open
Abstract
The activation of naïve B lymphocyte involves rapid and major changes in chromatin organization and gene expression; however, the complete repertoire of nuclear factors affecting these genomic changes is not known. We report that HMGN proteins, which bind to nucleosomes and affect chromatin structure and function, co-localize with, and maintain the intensity of DNase I hypersensitive sites genome wide, in resting but not in activated B cells. Transcription analyses of resting and activated B cells from wild-type and Hmgn−/− mice, show that loss of HMGNs dampens the magnitude of the transcriptional response and alters the pattern of gene expression during the course of B-cell activation; defense response genes are most affected at the onset of activation. Our study provides insights into the biological function of the ubiquitous HMGN chromatin binding proteins and into epigenetic processes that affect the fidelity of the transcriptional response during the activation of B cell lymphocytes.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Garfinkel BP, Arad S, Le PT, Bustin M, Rosen CJ, Gabet Y, Orly J. Proportionate Dwarfism in Mice Lacking Heterochromatin Protein 1 Binding Protein 3 (HP1BP3) Is Associated With Alterations in the Endocrine IGF-1 Pathway. Endocrinology 2015; 156:4558-70. [PMID: 26402843 PMCID: PMC5393342 DOI: 10.1210/en.2015-1668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heterochromatin protein 1 binding protein 3 (HP1BP3) is a recently described histone H1-related protein with roles in chromatin structure and transcriptional regulation. To explore the potential physiological role of HP1BP3, we have previously described an Hp1bp3(-/-) mouse model with reduced postnatal viability and growth. We now find that these mice are proportionate dwarfs, with reduction in body weight, body length, and organ weight. In addition to their small size, microcomputed tomography analysis showed that Hp1bp3(-/-) mice present a dramatic impairment of their bone development and structure. By 3 weeks of age, mice of both sexes have severely impaired cortical and trabecular bone, and these defects persist into adulthood and beyond. Primary cultures of both osteoblasts and osteoclasts from Hp1bp3(-/-) bone marrow and splenocytes, respectively, showed normal differentiation and function, strongly suggesting that the impaired bone accrual is due to noncell autonomous systemic cues in vivo. One major endocrine pathway regulating both body growth and bone acquisition is the IGF regulatory system, composed of IGF-1, the IGF receptors, and the IGF-binding proteins (IGFBPs). At 3 weeks of age, Hp1bp3(-/-) mice exhibited a 60% reduction in circulating IGF-1 and a 4-fold increase in the levels of IGFBP-1 and IGFBP-2. These alterations were reflected in similar changes in the hepatic transcripts of the Igf1, Igfbp1, and Igfbp2 genes. Collectively, these results suggest that HP1BP3 plays a key role in normal growth and bone development by regulating transcription of endocrine IGF-1 components.
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21
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Affiliation(s)
- De Yang
- Laboratory of Molecular Immunoregulation, Cancer & Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute at Bethesda, Bethesda, MD 20892, USA
| | - Joost J Oppenheim
- Laboratory of Molecular Immunoregulation, Cancer & Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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22
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Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M. Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers. Genome Res 2015; 25:1295-308. [PMID: 26156321 PMCID: PMC4561489 DOI: 10.1101/gr.192229.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 12/29/2022]
Abstract
DNase I hypersensitive sites (DHSs) are a hallmark of chromatin regions containing regulatory DNA such as enhancers and promoters; however, the factors affecting the establishment and maintenance of these sites are not fully understood. We now show that HMGN1 and HMGN2, nucleosome-binding proteins that are ubiquitously expressed in vertebrate cells, maintain the DHS landscape of mouse embryonic fibroblasts (MEFs) synergistically. Loss of one of these HMGN variants led to a compensatory increase of binding of the remaining variant. Genome-wide mapping of the DHSs in Hmgn1(-/-), Hmgn2(-/-), and Hmgn1(-/-)n2(-/-) MEFs reveals that loss of both, but not a single HMGN variant, leads to significant remodeling of the DHS landscape, especially at enhancer regions marked by H3K4me1 and H3K27ac. Loss of HMGN variants affects the induced expression of stress-responsive genes in MEFs, the transcription profiles of several mouse tissues, and leads to altered phenotypes that are not seen in mice lacking only one variant. We conclude that the compensatory binding of HMGN variants to chromatin maintains the DHS landscape, and the transcription fidelity and is necessary to retain wild-type phenotypes. Our study provides insight into mechanisms that maintain regulatory sites in chromatin and into functional compensation among nucleosome binding architectural proteins.
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Affiliation(s)
- Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Z Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Martin Klingenspor
- Molecular Nutritional Medicine, Technische Universität München, 85350 Freising, Germany; Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising, Germany
| | - Oana Amarie
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Developmental Genetics (IDG), 85764 Neuherberg, Germany
| | - Jochen Graw
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Developmental Genetics (IDG), 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, 81377 Munich, Germany
| | - Eckhard Wolf
- Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, 81377 Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, 81675 Munich, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Arjan van der Velde
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Ivan Ovcherenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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23
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Garfinkel BP, Melamed-Book N, Anuka E, Bustin M, Orly J. HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth. Nucleic Acids Res 2015; 43:2074-90. [PMID: 25662603 PMCID: PMC4344522 DOI: 10.1093/nar/gkv089] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/28/2022] Open
Abstract
The dynamic architecture of chromatin is vital for proper cellular function, and is maintained by the concerted action of numerous nuclear proteins, including that of the linker histone H1 variants, the most abundant family of nucleosome-binding proteins. Here we show that the nuclear protein HP1BP3 is widely expressed in most vertebrate tissues and is evolutionarily and structurally related to the H1 family. HP1BP3 contains three globular domains and a highly positively charged C-terminal domain, resembling similar domains in H1. Fluorescence recovery after photobleaching (FRAP) studies indicate that like H1, binding of HP1BP3 to chromatin depends on both its C and N terminal regions and is affected by the cell cycle and post translational modifications. HP1BP3 contains functional motifs not found in H1 histones, including an acidic stretch and a consensus HP1-binding motif. Transcriptional profiling of HeLa cells lacking HP1BP3 showed altered expression of 383 genes, suggesting a role for HP1BP3 in modulation of gene expression. Significantly, Hp1bp3(-/-) mice present a dramatic phenotype with 60% of pups dying within 24 h of birth and the surviving animals exhibiting a lifelong 20% growth retardation. We suggest that HP1BP3 is a ubiquitous histone H1 like nuclear protein with distinct and non-redundant functions necessary for survival and growth.
