1
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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] [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] [Abstract] [Key Words] [MESH Headings] [Grants] [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
- 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
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bing He
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Carol Xie
- Nucleic Acid Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kimia Dadkhah
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD, 20892, USA
| | - Michael C Kelly
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD, 20892, USA
| | - Oksana Gavrilova
- Mouse Metabolism Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Frank J Gonzalez
- Nucleic Acid 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.
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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] [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] [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] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
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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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Geng F, Liu Z, Chen X, Chen H, Liu Y, Yang J, Zheng M, Yang L, Teng Y. High mobility group nucleosomal binding 2 reduces integrin α5/β1-mediated adhesion of Klebsiella pneumoniae on human pulmonary epithelial cells via nuclear factor I. Microbiol Immunol 2020; 64:825-834. [PMID: 33034909 DOI: 10.1111/1348-0421.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/12/2020] [Accepted: 10/07/2020] [Indexed: 11/28/2022]
Abstract
It has been reported that high mobility group nucleosomal binding domain 2 (HMGN2) is a nucleus-related protein that regulates gene transcription and plays a critical role in bacterial clearance. An elevated level of HMGN2 reduced integrin α5/β1 expression of human pulmonary epithelial A549 cells was demonstrated during Klebsiella pneumoniae infection, thus weakening bacterial adhesion and invasion. However, the mechanism by which HMGN2 regulates integrin expression remains unclear. This study found that a transcription factor-nuclear factor I (NFI), which serves as the potential target of HMGN2 regulated integrin expression. The results showed that HMGN2 was able to promote NFIA and NFIB expression by increasing H3K27 acetylation of NFIA/B promoter regions. The integrin α5/β1 expression was significantly enhanced by knockdown of NFIA/B via a siRNA approach. Meanwhile, NFIA/B silence could also compromise the inhibition effect of HMGN2 on the integrin α5/β1 expression. Mechanistically, it was demonstrated that HMGN2 facilitated the recruitment of NFI on the promoter regions of integrin α5/β1 according to the chromatin immunoprecipitation assay. In addition, it was further demonstrated that the knockdown of NFIA/B induced more adhesion of Klebsiella pneumoniae on pulmonary epithelial A549 cells, which could be reversed by the application of an integrin inhibitor RGD. The results revealed a regulatory role of HMGN2 on the transcription level of integrin α5/β1, indicating a potential treatment strategy against Klebsiella pneumoniae-induced infectious lung diseases.
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Affiliation(s)
- Fan Geng
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Zhihao Liu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Xingmin Chen
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Huan Chen
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Yanzhuo Liu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Jing Yang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Min Zheng
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Lu Yang
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Yan Teng
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
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7
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Human HMGN1 and HMGN2 are not required for transcription-coupled DNA repair. Sci Rep 2020; 10:4332. [PMID: 32152397 PMCID: PMC7062826 DOI: 10.1038/s41598-020-61243-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription-coupled repair (TCR) removes DNA lesions from the transcribed strand of active genes. Stalling of RNA polymerase II (RNAPII) at DNA lesions initiates TCR through the recruitment of the CSB and CSA proteins. The full repertoire of proteins required for human TCR – particularly in a chromatin context - remains to be determined. Studies in mice have revealed that the nucleosome-binding protein HMGN1 is required to enhance the repair of UV-induced lesions in transcribed genes. However, whether HMGN1 is required for human TCR remains unaddressed. Here, we show that knockout or knockdown of HMGN1, either alone or in combination with HMGN2, does not render human cells sensitive to UV light or Illudin S-induced transcription-blocking DNA lesions. Moreover, transcription restart after UV irradiation was not impaired in HMGN-deficient cells. In contrast, TCR-deficient cells were highly sensitive to DNA damage and failed to restart transcription. Furthermore, GFP-tagged HMGN1 was not recruited to sites of UV-induced DNA damage under conditions where GFP-CSB readily accumulated. In line with this, HMGN1 did not associate with the TCR complex, nor did TCR proteins require HMGN1 to associate with DNA damage-stalled RNAPII. Together, our findings suggest that HMGN1 and HMGN2 are not required for human TCR.
