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Jamge B, Lorković ZJ, Axelsson E, Osakabe A, Shukla V, Yelagandula R, Akimcheva S, Kuehn AL, Berger F. Histone variants shape chromatin states in Arabidopsis. eLife 2023; 12:RP87714. [PMID: 37467143 PMCID: PMC10393023 DOI: 10.7554/elife.87714] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Akihisa Osakabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-kuTokyoJapan
- PRESTO, Japan Science and Technology Agency, HonchoKawaguchiJapan
| | - Vikas Shukla
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3ViennaAustria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
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2
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Nishimura M, Arimura Y, Nozawa K, Kurumizaka H. Linker DNA and histone contributions in nucleosome binding by p53. J Biochem 2021; 168:669-675. [PMID: 32702132 PMCID: PMC7763433 DOI: 10.1093/jb/mvaa081] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
The tumour suppressor protein p53 regulates various genes involved in cell-cycle arrest, apoptosis and DNA repair in response to cellular stress, and apparently functions as a pioneer transcription factor. The pioneer transcription factors can bind nucleosomal DNA, where many transcription factors are largely restricted. However, the mechanisms by which p53 recognizes the nucleosomal DNA are poorly understood. In the present study, we found that p53 requires linker DNAs for the efficient formation of p53-nucleosome complexes. p53 forms an additional specific complex with the nucleosome, when the p53 binding sequence is located around the entry/exit region of the nucleosomal DNA. We also showed that p53 directly binds to the histone H3-H4 complex via its N-terminal 1–93 amino acid region. These results shed light on the mechanism of nucleosome recognition by p53.
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Affiliation(s)
- Masahiro Nishimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences
| | - Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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3
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Osakabe A, Jamge B, Axelsson E, Montgomery SA, Akimcheva S, Kuehn AL, Pisupati R, Lorković ZJ, Yelagandula R, Kakutani T, Berger F. The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Nat Cell Biol 2021; 23:391-400. [PMID: 33833428 DOI: 10.1038/s41556-021-00658-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
Mobile transposable elements (TEs) not only participate in genome evolution but also threaten genome integrity. In healthy cells, TEs that encode all of the components that are necessary for their mobility are specifically silenced, yet the precise mechanism remains unknown. Here, we characterize the mechanism used by a conserved class of chromatin remodelers that prevent TE mobility. In the Arabidopsis chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), we identify two conserved binding domains for the histone variant H2A.W, which marks plant heterochromatin. DDM1 is necessary and sufficient for the deposition of H2A.W onto potentially mobile TEs, yet does not act on TE fragments or host protein-coding genes. DDM1-mediated H2A.W deposition changes the properties of chromatin, resulting in the silencing of TEs and, therefore, prevents their mobility. This distinct mechanism provides insights into the interplay between TEs and their host in the contexts of evolution and disease, and potentiates innovative strategies for targeted gene silencing.
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Affiliation(s)
- Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Bhagyshree Jamge
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Rahul Pisupati
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ramesh Yelagandula
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Tetsuji Kakutani
- National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life science, The Graduate University of Advanced Studies (SOKENDAI), Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
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4
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Reed CR, McCoy CC, Nag U, Nixon AB, Otto J, Lawson JH, Lodge AJ, Turek JW, Tracy ET. Proteomic Analysis of Infants Undergoing Cardiopulmonary Bypass Using Contemporary Ontological Tools. J Surg Res 2019; 246:83-92. [PMID: 31562990 DOI: 10.1016/j.jss.2019.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/08/2019] [Accepted: 08/29/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Cardiopulmonary bypass (CPB) is essential for the repair of many congenital cardiac defects in infants but is associated with significant derangements in hemostasis and systemic inflammation. As a result, hemorrhagic complications and thrombosis are major challenges in the management of children requiring CPB or extracorporeal membrane oxygenation. Conventional clinical laboratory tests capture individual hemostatic derangements (low platelets, elevated fibrinogen) but fail to describe the complex, overlapping interactions among the various components of coagulation, including cellular interactions, contact activation, fibrinolysis, and inflammation. Given recent advances in analytic tools for identifying protein-protein interactions in the plasma proteome, we hypothesized that an unbiased proteomic analysis would help identify networks of interacting proteins for further investigation in pediatric CPB. MATERIALS AND METHODS Infants up to 1 y of age were enrolled. Plasma samples were collected at 0, 1, 4, and 24 h after CPB. Mass spectrometry was used to identify proteins undergoing changes in concentration after CPB, and STRING and ToppGene tools were used to identify biological networks. Two-dimensional difference gel electrophoresis identified changes in protein concentrations. Inflammatory markers were assessed by enzyme-linked immunosorbent assay at the same time points. RESULTS Ten infants with cardiac anomalies requiring surgery and CPB were enrolled; no major complications were recorded (median age, 127.5 d; interquartile range, 181.25 d). Using two-dimensional difference gel electrophoresis, >1400 individual protein spots were observed, and 89 proteins demonstrated change in concentration >30% with P < 0.02 when comparing 1, 4, or 24 h to baseline. Among protein spots with significant changes in concentration after CPB, 29 were identified with mass spectrometry (33%). In our interrogation of functional associations among these differentially expressed proteins, our results were dominated by the acute phase response, coagulation, and cell signaling functional categories. Among cytokines analyzed by enzyme-linked immunosorbent assay, IL-2, IL-8, and IL-10 were elevated at 4 h but normalized by 24 h, whereas IL-6 was persistently elevated. CONCLUSIONS Infants manifest a robust response to CPB that includes overlapping, complex pathways. Further investigation of interactions among immune, coagulation, and cell signaling systems may lead to novel therapeutics or biomarkers useful in the management of infants requiring CPB.