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Affiliation(s)
- Benjamin P Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Naomi Melamed-Book
- Bio-Imaging Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eli Anuka
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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24
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Furusawa T, Rochman M, Taher L, Dimitriadis EK, Nagashima K, Anderson S, Bustin M. Chromatin decompaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness. Nat Commun 2015; 6:6138. [PMID: 25609380 PMCID: PMC4304400 DOI: 10.1038/ncomms7138] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/15/2014] [Indexed: 12/19/2022] Open
Abstract
In most metazoan nuclei, heterochromatin is located at the nuclear periphery in contact with the nuclear lamina, which provides mechanical stability to the nucleus. We show that in cultured cells, chromatin de-compaction by the nucleosome binding protein HMGN5 decreases the sturdiness, elasticity, and rigidity of the nucleus. Mice overexpressing HMGN5, either globally or only in the heart, are normal at birth but develop hypertrophic heart with large cardiomyoctyes, deformed nuclei and disrupted lamina, and die of cardiac malfunction. Chromatin de-compaction is seen in cardiomyocytes of newborn mice but misshaped nuclei with disrupted lamina are seen only in adult cardiomyocytes, suggesting that loss of heterochromatin diminishes the ability of the nucleus to withstand the mechanical forces of the contracting heart. Thus, heterochromatin enhances the ability of the nuclear lamina to maintain the sturdiness and shape of the eukaryotic nucleus; a structural role for chromatin that is distinct from its genetic functions.
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Affiliation(s)
- Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Leila Taher
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock 18057, Germany
| | - Emilios K Dimitriadis
- Biomedical Engineering and Physical Science Shared Resource Program, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kunio Nagashima
- Electron microscopy laboratory, Leidos Biomedical Research Inc., SAIC-Frederick Inc.,Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Stasia Anderson
- Animal Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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25
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Abstract
Alarmins are endogenous mediators that are elicited rapidly in response to danger signals, enhancing innate and adaptive immune responses by promoting the recruitment and maturation of antigen-presenting cells (APC). The nucleosome-binding protein HMGN1 is a potent alarmin that binds TLR4 and induces antigen-specific Th1 immune responses, but its contributions to antitumor immunity have not been explored. We found that ovalbumin (OVA)-expressing EG7 mouse thymoma cells grew much faster in Hmgn1-deficient mice than littermate-matched controls. Tumor-bearing Hmgn1(-/-) mice generated fewer OVA-specific CD8 cells in the spleen than EG7-bearing Hmgn1(+/+) mice, suggesting that HMGN1 supported T cell-mediated antitumor immunity. In addition, EG7 tumors expressing HMGN1 grew more slowly than control EG7 tumors, suggesting greater resistance to HMGN1-expressing tumors. This resistance relied on T cell-mediated immunity because it was abolished by in vivo depletion of CD4(+) and CD8(+) T cells. Moreover, mice vaccinated with a DNA vector expressing an HMGN1-gp100 fusion protein manifested gp100-specific, Th1-polarized immune responses, acquiring resistance to challenge with mouse B16F1 melanoma. Overall, our findings show that HMGN1 contributes to antitumor immunity and it may offer an effective adjuvant to heighten responses to cancer vaccines.
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Affiliation(s)
- Feng Wei
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300060, China
| | - De Yang
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300060, China
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, MD 21702, USA
| | - Poonam Tewary
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, MD 21702, USA
| | - Yana Li
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Sandra Li
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Xin Chen
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, MD 21702, USA
| | - O. M. Zack Howard
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joost J. Oppenheim
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
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Lane AA, Chapuy B, Lin CY, Tivey T, Li H, Townsend E, Bodegom DV, Day TA, Wu SC, Liu H, Yoda A, Alexe G, Schinzel A, Sullivan TJ, Malinge S, Taylor J, Stegmaier K, Jaffe J, Bustin M, Kronnie GT, Izraeli S, Harris M, Stevenson K, Neuberg D, Silverman LB, Sallan SE, Bradner JE, Hahn WC, Crispino JD, Pellman D, Weinstock DM. Abstract 433: Triplication of HMGN1 promotes B cell acute lymphoblastic leukemia (B-ALL) through suppression of H3K27me3. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Our goal is to identify oncogenic loci in regions of recurrent DNA copy number alterations in cancer. Constitutional trisomy 21 (Down syndrome) carries a 20-fold increased risk of B-ALL, and chr.21 gains are the most common acquired aneuploidy in B-ALL. Interstitial amplification in the chr.21q22 region (iAMP21) is also a recurrent finding in B-ALL and carries a poor prognosis. However, the gene(s) on chr.21 responsible for this association remain unclear. We studied the Ts1Rhr mouse, which carries germline triplication of 31 genes homologous to human chr.21q22. Chr.21q22 triplication was sufficient to promote B cell autonomous self-renewal and maturation defects, and cooperated with BCR-ABL or CRLF2 with JAK2 R683G to accelerate leukemogenesis. Chr.21q22 triplication also resulted in histone H3K27 hypomethylation at gene promoters, and the expression signature of triplicated B cells was enriched for genes targeted by polycomb repressor complex 2 (PRC2), which trimethylates H3K27. Thus, chr.21q22 triplication may deregulate B cell development by causing H3K27 hypomethylation at genes critical for progenitor cell growth. In support of this hypothesis, pharmacologic inhibition of PRC2 function was sufficient to confer self-renewal in wild-type B cells, while inhibition of H3K27 demethylases blocked self-renewal induced by chr.21q22 triplication. In three independent B-ALL cohorts, PRC2/H3K27 gene signatures distinguished leukemias with +21 from those without, validating the same biology in human disease. One of the 31 triplicated genes, HMGN1, encodes a nucleosome binding protein known to modulate chromatin structure and facilitate transcriptional activation. When we overexpressed HMGN1 in BaF3 proB cells, H3K27me3 decreased proportionally to the level of overexpression. We next knocked down each of the 31 triplicated genes with lentivirally-expressed shRNAs (5 per gene) and assessed the effects on growth of Ts1Rhr and wild-type primary B cells. Strikingly, Hmgn1 was the top scoring gene and all 5 hairpins targeting Hmgn1 were depleted in the assay. Finally, we studied transgenic mice (HMGN1_OE) that overexpress human HMGN1 (∼2-fold total overexpression). HMGN1_OE mice had a defect in B cell maturation, increased proB colony forming capacity, and a transcriptional signature overlapping with that of triplication of all 31 Ts1Rhr genes. In a bone marrow transplant model driven by BCR-ABL, recipients of HMGN1_OE bone marrow developed B-ALL with decreased latency (median 33 days vs not reached) and increased penetrance (17/18 vs 4/17 mice died by 80 days; leukemia-free survival difference P<0.001) compared to recipients of wild-type bone marrow. These data indicate that HMGN1 is a B-ALL oncogene, and therapies targeting HMGN1 or the downstream effects of HMGN1 overexpression on epigenetic histone modifications may be effective in B-ALL with copy number gains involving chr.21q22.