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8
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Biological Functions of HMGN Chromosomal Proteins. Int J Mol Sci 2020; 21:ijms21020449. [PMID: 31936777 PMCID: PMC7013550 DOI: 10.3390/ijms21020449] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Chromatin plays a key role in regulating gene expression programs necessary for the orderly progress of development and for preventing changes in cell identity that can lead to disease. The high mobility group N (HMGN) is a family of nucleosome binding proteins that preferentially binds to chromatin regulatory sites including enhancers and promoters. HMGN proteins are ubiquitously expressed in all vertebrate cells potentially affecting chromatin function and epigenetic regulation in multiple cell types. Here, we review studies aimed at elucidating the biological function of HMGN proteins, focusing on their possible role in vertebrate development and the etiology of disease. The data indicate that changes in HMGN levels lead to cell type-specific phenotypes, suggesting that HMGN optimize epigenetic processes necessary for maintaining cell identity and for proper execution of specific cellular functions. This manuscript contains tables that can be used as a comprehensive resource for all the English written manuscripts describing research aimed at elucidating the biological function of the HMGN protein family.
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9
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Garza-Manero S, Sindi AAA, Mohan G, Rehbini O, Jeantet VHM, Bailo M, Latif FA, West MP, Gurden R, Finlayson L, Svambaryte S, West AG, West KL. Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model. Epigenetics Chromatin 2019; 12:73. [PMID: 31831052 PMCID: PMC6907237 DOI: 10.1186/s13072-019-0320-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
Background Members of the HMGN protein family modulate chromatin structure and influence epigenetic modifications. HMGN1 and HMGN2 are highly expressed during early development and in the neural stem/progenitor cells of the developing and adult brain. Here, we investigate whether HMGN proteins contribute to the chromatin plasticity and epigenetic regulation that is essential for maintaining pluripotency in stem cells. Results We show that loss of Hmgn1 or Hmgn2 in pluripotent embryonal carcinoma cells leads to increased levels of spontaneous neuronal differentiation. This is accompanied by the loss of pluripotency markers Nanog and Ssea1, and increased expression of the pro-neural transcription factors Neurog1 and Ascl1. Neural stem cells derived from these Hmgn-knockout lines also show increased spontaneous neuronal differentiation and Neurog1 expression. The loss of HMGN2 leads to a global reduction in H3K9 acetylation, and disrupts the profile of H3K4me3, H3K9ac, H3K27ac and H3K122ac at the Nanog and Oct4 loci. At endodermal/mesodermal genes, Hmgn2-knockout cells show a switch from a bivalent to a repressive chromatin configuration. However, at neuronal lineage genes whose expression is increased, no epigenetic changes are observed and their bivalent states are retained following the loss of HMGN2. Conclusions We conclude that HMGN1 and HMGN2 maintain the identity of pluripotent embryonal carcinoma cells by optimising the pluripotency transcription factor network and protecting the cells from precocious differentiation. Our evidence suggests that HMGN2 regulates active and bivalent genes by promoting an epigenetic landscape of active histone modifications at promoters and enhancers.
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Affiliation(s)
- Sylvia Garza-Manero
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Abdulmajeed Abdulghani A Sindi
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.,Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Albaha University, Albaha-Alaqiq, Saudi Arabia
| | - Gokula Mohan
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.,Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Ohoud Rehbini
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Valentine H M Jeantet
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Mariarca Bailo
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Faeezah Abdul Latif
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Maureen P West
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Ross Gurden
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Lauren Finlayson
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Silvija Svambaryte
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Adam G West
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Katherine L West
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK. .,School of Life Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.