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Affiliation(s)
| | | | - Uttara Nag
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Andrew B Nixon
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - James Otto
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | | | - Andrew J Lodge
- Section of Pediatric Cardiac Surgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Joseph W Turek
- Section of Pediatric Cardiac Surgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina
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5
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Long M, Sun X, Shi W, Yanru A, Leung STC, Ding D, Cheema MS, MacPherson N, Nelson CJ, Ausio J, Yan Y, Ishibashi T. A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. Nucleic Acids Res 2019; 47:8399-8409. [PMID: 31219579 PMCID: PMC6895281 DOI: 10.1093/nar/gkz547] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Histone variants, present in various cell types and tissues, are known to exhibit different functions. For example, histone H3.3 and H2A.Z are both involved in gene expression regulation, whereas H2A.X is a specific variant that responds to DNA double-strand breaks. In this study, we characterized H4G, a novel hominidae-specific histone H4 variant. We found that H4G is expressed in a variety of human cell lines and exhibit tumor-stage dependent overexpression in tissues from breast cancer patients. We found that H4G localized primarily to the nucleoli of the cell nucleus. This localization was controlled by the interaction of the alpha-helix 3 of the histone fold motif with a histone chaperone, nucleophosmin 1. In addition, we found that modulating H4G expression affects rRNA expression levels, protein synthesis rates and cell-cycle progression. Our data suggest that H4G expression alters nucleolar chromatin in a way that enhances rDNA transcription in breast cancer tissues.
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Affiliation(s)
- Mengping Long
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Xulun Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Wenjin Shi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - An Yanru
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Sophia T C Leung
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Dongbo Ding
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Nicol MacPherson
- Department of Medical Oncology, BC Cancer Vancouver Island Centre, Victoria, BC V8R 6V5, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Yan Yan
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
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6
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Zhou Y, Tang Q, Wu M, Mou D, Liu H, Wang S, Zhang C, Ding L, Luo J. Comparative transcriptomics provides novel insights into the mechanisms of selenium tolerance in the hyperaccumulator plant Cardamine hupingshanensis. Sci Rep 2018; 8:2789. [PMID: 29434336 PMCID: PMC5809607 DOI: 10.1038/s41598-018-21268-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
Selenium (Se) is an essential mineral element for animals and humans. Cardamine hupingshanensis (Brassicaceae), found in the Wuling mountain area of China, has been identified as a novel Se hyperaccumulator plant. However, the mechanism for selenium tolerance in Cardamine plants remains unknown. In this study, two cDNA libraries were constructed from seedlings of C. hupingshanensis treated with selenite. Approximately 100 million clean sequencing reads were de novo assembled into 48,989 unigenes, of which 39,579 and 33,510 were expressed in the roots and leaves, respectively. Biological pathways and candidate genes involved in selenium tolerance mechanisms were identified. Differential expression analysis identified 25 genes located in four pathways that were significantly responsive to selenite in C. hupingshanensis seedlings. The results of RNA sequencing (RNA-Seq) and quantitative real-time PCR (RT-qPCR) confirmed that storage function, oxidation, transamination and selenation play very important roles in the selenium tolerance in C. hupingshanensis. Furthermore, a different degradation pathway synthesizing malformed or deformed selenoproteins increased selenium tolerance at different selenite concentrations. This study provides novel insights into the mechanisms of selenium tolerance in a hyperaccumulator plant, and should serve as a rich gene resource for C. hupingshanensis.
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Affiliation(s)
- Yifeng Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China.,Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Qiaoyu Tang
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Meiru Wu
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Di Mou
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Hui Liu
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chi Zhang
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Li Ding
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
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7
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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8
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Ishiguro T, Amamoto Y, Tanabe K, Liu J, Kajino H, Fujimura A, Aoi Y, Osakabe A, Horikoshi N, Kurumizaka H, Yamatsugu K, Kawashima SA, Kanai M. Synthetic Chromatin Acylation by an Artificial Catalyst System. Chem 2017. [DOI: 10.1016/j.chempr.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 2017; 18:141-158. [PMID: 28053344 DOI: 10.1038/nrm.2016.159] [Citation(s) in RCA: 347] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The association of histones with specific chaperone complexes is important for their folding, oligomerization, post-translational modification, nuclear import, stability, assembly and genomic localization. In this way, the chaperoning of soluble histones is a key determinant of histone availability and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin.