Citation Format: Andrew A. Lane, Bjoern Chapuy, Charles Y. Lin, Trevor Tivey, Hubo Li, Elizabeth Townsend, Diederik van Bodegom, Tovah A. Day, Shuo-Chieh Wu, Huiyun Liu, Akinori Yoda, Gabriela Alexe, Anna Schinzel, Timothy J. Sullivan, Sebastien Malinge, Jordan Taylor, Kimberly Stegmaier, Jacob Jaffe, Michael Bustin, Geertruy te Kronnie, Shai Izraeli, Marian Harris, Kristen Stevenson, Donna Neuberg, Lewis B. Silverman, Steven E. Sallan, James E. Bradner, William C. Hahn, John D. Crispino, David Pellman, David M. Weinstock. Triplication of HMGN1 promotes B cell acute lymphoblastic leukemia (B-ALL) through suppression of H3K27me3. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 433. doi:10.1158/1538-7445.AM2014-433
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Affiliation(s)
| | | | | | | | - Hubo Li
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | - Huiyun Liu
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | | | | | - Shai Izraeli
- 6Sheba Medical Center Tel Hashomer and Tel Aviv University, Tel Hashomer, Israel
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27
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Lane AA, Chapuy B, Lin CY, Tivey T, Li H, Townsend EC, van Bodegom D, Day TA, Wu SC, Liu H, Yoda A, Alexe G, Schinzel AC, Sullivan TJ, Malinge S, Taylor JE, Stegmaier K, Jaffe JD, Bustin M, te Kronnie G, Izraeli S, Harris MH, Stevenson KE, Neuberg D, Silverman LB, Sallan SE, Bradner JE, Hahn WC, Crispino JD, Pellman D, Weinstock DM. Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation. Nat Genet 2014; 46:618-23. [PMID: 24747640 PMCID: PMC4040006 DOI: 10.1038/ng.2949] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/13/2014] [Indexed: 12/14/2022]
Abstract
Down syndrome confers a 20-fold increased risk of B cell acute lymphoblastic leukemia (B-ALL)1 and polysomy 21 is the most frequent somatic aneuploidy amongst all B-ALLs2. Yet, the mechanistic links between chr.21 triplication and B-ALL remain undefined. Here we show that germline triplication of only 31 genes orthologous to human chr.21q22 confers murine progenitor B cell self-renewal in vitro, maturation defects in vivo, and B-ALL with either BCR-ABL or CRLF2 with activated JAK2. Chr.21q22 triplication suppresses H3K27me3 in progenitor B cells and B-ALLs, and “bivalent” genes with both H3K27me3 and H3K4me3 at their promoters in wild-type progenitor B cells are preferentially overexpressed in triplicated cells. Strikingly, human B-ALLs with polysomy 21 are distinguished by their overexpression of genes marked with H3K27me3 in multiple cell types. Finally, overexpression of HMGN1, a nucleosome remodeling protein encoded on chr.21q223–5, suppresses H3K27me3 and promotes both B cell proliferation in vitro and B-ALL in vivo.
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Affiliation(s)
- Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Trevor Tivey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Hubo Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth C Townsend
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Diederik van Bodegom
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Tovah A Day
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shuo-Chieh Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Huiyun Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Akinori Yoda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Anna C Schinzel
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - Timothy J Sullivan
- Microarray Core, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Sébastien Malinge
- Institut National de la Santé et de la Recherche Médicale (INSERM) U985, Institut Gustave Roussy, Villejuif, France
| | | | - Kimberly Stegmaier
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | | | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Shai Izraeli
- 1] Department of Pediatric Hemato-Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. [2] Department of Human Molecular Genetics and Biochemsitry, Tel Aviv University, Tel Aviv, Israel
| | - Marian H Harris
- Department of Pathology, Children's Hospital Boston, Boston, Massachusetts, USA
| | - Kristen E Stevenson
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - William C Hahn
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois, USA
| | - David Pellman
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - David M Weinstock
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
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Ciappio ED, Krausz KW, Rochman M, Furusawa T, Bonzo JA, Tessarollo L, Gonzalez FJ, Bustin M. Metabolomics reveals a role for the chromatin-binding protein HMGN5 in glutathione metabolism. PLoS One 2014; 9:e84583. [PMID: 24392144 PMCID: PMC3879345 DOI: 10.1371/journal.pone.0084583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/18/2013] [Indexed: 11/26/2022] Open
Abstract
High mobility group nucleosome-binding protein 5 (HMGN5) is a chromatin architectural protein that binds specifically to nucleosomes and reduces the compaction of the chromatin fiber. The protein is present in most vertebrate tissues however the physiological function of this protein is unknown. To examine the function of HMGN5 in vivo, mice lacking the nucleosome-binding domain of HMGN5 were generated and characterized. Serological analysis revealed that compared to wild-type littermates (Hmgn5+/Y), mice with a targeted mutation in the HMGN5 gene (Hmgn5tm1/Y), had elevated serum albumin, non-HDL cholesterol, triglycerides, and alanine transaminase, suggesting mild hepatic abnormalities. Metabolomics analysis of liver extracts and urine revealed clear differences in metabolites between Hmgn5tm1/Y and their Hmgn5+/Y littermates. Hmgn5tm1/Y mice had a significant increase in hepatic glutathione levels and decreased urinary concentrations of betaine, phenylacetylglycine, and creatine, all of which are metabolically related to the glutathione precursor glycine. Microarray and qPCR analysis revealed that expression of two genes affecting glutathione metabolism, glutathione peroxidase 6 (Gpx6) and hexokinase 1 (Hk1), was significantly decreased in Hmgn5tm1/Y mouse liver tissue. Analysis of chromatin structure by DNase I digestion revealed alterations in the chromatin structure of these genes in the livers of Hmgn5tm1/Y mice. Thus, functional loss of HMGN5 leads to changes in transcription of Gpx6 and Hk1 that alter glutathione metabolism.