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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] [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] [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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Gao XL, Tian WJ, Liu B, Wu J, Xie W, Shen Q. High-mobility group nucleosomal binding domain 2 protects against microcephaly by maintaining global chromatin accessibility during corticogenesis. J Biol Chem 2019; 295:468-480. [PMID: 31699896 DOI: 10.1074/jbc.ra119.010616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/30/2019] [Indexed: 11/06/2022] Open
Abstract
The surface area of the human cerebral cortex undergoes dramatic expansion during late fetal development, leading to cortical folding, an evolutionary feature not present in rodents. Microcephaly is a neurodevelopmental disorder defined by an abnormally small brain, and many gene mutations have been found to be associated with primary microcephaly. However, mouse models generated by ablating primary microcephaly-associated genes often fail to recapitulate the severe loss of cortical surface area observed in individuals with this pathology. Here, we show that a mouse model with deficient expression of high-mobility group nucleosomal binding domain 2 (HMGN2) manifests microcephaly with reduced cortical surface area and almost normal radial corticogenesis, with a pattern of incomplete penetrance. We revealed that altered cleavage plane and mitotic delay of ventricular radial glia may explain the rising ratio of intermediate progenitor cells to radial glia and the displacement of neural progenitor cells in microcephalic mutant mice. These led to decreased self-renewal of the radial glia and reduction in lateral expansion. Furthermore, we found that HMGN2 protected corticogenesis by maintaining global chromatin accessibility mainly at promoter regions, thereby ensuring the correct regulation of the transcriptome. Our findings underscore the importance of the regulation of chromatin structure in cortical development and highlight a mouse model with critical insights into the etiology of microcephaly.
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Affiliation(s)
- Xue-Ling Gao
- School of Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Ministry of Education, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Wen-Jia Tian
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Ministry of Education, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bofeng Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyi Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qin Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Ministry of Education, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Tongji University Brain and Spinal Cord Clinical Research Center, Shanghai 200092, China.
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13
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Chen Y, Chen A. Unveiling the gene regulatory landscape in diseases through the identification of DNase I-hypersensitive sites. Biomed Rep 2019; 11:87-97. [PMID: 31423302 PMCID: PMC6684942 DOI: 10.3892/br.2019.1233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/03/2019] [Indexed: 01/18/2023] Open
Abstract
DNase I-hypersensitive sites (DHSs) serve key roles in the regulation of gene transcription as markers of cis-regulatory elements (CREs). Recent advances in next-generation sequencing have enabled the genome-wide location and annotation of DHSs in a variety of cells. Numerous studies have confirmed that DHSs are involved in several processes in cell fate decision and development. DHSs have also been indicated in cancer and inherited diseases as driver distal regulatory elements. Here, the definition of DHSs is reviewed, in addition to high-throughput methods of DHS identification. Furthermore, the function of DHSs in gene expression is probed. The roles of DHSs in disease occurrence are also reviewed and discussed. Concomitant advances in the identification of essential roles of DHSs will assist in disclosing the underlying molecular mechanisms, supplementing gene transcription and enlarging the molecular basis of DHS-related bioprocesses, phenotypes, distinct traits and diseases.
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Affiliation(s)
- Ying Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Ailing Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
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14
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Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019; 19:e1800438. [PMID: 30901150 DOI: 10.1002/pmic.201800438] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/24/2019] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
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15
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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] [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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16
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Yang D, Han Z, Alam MM, Oppenheim JJ. High-mobility group nucleosome binding domain 1 (HMGN1) functions as a Th1-polarizing alarmin. Semin Immunol 2018; 38:49-53. [PMID: 29503123 DOI: 10.1016/j.smim.2018.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/26/2018] [Indexed: 12/16/2022]
Abstract
High-mobility group (HMG) nucleosome binding domain 1 (HMGN1), which previously was thought to function only as a nucleosome-binding protein that regulates chromatin structure, histone modifications, and gene expression, was recently discovered to be an alarmin that contributes extracellularly to the generation of innate and adaptive immune responses. HMGN1 promotes DC recruitment through interacting with a Gαi protein-coupled receptor (GiPCR) and activates DCs predominantly through triggering TLR4. HMGN1 preferentially promotes Th1-type immunity, which makes it relevant for the fields of vaccinology, autoimmunity, and oncoimmunology. Here, we discuss the alarmin properties of HMGN1 and update recent advances on its roles in immunity and potential applications for immunotherapy of tumors.
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Affiliation(s)
- De Yang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA.
| | - Zhen Han
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA
| | - Md Masud Alam
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA
| | - Joost J Oppenheim
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA.