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Affiliation(s)
- Eric D. Ciappio
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kristopher W. Krausz
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Rochman
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Takashi Furusawa
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jessica A. Bonzo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Frank J. Gonzalez
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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29
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Postnikov YV, Furusawa T, Haines DC, Factor VM, Bustin M. Loss of the nucleosome-binding protein HMGN1 affects the rate of N-nitrosodiethylamine-induced hepatocarcinogenesis in mice. Mol Cancer Res 2013; 12:82-90. [PMID: 24296759 DOI: 10.1158/1541-7786.mcr-13-0392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
UNLABELLED We report that HMGN1, a nucleosome-binding protein that affects chromatin structure and function, affects the growth of N-nitrosodiethylamine (DEN)-induced liver tumors. Following a single DEN injection at 2 weeks of age, Hmgn1(tm1/tm1) mice, lacking the nucleosome-binding domain of HMGN1, had earlier signs of liver tumorigenesis than their Hmgn1(+/+) littermates. Detailed gene expression profiling revealed significant differences between DEN-injected and control saline-injected mice, but only minor differences between the injected Hmgn1(tm1/tm1) mice and their Hmgn1(+/+) littermates. Pathway analysis revealed that the most significant process affected by loss of HMGN1 involves the lipid/sterol metabolic pathway. Our study indicates that in mice, loss of HMGN1 leads to transcription changes that accelerate the progression of DEN-induced hepatocarcinogenesis, without affecting the type of tumors or the final total tumor burden of these mice. IMPLICATIONS Loss of HMGN1 leads to accelerated progression of DEN-induced hepatocarcinogenesis in mice.
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30
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Zhang S, Schones DE, Malicet C, Rochman M, Zhou M, Foisner R, Bustin M. High mobility group protein N5 (HMGN5) and lamina-associated polypeptide 2α (LAP2α) interact and reciprocally affect their genome-wide chromatin organization. J Biol Chem 2013; 288:18104-9. [PMID: 23673662 DOI: 10.1074/jbc.c113.469544] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The interactions of nuclear lamins with the chromatin fiber play an important role in regulating nuclear architecture and chromatin function; however, the full spectrum of these interactions is not known. We report that the N-terminal domain of the nucleosome-binding protein HMGN5 interacts with the C-terminal domain of the lamin-binding protein LAP2α and that these proteins reciprocally alter their interaction with chromatin. Chromatin immunoprecipitation analysis of cells lacking either HMGN5 or LAP2α reveals that loss of either protein affects the genome-wide distribution of the remaining partner. Our study identifies a new functional link between chromatin-binding and lamin-binding proteins.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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31
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Kugler JE, Horsch M, Huang D, Furusawa T, Rochman M, Garrett L, Becker L, Bohla A, Hölter SM, Prehn C, Rathkolb B, Racz I, Aguilar-Pimentel JA, Adler T, Adamski J, Beckers J, Busch DH, Eickelberg O, Klopstock T, Ollert M, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Garfinkel B, Orly J, Ovcharenko I, Bustin M. High mobility group N proteins modulate the fidelity of the cellular transcriptional profile in a tissue- and variant-specific manner. J Biol Chem 2013; 288:16690-16703. [PMID: 23620591 DOI: 10.1074/jbc.m113.463315] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nuclei of most vertebrate cells contain members of the high mobility group N (HMGN) protein family, which bind specifically to nucleosome core particles and affect chromatin structure and function, including transcription. Here, we study the biological role of this protein family by systematic analysis of phenotypes and tissue transcription profiles in mice lacking functional HMGN variants. Phenotypic analysis of Hmgn1(tm1/tm1), Hmgn3(tm1/tm1), and Hmgn5(tm1/tm1) mice and their wild type littermates with a battery of standardized tests uncovered variant-specific abnormalities. Gene expression analysis of four different tissues in each of the Hmgn(tm1/tm1) lines reveals very little overlap between genes affected by specific variants in different tissues. Pathway analysis reveals that loss of an HMGN variant subtly affects expression of numerous genes in specific biological processes. We conclude that within the biological framework of an entire organism, HMGNs modulate the fidelity of the cellular transcriptional profile in a tissue- and HMGN variant-specific manner.
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Affiliation(s)
- Jamie E Kugler
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Di Huang
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Lillian Garrett
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alexander Bohla
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Prehn
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ildikó Racz
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Juan Antonio Aguilar-Pimentel
- Center of Allergy and Environment, Technische Universität München, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Jerzy Adamski
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Dirk H Busch
- Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Oliver Eickelberg
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany
| | - Markus Ollert
- Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Tobias Stöger
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany; Max Planck Institute of Psychiatry, Munich, Germany; Developmental Genetics, Technische Universität München c/o Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ali Önder Yildirim
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Andreas Zimmer
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Benny Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ivan Ovcharenko
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.