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17
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Chen A, Chen D, Chen Y. Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals. Gene 2018; 667:83-94. [DOI: 10.1016/j.gene.2018.05.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/04/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022]
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18
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Gao Y, Du X, Zeng J, Wu R, Chen Y, Li F, Li W, Zhou H, Yang Y, Pei Z. Prediction and identification of transcriptional regulatory elements at the lung cancer-specific DKK1 locus. Oncol Lett 2018; 16:137-144. [PMID: 29928394 PMCID: PMC6006444 DOI: 10.3892/ol.2018.8638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/23/2018] [Indexed: 12/29/2022] Open
Abstract
The glycoprotein dickkopf 1 (DKK1) is highly expressed in lung cancer cell lines and tissues. Our previous study demonstrated that DKK1 promoter activity is low in lung cancer cell lines. This may be because it lacks the necessary transcriptional regulatory elements (TREs) required for higher activity levels. However, it is difficult to computationally predict functionally significant TREs, as TREs from different locations can affect large segments of distant DNA. The Encyclopedia of DNA Elements project features multiple integrated technologies and approaches for the discovery and definition of functional elements, including enhancer elements and enhancer-blocking insulators. In the present study, DNase I hypersensitive sites and histone modifications of DKK1 were investigated in the A549 lung cancer cell line using the UCSC Genome Browser. A set of cis-acting enhancer elements were identified by a dual-luciferase reporter gene assay system to increase activity of the DKK1 promoter with lung cancer specificity. To the best of our knowledge, these data provide the first insight into the role of the DKK1 locus in lung cancer, and confirm the contribution of intronic cis-acting elements to the regulation of DKK1 expression, providing a new insight into gene regulation in lung cancer, which could inform the development of targeted therapy.
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Affiliation(s)
- Yan Gao
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Xian Du
- Department of General Surgery II, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Jing Zeng
- Department of Infection Control, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Ruimin Wu
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yijia Chen
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Fuyan Li
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Wei Li
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Hong Zhou
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yi Yang
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zhijun Pei
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
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19
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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] [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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20
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Fuchs H, Aguilar-Pimentel JA, Amarie OV, Becker L, Calzada-Wack J, Cho YL, Garrett L, Hölter SM, Irmler M, Kistler M, Kraiger M, Mayer-Kuckuk P, Moreth K, Rathkolb B, Rozman J, da Silva Buttkus P, Treise I, Zimprich A, Gampe K, Hutterer C, Stöger C, Leuchtenberger S, Maier H, Miller M, Scheideler A, Wu M, Beckers J, Bekeredjian R, Brielmeier M, Busch DH, Klingenspor M, Klopstock T, Ollert M, Schmidt-Weber C, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Gailus-Durner V, Hrabě de Angelis M. Understanding gene functions and disease mechanisms: Phenotyping pipelines in the German Mouse Clinic. Behav Brain Res 2017; 352:187-196. [PMID: 28966146 DOI: 10.1016/j.bbr.2017.09.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
Abstract
Since decades, model organisms have provided an important approach for understanding the mechanistic basis of human diseases. The German Mouse Clinic (GMC) was the first phenotyping facility that established a collaboration-based platform for phenotype characterization of mouse lines. In order to address individual projects by a tailor-made phenotyping strategy, the GMC advanced in developing a series of pipelines with tests for the analysis of specific disease areas. For a general broad analysis, there is a screening pipeline that covers the key parameters for the most relevant disease areas. For hypothesis-driven phenotypic analyses, there are thirteen additional pipelines with focus on neurological and behavioral disorders, metabolic dysfunction, respiratory system malfunctions, immune-system disorders and imaging techniques. In this article, we give an overview of the pipelines and describe the scientific rationale behind the different test combinations.