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32
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Ciappio ED, Rochman M, Horsch M, Beckers J, Krausz KW, Bonzo JA, Gonzalez FJ, Bustin M. Targeted disruption of the nucleosomal binding protein HMGN5 results in altered glutathione metabolism and mild hepatic dysfunction. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1073.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Eric D Ciappio
- Laboratory of MetabolismNational Cancer InstituteBethesdaMD
| | - Mark Rochman
- Laboratory of MetabolismNational Cancer InstituteBethesdaMD
| | - Marion Horsch
- German Mouse ClinicGerman Research Center for Environmental HealthNeuherbergGermany
| | - Johannes Beckers
- German Mouse ClinicGerman Research Center for Environmental HealthNeuherbergGermany
| | | | | | | | - Michael Bustin
- Laboratory of MetabolismNational Cancer InstituteBethesdaMD
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33
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Mine KL, Shulzhenko N, Yambartsev A, Rochman M, Sanson GFO, Lando M, Varma S, Skinner J, Volfovsky N, Deng T, Brenna SMF, Carvalho CRN, Ribalta JCL, Bustin M, Matzinger P, Silva IDCG, Lyng H, Gerbase-DeLima M, Morgun A. Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer. Nat Commun 2013; 4:1806. [PMID: 23651994 PMCID: PMC4237593 DOI: 10.1038/ncomms2693] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 03/04/2013] [Indexed: 01/04/2023] Open
Abstract
Although human papillomavirus was identified as an aetiological factor in cervical cancer, the key human gene drivers of this disease remain unknown. Here we apply an unbiased approach integrating gene expression and chromosomal aberration data. In an independent group of patients, we reconstruct and validate a gene regulatory meta-network, and identify cell cycle and antiviral genes that constitute two major subnetworks upregulated in tumour samples. These genes are located within the same regions as chromosomal amplifications, most frequently on 3q. We propose a model in which selected chromosomal gains drive activation of antiviral genes contributing to episomal virus elimination, which synergizes with cell cycle dysregulation. These findings may help to explain the paradox of episomal human papillomavirus decline in women with invasive cancer who were previously unable to clear the virus.
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Affiliation(s)
- Karina L. Mine
- Instituto de Imunogenética - Associação Fundo de Incentivo à Pesquisa (IGEN-AFIP), São Paulo SP, Brazil
- Universidade Federal de São Paulo, SP, Brazil
| | - Natalia Shulzhenko
- Instituto de Imunogenética - Associação Fundo de Incentivo à Pesquisa (IGEN-AFIP), São Paulo SP, Brazil
- Laboratory of Cellular and Molecular Immunology, NIAID, NIH, Bethesda, MD, United States
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Anatoly Yambartsev
- Institute of Mathematics and Statistics, Department of Statistics, University of Sao Paulo, SP, Brazil
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States
| | - Gerdine F. O. Sanson
- Instituto de Imunogenética - Associação Fundo de Incentivo à Pesquisa (IGEN-AFIP), São Paulo SP, Brazil
| | - Malin Lando
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo, Norway
| | - Sudhir Varma
- Bioinformatics and Computational Biosciences Branch, NIAID, NIH, Bethesda, MD, United States
| | - Jeff Skinner
- Bioinformatics and Computational Biosciences Branch, NIAID, NIH, Bethesda, MD, United States
| | - Natalia Volfovsky
- Advanced Biomedical Computing Center, SAIC-Frederick, Inc., Frederick, MD, United States
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States
| | - Sylvia M. F. Brenna
- Medical School of Universidade Cidade de São Paulo (UNICID), Sao Paulo, Brazil
| | | | | | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States
| | - Polly Matzinger
- Laboratory of Cellular and Molecular Immunology, NIAID, NIH, Bethesda, MD, United States
| | | | - Heidi Lyng
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo, Norway
| | - Maria Gerbase-DeLima
- Instituto de Imunogenética - Associação Fundo de Incentivo à Pesquisa (IGEN-AFIP), São Paulo SP, Brazil
- Universidade Federal de São Paulo, SP, Brazil
| | - Andrey Morgun
- Instituto de Imunogenética - Associação Fundo de Incentivo à Pesquisa (IGEN-AFIP), São Paulo SP, Brazil
- Laboratory of Cellular and Molecular Immunology, NIAID, NIH, Bethesda, MD, United States
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
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34
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Gerlitz G, Reiner O, Bustin M. Microtubule dynamics alter the interphase nucleus. Cell Mol Life Sci 2012; 70:1255-68. [PMID: 23117601 DOI: 10.1007/s00018-012-1200-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/09/2012] [Accepted: 10/15/2012] [Indexed: 11/30/2022]
Abstract
Microtubules are known to drive chromosome movements and to induce nuclear envelope breakdown during mitosis and meiosis. Here we show that microtubules can enforce nuclear envelope folding and alter the levels of nuclear envelope-associated heterochromatin during interphase, when the nuclear envelope is intact. Microtubule reassembly, after chemically induced depolymerization led to folding of the nuclear envelope and to a transient accumulation of condensed chromatin at the site nearest the microtubule organizing center (MTOC). This microtubule-dependent chromatin accumulation next to the MTOC is dependent on the composition of the nuclear lamina and the activity of the dynein motor protein. We suggest that forces originating from simultaneous polymerization of microtubule fibers deform the nuclear membrane and the underlying lamina. Whereas dynein motor complexes localized to the nuclear envelope that slide along the microtubules transfer forces and/or signals into the nucleus to induce chromatin reorganization and accumulation at the nuclear membrane folds. Thus, our study identified a molecular mechanism by which mechanical forces generated in the cytoplasm reshape the nuclear envelope, alter the intranuclear organization of chromatin, and affect the architecture of the interphase nucleus.
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Affiliation(s)
- Gabi Gerlitz
- Protein Section, Laboratory of Metabolism, National Cancer Institute, US National Institutes of Health, Bethesda, MD 20892, USA.
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35
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Kurth PD, Bustin M, Moudrianakis EN. Concanavalin A binds to puffs in polytene chromosomes. Nature 2012; 279:448-50. [PMID: 16068191 DOI: 10.1038/279448a0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/1978] [Accepted: 04/04/1979] [Indexed: 11/09/2022]
Abstract
CHANGES in transcriptional activity at defined loci are often correlated with significant local structural changes in the genome(1), and in polytene chromosomes, such changes are thought to be associated with compositional or conformational changes in the protein complement at these particular bands(2,3). Thus, various studies on Balfoiani rings and specific 'puffs' in such chromosomes are useful for elucidating the role of defined chromosomal components in both chromosome structure and gene activity. Such studies require specific probes which will allow in situ localisation of a chromosomal component during the various stages of puffing. Antibodies specific to purified histone fractions(4-7), HMG proteins(8), RNA polymerase(9) and non-histone protein subfractions(10) have been used in studies on chromatin and chromosome structure. We reported previously that concanavalin A (Con A) specifically binds to three types of non-histone proteins present in chromatin purified from rat liver nuclei and suggested that derivatives of Con A might serve as specific probes to study the in situ organisation of these non-histone proteins(11). We have now reacted fluorescein-labelled Con A with polytene chromosomes isolated from different developmental stages of Chironomus thummi and visualised the location of the bound Con A by fluorescence microscopy. We observed that the fluorescent lectin, which has an affinity for glucose- and mannose-containing molecules, specifically bound to the transcriptionally active regions of chromosome IV. The extent of binding of Con A to the Balbiani rings present in regions b and c of chromosome IV is proportional to the size of the respective ring. Our results indicate that glucose- or mannose-containing molecules are present in these Balbiani rings and that the availability of these sugars to interact with Con A can be correlated with the developmental stage of a puff. We suggest that lectins can be useful cytological tools with which to study the in situ organisation of defined chromosomal components during various functional states of the genome.
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Masaoka A, Gassman NR, Kedar PS, Prasad R, Hou EW, Horton JK, Bustin M, Wilson SH. HMGN1 protein regulates poly(ADP-ribose) polymerase-1 (PARP-1) self-PARylation in mouse fibroblasts. J Biol Chem 2012; 287:27648-58. [PMID: 22736760 DOI: 10.1074/jbc.m112.370759] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In mammalian cells, the nucleosome-binding protein HMGN1 (high mobility group N1) affects the structure and function of chromatin and plays a role in repair of damaged DNA. HMGN1 affects the interaction of DNA repair factors with chromatin and their access to damaged DNA; however, not all of the repair factors affected have been identified. Here, we report that HMGN1 affects the self-poly(ADP-ribosyl)ation (i.e., PARylation) of poly(ADP-ribose) polymerase-1 (PARP-1), a multifunctional and abundant nuclear enzyme known to recognize DNA lesions and promote chromatin remodeling, DNA repair, and other nucleic acid transactions. The catalytic activity of PARP-1 is activated by DNA with a strand break, and this results in self-PARylation and PARylation of other chromatin proteins. Using cells obtained from Hmgn1(-/-) and Hmgn1(+/+) littermate mice, we find that in untreated cells, loss of HMGN1 protein reduces PARP-1 self-PARylation. A similar result was obtained after MMS treatment of these cells. In imaging experiments after low energy laser-induced DNA damage, less PARylation at lesion sites was observed in Hmgn1(-/-) than in Hmgn1(+/+) cells. The HMGN1 regulation of PARP-1 activity could be mediated by direct protein-protein interaction as HMGN1 and PARP-1 were found to interact in binding assays. Purified HMGN1 was able to stimulate self-PARylation of purified PARP-1, and in experiments with cell extracts, self-PARylation was greater in Hmgn1(+/+) than in Hmgn1(-/-) extract. The results suggest a regulatory role for HMGN1 in PARP-1 activation.
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Affiliation(s)
- Aya Masaoka
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
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37
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Yang D, Postnikov YV, Li Y, Tewary P, de la Rosa G, Wei F, Klinman D, Gioannini T, Weiss JP, Furusawa T, Bustin M, Oppenheim JJ. High-mobility group nucleosome-binding protein 1 acts as an alarmin and is critical for lipopolysaccharide-induced immune responses. ACTA ACUST UNITED AC 2011; 209:157-71. [PMID: 22184635 PMCID: PMC3260868 DOI: 10.1084/jem.20101354] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
HMGN1 is a novel alarmin that signals through TLR4 and is required for LPS-induced immune responses in vivo. Alarmins are endogenous mediators capable of promoting the recruitment and activation of antigen-presenting cells (APCs), including dendritic cells (DCs), that can potentially alert host defense against danger signals. However, the relevance of alarmins to the induction of adaptive immune responses remains to be demonstrated. In this study, we report the identification of HMGN1 (high-mobility group nucleosome-binding protein 1) as a novel alarmin and demonstrate that it contributes to the induction of antigen-specific immune responses. HMGN1 induced DC maturation via TLR4 (Toll-like receptor 4), recruitment of APCs at sites of injection, and activation of NF-κB and multiple mitogen-activated protein kinases in DCs. HMGN1 promoted antigen-specific immune response upon co-administration with antigens, and Hmgn1−/− mice developed greatly reduced antigen-specific antibody and T cell responses when immunized with antigens in the presence of lipopolysaccharide (LPS). The impaired ability of Hmgn1−/− mice to mount antigen-specific immune responses was accompanied by both deficient DC recruitment at sites of immunization and reduced production of inflammatory cytokines. Bone marrow chimera experiments revealed that HMGN1 derived from nonleukocytes was critical for the induction of antigen-specific antibody and T cell responses. Thus, extracellular HMGN1 acts as a novel alarmin critical for LPS-induced development of innate and adaptive immune responses.
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Affiliation(s)
- De Yang
- Basic Research Program, Scientific Application and International Corporation–Frederick, Inc, Frederick, Frederick, MD 21702, USA.
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38
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Abuhatzira L, Shamir A, Schones DE, Schäffer AA, Bustin M. The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice. J Biol Chem 2011; 286:42051-42062. [PMID: 22009741 PMCID: PMC3234940 DOI: 10.1074/jbc.m111.300541] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/05/2011] [Indexed: 11/06/2022] Open
Abstract
High mobility group N1 protein (HMGN1), a nucleosomal-binding protein that affects the structure and function of chromatin, is encoded by a gene located on chromosome 21 and is overexpressed in Down syndrome, one of the most prevalent genomic disorders. Misexpression of HMGN1 affects the cellular transcription profile; however, the biological function of this protein is still not fully understood. We report that HMGN1 modulates the expression of methyl CpG-binding protein 2 (MeCP2), a DNA-binding protein known to affect neurological functions including autism spectrum disorders, and whose alterations in HMGN1 levels affect the behavior of mice. Quantitative PCR and Western analyses of cell lines and brain tissues from mice that either overexpress or lack HMGN1 indicate that HMGN1 is a negative regulator of MeCP2 expression. Alterations in HMGN1 levels lead to changes in chromatin structure and histone modifications in the MeCP2 promoter. Behavior analyses by open field test, elevated plus maze, Reciprocal Social Interaction, and automated sociability test link changes in HMGN1 levels to abnormalities in activity and anxiety and to social deficits in mice. Targeted analysis of the Autism Genetic Resource Exchange genotype collection reveals a non-random distribution of genotypes within 500 kbp of HMGN1 in a region affecting its expression in families predisposed to autism spectrum disorders. Our results reveal that HMGN1 affects the behavior of mice and suggest that epigenetic changes resulting from altered HMGN1 levels could play a role in the etiology of neurodevelopmental disorders.