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Affiliation(s)
- Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Oana V Amarie
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Julia Calzada-Wack
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Yi-Li Cho
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Lillian Garrett
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Irmler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Kistler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Markus Kraiger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Kristin Moreth
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Patricia da Silva Buttkus
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Irina Treise
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Annemarie Zimprich
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Kristine Gampe
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Christine Hutterer
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Claudia Stöger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Miller
- Research Unit Comparative Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Angelika Scheideler
- Research Unit Comparative Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Moya Wu
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Raffi Bekeredjian
- Department of Cardiology, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Markus Brielmeier
- Research Unit Comparative Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstr. 30, 81675 Munich, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, Technical University Munich, EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Gregor-Mendel-Str. 2, 85350 Freising-Weihenstephan, Germany; ZIEL - Institute for Food and Health, Technical University Munich, Gregor-Mendel-Str. 2, 85350 Freising-Weihenstephan, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Ziemssenstr. 1a, 80336 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 80336 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 Munich, Germany; German Center for Vertigo and Balance Disorders, 81377 Munich, Germany
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, 29, Rue Henri Koch, 4354 Esch-sur-Alzette, Luxembourg; Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, 5000 Odense C, Denmark
| | - Carsten Schmidt-Weber
- Center of Allergy & Environment (ZAUM), Technische Universität München, and Helmholtz Zentrum München, Ingolstädter-Landstr., 85764 Neuherberg, Germany
| | - Tobias Stöger
- Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, D-85764 Neuherberg, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE), 80336 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 Munich, Germany; Chair of Developmental Genetics, Technische Universität München Freising-Weihenstephan, c/o Helmholtz Zentrum München Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany
| | - Ali Önder Yildirim
- Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 1, D-85764 Neuherberg, Germany
| | - Andreas Zimmer
- Institute of Molecular Psychiatry, Medical Faculty, University of Bonn, Sigmund Freud Str. 25, 53127 Bonn, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter-Landstr. 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-Landstr. 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstädter-Landstr. 1, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany.
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21
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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] [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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22
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Liu K, Wang X, Sha K, Zhang F, Xiong F, Wang X, Chen J, Li J, Churilov LP, Chen S, Wang Y, Huang N. Nuclear protein HMGN2 attenuates pyocyanin-induced oxidative stress via Nrf2 signaling and inhibits Pseudomonas aeruginosa internalization in A549 cells. Free Radic Biol Med 2017; 108:404-417. [PMID: 28408162 DOI: 10.1016/j.freeradbiomed.2017.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/17/2017] [Accepted: 04/07/2017] [Indexed: 12/21/2022]
Abstract
Pyocyanin (PCN, 1-hydroxy-5-methyl-phenazine) is one of the most essential virulence factors of Pseudomonas aeruginosa (PA) to cause various cytotoxic effects in long-term lung infectious diseases, however the early effect of this bacterial toxin during PA infection and subsequent autonomous immune response in host cells have not been fully understood yet. Our results display that early onset of PCN stimulates Pseudomonas aeruginosa PAO1 adhesion and invasion in A549 cells via ROS production. Non-histone nuclear protein HMGN2 is found to be involved in the regulation of PCN-induced oxidative stress by promoting intracellular ROS clearance. Mechanistically, HMGN2 facilitates nuclear translocation of transcription factor Nrf2 upon PCN stimulation and in turn elevates antioxidant gene expression. We also found that actin cytoskeleton dynamics is targeted by ROS, which is to be exploited by PAO1 for host cell internalization. HMGN2 regulates actin skeleton rearrangement in both PCN-dependent and independent manners and specifically attenuates PCN-mediated PAO1 infection via ROS elimination. These results uncover a novel link between nuclear protein HMGN2 and Nrf2-mediated cellular redox circumstance and suggest roles of HMGN2 in autonomous immune response to PA infection.
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Affiliation(s)
- Keyun Liu
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China; Department of Physiology, School of Medicine, Hubei University for Nationalities, Enshi 445000, China
| | - Xinyuan Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Kaihui Sha
- School of Nursing, Binzhou Medical University, Binzhou 256600, China
| | - Fumei Zhang
- Experimental Center, Northwest University for Nationalities, Lanzhou 730030, China
| | - Feng Xiong
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaoying Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Junli Chen
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jingyu Li
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Leonid P Churilov
- Department of Pathology, Faculty of Medicine, Saint Petersburg State University, Saint Petersburg 199034, Russia; Saint Petersburg State Research Institute of Phthisiopulmonology, Saint Petersburg 191036, Russia
| | - Shanze Chen
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yi Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Ning Huang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China.
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23
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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: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [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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24
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Schauwecker SM, Kim JJ, Licht JD, Clevenger CV. Histone H1 and Chromosomal Protein HMGN2 Regulate Prolactin-induced STAT5 Transcription Factor Recruitment and Function in Breast Cancer Cells. J Biol Chem 2016; 292:2237-2254. [PMID: 28035005 DOI: 10.1074/jbc.m116.764233] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/28/2016] [Indexed: 01/10/2023] Open
Abstract
The hormone prolactin (PRL) contributes to breast cancer pathogenesis through various signaling pathways, one of the most notable being the JAK2/signal transducer and activator of transcription 5 (STAT5) pathway. PRL-induced activation of the transcription factor STAT5 results in the up-regulation of numerous genes implicated in breast cancer pathogenesis. However, the molecular mechanisms that enable STAT5 to access the promoters of these genes are not well understood. Here, we show that PRL signaling induces chromatin decompaction at promoter DNA, corresponding with STAT5 binding. The chromatin-modifying protein high mobility group nucleosomal binding domain 2 (HMGN2) specifically promotes STAT5 accessibility at promoter DNA by facilitating the dissociation of the linker histone H1 in response to PRL. Knockdown of H1 rescues the decrease in PRL-induced transcription following HMGN2 knockdown, and it does so by allowing increased STAT5 recruitment. Moreover, H1 and STAT5 are shown to function antagonistically in regulating PRL-induced transcription as well as breast cancer cell biology. While reduced STAT5 activation results in decreased PRL-induced transcription and cell proliferation, knockdown of H1 rescues both of these effects. Taken together, we elucidate a novel mechanism whereby the linker histone H1 prevents STAT5 binding at promoter DNA, and the PRL-induced dissociation of H1 mediated by HMGN2 is necessary to allow full STAT5 recruitment and promote the biological effects of PRL signaling.
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Affiliation(s)
| | - J Julie Kim
- the Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Jonathan D Licht
- the Division of Hematology and Oncology, Department of Medicine, University of Florida Health Cancer Center, Gainesville, Florida 32610, and
| | - Charles V Clevenger
- the Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298
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25
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Jeffers TE, Lieb JD. Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans. Genome Res 2016; 27:75-86. [PMID: 27979995 PMCID: PMC5204346 DOI: 10.1101/gr.208173.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone–DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development in Caenorhabditis elegans embryos. We performed a time-course of micrococcal nuclease (MNase) digestion and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments that were recovered preferentially in early MNase-digestion time points. Nucleosome fragility was strongly and positively correlated with the AT content of the underlying DNA sequence. There was no correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Genes with fragile nucleosomes in their promoters tended to be lowly expressed and expressed in a context-specific way, operating in neuronal response, the immune system, and stress response. In addition to DNA-encoded nucleosome fragility, we also found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, for example, at transcription factor binding sites where nucleosomes compete with DNA-binding factors. Our data suggest that in C. elegans promoters, nucleosome fragility is in large part DNA-encoded and that it poises genes for future context-specific activation in response to environmental stress and developmental cues.
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Affiliation(s)
- Tess E Jeffers
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason D Lieb
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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26
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Teng Y, Miao J, Shen X, Yang X, Wang X, Ren L, Wang X, Chen J, Li J, Chen S, Wang Y, Huang N. The modulation of MiR-155 and MiR-23a manipulates Klebsiella pneumoniae Adhesion on Human pulmonary Epithelial cells via Integrin α5β1 Signaling. Sci Rep 2016; 6:31918. [PMID: 27534887 PMCID: PMC4989230 DOI: 10.1038/srep31918] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/29/2016] [Indexed: 12/14/2022] Open
Abstract
Micro-RNAs (miRNAs) critically regulate several host defense mechanisms, but their roles in the bacteria-epithelium interplay remain unclear. Our results displayed that the expression of miR-155 and miR-23a were down-regulated in K. pneumoniae-infected pulmonary epithelial cells. The elevated bacterial adhesion on A549 cells followed the enhancement of the cellular levels of these two miRNAs. Meanwhile, a mechanistic study demonstrated that miR-155 promoted integrin α5β1 function and resulted in the increased actin polymerization. Moreover, a non-histone nuclear protein, high mobility group nucleosomal-binding domain 2 (HMGN2) served as the potential target of miR-155 and miR-23a to regulate the integrin α5β1 expression and K. pneumoniae adhesion. Furthermore, the expression of a known integrin transcription suppressor-Nuclear Factor-I (NFI) was also repressed by miR-155, which paralleled with its chromatin location in the promoter regions of integrin α5 and β1. These results uncover novel links between miRNAs and integrin function to regulate bacterial adhesion, indicating a potential mechanism of host cell autonomous immune response to K. pneumoniae infection.