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Affiliation(s)
- Liron Abuhatzira
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, Bethesda, Maryland 20892
| | | | | | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, Bethesda, Maryland 20892.
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39
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Rochman M, Furusawa T, Bustin M. Elevated embryonic expression of chromatin architectural protein HMGN5 alters higher order chromatin organization and leads to postnatal cardiac malfunction. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.890.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mark Rochman
- Laboratory of MetabolismNational Cancer InstituteBethesdaMD
| | | | - Michael Bustin
- Laboratory of MetabolismNational Cancer InstituteBethesdaMD
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40
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Yang D, Postnikov Y, Li Y, Tewary P, de la Rosa G, Kliman D, Furusawa T, Bustin M, Wei F, Oppenheim J. High mobility group nucleosome-binding protein 1 acts as an alarmin critical for the induction of immune response (113.7). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.113.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Alarmins, defined as endogenous mediator(s) capable of promoting the recruitment and activation of antigen-presenting cells (APCs) including dendritic cells (DCs), can potentially promote immunity, however, their essential contribution to the induction immune responses remain to be demonstrated. Here we report the identification of HMGN1 as a novel alarmin that is critical to the induction of antigen-specific immune response. HMGN1 induced DC maturation and recruitment of APCs and activated NF-κB and multiple MAPKs, in a MyD88-dependent manner. HMGN1 promoted antigen-specific immune response upon co-administration with an antigen. Furthermore, knockout of HMGN1 in mice greatly reduced antigen-specific antibody and T cell responses upon intraperitoneal immunization with an antigen using LPS as an adjuvant. The impaired ability of HMGN1 KO mice to mount antigen-specific immune responses was accompanied by both deficient DC recruitment at sites of immunization and reduced production of inflammatory cytokines. Bone marrow chimera experiments revealed that HMGN1 derived from non-leukocytes played a more critical role in the induction of antigen-specific antibody and T cell responses. Thus, HMGN1 acts as a novel alarmin critical for the induction of adaptive immune response.
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Affiliation(s)
- De Yang
- 1SAIC Frederick, Frederick, MD
- 2NCI - Frederick, Frederick, MD
| | | | - Yana Li
- 2NCI - Frederick, Frederick, MD
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41
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Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M. Effects of HMGN variants on the cellular transcription profile. Nucleic Acids Res 2011; 39:4076-87. [PMID: 21278158 PMCID: PMC3105402 DOI: 10.1093/nar/gkq1343] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
High mobility group N (HMGN) is a family of intrinsically disordered nuclear proteins that bind to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here, we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. We find that both up- and downregulation of HMGN expression altered the cellular transcription profile. Most, but not all of the changes were variant specific, suggesting limited redundancy in transcriptional regulation. Analysis of point and swap HMGN mutants revealed that the transcriptional specificity is determined by a unique combination of a functional nucleosome-binding domain and C-terminal domain. Doubling the amount of HMGN had a significantly larger effect on the transcription profile than total deletion, suggesting that the intrinsically disordered structure of HMGN proteins plays an important role in their function. The results reveal an HMGN-variant-specific effect on the fidelity of the cellular transcription profile, indicating that functionally the various HMGN subtypes are not fully redundant.
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Affiliation(s)
- Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA
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42
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Gerlitz G, Bustin M. The role of chromatin structure in cell migration. Trends Cell Biol 2010; 21:6-11. [PMID: 20951589 DOI: 10.1016/j.tcb.2010.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/24/2010] [Accepted: 09/01/2010] [Indexed: 10/18/2022]
Abstract
Chromatin dynamics play a major role in regulating genetic processes. Now, accumulating data suggest that chromatin structure may also affect the mechanical properties of the nucleus and cell migration. Global chromatin organization appears to modulate the shape, the size and the stiffness of the nucleus. Directed-cell migration, which often requires nuclear reshaping to allow passage of cells through narrow openings, is dependent not only on changes in cytoskeletal elements but also on global chromatin condensation. Conceivably, during cell migration a physical link between the chromatin and the cytoskeleton facilitates coordinated structural changes in these two components. Thus, in addition to regulating genetic processes, we suggest that alterations in chromatin structure could facilitate cellular reorganizations necessary for efficient migration.
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Affiliation(s)
- Gabi Gerlitz
- Protein Section, Laboratory of Metabolism, National Cancer Institute, US National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Oh KS, Bustin M, Mazur SJ, Appella E, Kraemer KH. UV-induced histone H2AX phosphorylation and DNA damage related proteins accumulate and persist in nucleotide excision repair-deficient XP-B cells. DNA Repair (Amst) 2010; 10:5-15. [PMID: 20947453 DOI: 10.1016/j.dnarep.2010.09.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 09/03/2010] [Accepted: 09/13/2010] [Indexed: 10/19/2022]
Abstract
DNA double strand breaks (DSB) may be caused by ionizing radiation. In contrast, UV exposure forms dipyrimidine photoproducts and is not considered an inducer of DSB. We found that uniform or localized UV treatment induced phosphorylation of the DNA damage related (DDR) proteins H2AX, ATM and NBS1 and co-localization of γ-H2AX with the DDR proteins p-ATM, p-NBS1, Rad51 and FANCD2 that persisted for about 6h in normal human fibroblasts. This post-UV phosphorylation was observed in the absence of nucleotide excision repair (NER), since NER deficient XP-B cells (lacking functional XPB DNA repair helicase) and global genome repair-deficient rodent cells also showed phosphorylation and localization of these DDR proteins. Resolution of the DDR proteins was dependent on NER, since they persisted for 24h in the XP-B cells. In the normal and XP-B cells p53 and p21 was detected at 6h and 24h but Mdm2 was not induced in the XP-B cells. Post-UV induction of Wip1 phosphatase was detected in the normal cells but not in the XP-B cells. DNA DSB were detected with a neutral comet assay at 6h and 24h post-UV in the normal and XP-B cells. These results indicate that UV damage can activate the DDR pathway in the absence of NER. However, a later step in DNA damage processing involving induction of Wip1 and resolution of DDR proteins was not observed in the absence of NER.