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Affiliation(s)
- Yan Teng
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Junming Miao
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaofei Shen
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaolong Yang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xinyuan Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Laibin Ren
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaoying Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Junli Chen
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jingyu Li
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shanze Chen
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yi Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Ning Huang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
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27
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Wang X, Ma Z, Kong X, Lv Z. Effects of RNAs on chromatin accessibility and gene expression suggest RNA-mediated activation. Int J Biochem Cell Biol 2016; 79:24-32. [PMID: 27497987 DOI: 10.1016/j.biocel.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/20/2023]
Abstract
The study of the interaction between RNA and DNA sequences in activating genes has important significance for understanding the mechanisms of RNA-mediated activation. Here, we used in vitro chromatin reconstitution approach to observe whether RNAs increase DNase I digestion, plasmid transfection to observe whether RNAs promote gene expression, and bioinformatics analysis to predict the binding ability of RNAs to centromere DNA (constitutive heterochromatin). Synthetic RNAs (23nt) that were complementary to mouse albumin gene and total liver RNA increased DNase I digestion sensitivity of mouse albumin gene, suggesting that RNAs can increase chromatin accessibility. Transcribed sense-antisense tandem Alu elements activated an enhanced green fluorescent protein reporter gene after stable transfection. Bioinformatics analysis showed that the binding strength of RNA population to centromere DNAs is significantly lower than that of their flanking sequences, which suggests that the centromere is not easily affected by RNAs produced from other transcribed regions and may be the reason why centromeres consist of constitutive heterochromatin. The results in this paper illustrate that RNAs complementary to DNA sequences play roles in activating genes. Since RNA is mainly produced from the cell's own DNA, the work presented in this paper suggests that RNAs transcribed from DNA create feedback that activates DNA transcription.
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Affiliation(s)
- Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
| | - Zhihong Ma
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, The Second Hospital of Tangshan, 21 North Jianshe Road, Tangshan, Hebei Province, China.
| | - Xianglong Kong
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, Hebei Chest Hospital, 372 Shengli North Street, Shijiazhuang, Hebei Province, China.
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
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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] [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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29
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Abstract
The DNase I hypersensitive sites (DHSs) of chromatin constitute one of the best landmarks of eukaryotic genes that are poised and/or activated for transcription. For over 35 years, the high-mobility group nucleosome-binding chromosomal proteins HMGN1 and HMGN2 have been shown to play a role in the establishment of these chromatin-accessible domains at transcriptional regulatory elements, namely promoters and enhancers. The critical presence of HMGNs at enhancers, as highlighted by a recent publication, suggests a role for them in the structural and functional fine-tuning of the DHSs in vertebrates. As we review here, while preferentially out-competing histone H1 binding and invading neighbor nucleosomes, HMGNs may also modulate histone H3 at serine 10 (H3S10ph), which plays an important role in enhancer function and transcriptional initiation.
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Affiliation(s)
- Alexia Martínez de Paz
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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30
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Functional interplay between histone H1 and HMG proteins in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:462-7. [PMID: 26455954 DOI: 10.1016/j.bbagrm.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 11/22/2022]
Abstract
The dynamic interaction of nucleosome binding proteins with their chromatin targets is an important element in regulating the structure and function of chromatin. Histone H1 variants and High Mobility Group (HMG) proteins are ubiquitously expressed in all vertebrate cells, bind dynamically to chromatin, and are known to affect chromatin condensation and the ability of regulatory factors to access their genomic binding sites. Here, we review the studies that focus on the interactions between H1 and HMGs and highlight the functional consequences of the interplay between these architectural chromatin binding proteins. H1 and HMG proteins are mobile molecules that bind to nucleosomes as members of a dynamic protein network. All HMGs compete with H1 for chromatin binding sites, in a dose dependent fashion, but each HMG family has specific effects on the interaction of H1 with chromatin. The interplay between H1 and HMGs affects chromatin organization and plays a role in epigenetic regulation.
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