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Affiliation(s)
- Kyu-Seon Oh
- DNA Repair Section, Dermatology Branch, CCR, National Cancer Institute, Bethesda, MD 20892, USA
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44
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Gerlitz G, Bustin M. Efficient cell migration requires global chromatin condensation. Development 2010. [DOI: 10.1242/dev.055145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Abstract
Cell migration is a fundamental process that is necessary for the development and survival of multicellular organisms. Here, we show that cell migration is contingent on global condensation of the chromatin fiber. Induction of directed cell migration by the scratch-wound assay leads to decreased DNaseI sensitivity, alterations in the chromatin binding of architectural proteins and elevated levels of H4K20me1, H3K27me3 and methylated DNA. All these global changes are indicative of increased chromatin condensation in response to induction of directed cell migration. Conversely, chromatin decondensation inhibited the rate of cell migration, in a transcription-independent manner. We suggest that global chromatin condensation facilitates nuclear movement and reshaping, which are important for cell migration. Our results support a role for the chromatin fiber that is distinct from its known functions in genetic processes.
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Affiliation(s)
- Gabi Gerlitz
- Protein Section, Laboratory of Metabolism, National Cancer Institute, US National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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46
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47
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Rochman M, Malicet C, Bustin M. HMGN5/NSBP1: a new member of the HMGN protein family that affects chromatin structure and function. Biochim Biophys Acta 2010; 1799:86-92. [PMID: 20123071 DOI: 10.1016/j.bbagrm.2009.09.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 09/15/2009] [Accepted: 09/15/2009] [Indexed: 12/22/2022]
Abstract
The dynamic nature of the chromatin fiber provides the structural and functional flexibility required for the accurate transcriptional responses to various stimuli. In living cells, structural proteins such as the linker histone H1 and the high mobility group (HMG) proteins continuously modulate the local and global architecture of the chromatin fiber and affect the binding of regulatory factors to their nucleosomal targets. HMGN proteins specifically bind to the nucleosome core particle through a highly conserved "nucleosomal binding domain" (NBD) and reduce chromatin compaction. HMGN5 (NSBP1), a new member of the HMGN protein family, is ubiquitously expressed in mouse and human tissues. Similar to other HMGNs, HMGN5 is a nuclear protein which binds to nucleosomes via NBD, unfolds chromatin, and affects transcription. This protein remains mainly uncharacterized and its biological function is unknown. In this review, we describe the structure of the HMGN5 gene and the known properties of the HMGN5 protein. We present recent findings related to the expression pattern of the protein during development, the mechanism of HMGN5 action on chromatin, and discuss the possible role of HMGN5 in pathological and physiological processes.
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Affiliation(s)
- Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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48
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Kurahashi T, Furusawa T, Ueda T, Bustin M. The nucleosome binding protein HMGN3 is expressed in pancreatic alpha-cells and affects plasma glucagon levels in mice. J Cell Biochem 2010; 109:49-57. [PMID: 19885867 DOI: 10.1002/jcb.22377] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glucose homeostasis requires the coordinated actions of various organs and is critically dependent on the proper functioning of the various cell types present in the pancreatic Langerhans islets. Here we report that chromatin architectural protein HMGN3 is highly expressed in all pancreatic endocrine islet cells, and that Hmgn3-/- mice which have a mild diabetic phenotype, have reduced glucagon levels in their blood. To elucidate the mechanism leading to altered glucagon secretion of Hmgn3-/- mice, we tested whether HMGN3 affect glucagon synthesis and secretion in alphaTC1-9 cells, a glucagon secreting cell line that is used to study pancreatic alpha-cell function. We find that in these cells deletion of either HMGN3 or other HMGN variants, does not significantly affect glucagon gene expression or glucagon secretion. Our studies demonstrate a link between HMGN3 and glucagon blood levels that is not directly dependent of the function of pancreatic alpha-cells.
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Affiliation(s)
- Toshihiro Kurahashi
- Protein Section, Laboratory of Metabolism, Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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49
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Subramanian M, Gonzalez RW, Patil H, Ueda T, Lim JH, Kraemer KH, Bustin M, Bergel M. The nucleosome-binding protein HMGN2 modulates global genome repair. FEBS J 2009; 276:6646-57. [PMID: 19843163 DOI: 10.1111/j.1742-4658.2009.07375.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The HMGN family comprises nuclear proteins that bind to nucleosomes and alter the structure of chromatin. Here, we report that DT40 chicken cells lacking either HMGN2 or HMGN1a, or lacking both HMGN1a and HMGN2, are hypersensitive to killing by UV irradiation. Loss of both HMGN1a and HMGN2 or only HMGN2 increases the extent of UV-induced G(2)-M checkpoint arrest and the rate of apoptosis. HMGN null mutant cells showed slower removal of UV-induced DNA lesions from native chromatin, but the nucleotide excision repair remained intact, as measured by host cell reactivation assays. These results identify HMGN2 as a component of the global genome repair subpathway of the nucleotide excision repair pathway, and may indicate that HMGN2 facilitates the ability of the DNA repair proteins to access and repair UV-induced DNA lesions in chromatin. Our finding that HMGNs play a role in global DNA repair expands the role of these proteins in the maintenance of genome integrity.
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50
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Rochman M, Postnikov Y, Correll S, Malicet C, Wincovitch S, Karpova TS, McNally JG, Wu X, Bubunenko NA, Grigoryev S, Bustin M. The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription. Mol Cell 2009; 35:642-56. [PMID: 19748358 DOI: 10.1016/j.molcel.2009.07.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 05/01/2009] [Accepted: 07/08/2009] [Indexed: 10/20/2022]
Abstract
Structural changes in specific chromatin domains are essential to the orderly progression of numerous nuclear processes, including transcription. We report that the nuclear protein NSBP1 (HMGN5), a recently discovered member of the HMGN nucleosome-binding protein family, is specifically targeted by its C-terminal domain to nucleosomes in euchromatin. We find that the interaction of NSBP1 with nucleosomes alters the compaction of cellular chromatin and that in living cells, NSBP1 interacts with linker histones. We demonstrate that the negatively charged C-terminal domain of NSBP1 interacts with the positively charged C-terminal domain of H5 and that NSBP1 counteracts the linker histone-mediated compaction of a nucleosomal array. Dysregulation of the cellular levels of NSBP1 alters the transcription level of numerous genes. We suggest that mouse NSBP1 is an architectural protein that binds preferentially to euchromatin and modulates the fidelity of the cellular transcription profile by counteracting the chromatin-condensing activity of linker histones.
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Affiliation(s)
- Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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