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Affiliation(s)
- Colin M Hammond
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Caroline B Strømme
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Hongda Huang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
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10
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Ohtomo H, Akashi S, Moriwaki Y, Okuwaki M, Osakabe A, Nagata K, Kurumizaka H, Nishimura Y. C‐terminal acidic domain of histone chaperone human
NAP
1 is an efficient binding assistant for histone H2A‐H2B, but not H3‐H4. Genes Cells 2016; 21:252-63. [DOI: 10.1111/gtc.12339] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/13/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Hideaki Ohtomo
- Graduate School of Medical Life Science Yokohama City University 1‐7‐29 Suehiro‐cho, Tsurumi‐ku Yokohama 230‐0045 Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science Yokohama City University 1‐7‐29 Suehiro‐cho, Tsurumi‐ku Yokohama 230‐0045 Japan
| | - Yoshihito Moriwaki
- Graduate School of Medical Life Science Yokohama City University 1‐7‐29 Suehiro‐cho, Tsurumi‐ku Yokohama 230‐0045 Japan
| | - Mitsuru Okuwaki
- Faculty of Medicine and Graduate School of Comprehensive Human Sciences University of Tsukuba 1‐1‐1 Tennodai Tsukuba 305‐8575 Japan
| | - Akihisa Osakabe
- Graduate School of Advanced Science and Engineering/RISE Waseda University 2‐2 Wakamatsu‐cho, Shinjuku‐ku Tokyo 162‐8480 Japan
| | - Kyosuke Nagata
- Faculty of Medicine and Graduate School of Comprehensive Human Sciences University of Tsukuba 1‐1‐1 Tennodai Tsukuba 305‐8575 Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering/RISE Waseda University 2‐2 Wakamatsu‐cho, Shinjuku‐ku Tokyo 162‐8480 Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science Yokohama City University 1‐7‐29 Suehiro‐cho, Tsurumi‐ku Yokohama 230‐0045 Japan
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11
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Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome. Sci Rep 2015; 5:16330. [PMID: 26573481 PMCID: PMC4648065 DOI: 10.1038/srep16330] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/13/2015] [Indexed: 11/24/2022] Open
Abstract
UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes
6–4PP lesions through a base flipping mechanism. As genomic DNA is
almost entirely accommodated within nucleosomes, the flipping of the
6–4PP bases is supposed to be extremely difficult if the lesion occurs
in a nucleosome, especially on the strand directly contacting the histone surface.
Here we report that UV-DDB binds efficiently to nucleosomal 6–4PPs that
are rotationally positioned on the solvent accessible or occluded surface. We
determined the crystal structures of nucleosomes containing 6–4PPs in
these rotational positions, and found that the 6–4PP DNA regions were
flexibly disordered, especially in the strand exposed to the solvent. This
characteristic of 6–4PP may facilitate UV-DDB binding to the damaged
nucleosome. We present the first atomic-resolution pictures of the detrimental DNA
cross-links of neighboring pyrimidine bases within the nucleosome, and provide the
mechanistic framework for lesion recognition by UV-DDB in chromatin.
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12
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Chen S, Rufiange A, Huang H, Rajashankar KR, Nourani A, Patel DJ. Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. Genes Dev 2015; 29:1326-40. [PMID: 26109053 PMCID: PMC4495402 DOI: 10.1101/gad.261115.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this study, Patel and colleagues determined the crystal structure of the conserved C terminus of the hSpt2C histone chaperone bound to an H3/H4 tetramer. The results suggest that Spt2 interacts with the periphery of the H3/H4 tetramer and promotes its recycling. Cells use specific mechanisms such as histone chaperones to abrogate the inherent barrier that the nucleosome poses to transcribing polymerases. The current model postulates that nucleosomes can be transiently disrupted to accommodate passage of RNA polymerases and that histones H3 and H4 possess their own chaperones dedicated to the recovery of nucleosomes. Here, we determined the crystal structure of the conserved C terminus of human Suppressors of Ty insertions 2 (hSpt2C) chaperone bound to an H3/H4 tetramer. The structural studies demonstrate that hSpt2C is bound to the periphery of the H3/H4 tetramer, mimicking the trajectory of nucleosomal-bound DNA. These structural studies have been complemented with in vitro binding and in vivo functional studies on mutants that disrupt key intermolecular contacts involving two acidic patches and hydrophobic residues on Spt2C. We show that contacts between both human and yeast Spt2C with the H3/H4 tetramer are required for the suppression of H3/H4 exchange as measured by H3K56ac and new H3 deposition. These interactions are also crucial for the inhibition of spurious transcription from within coding regions. Together, our data indicate that Spt2 interacts with the periphery of the H3/H4 tetramer and promotes its recycling in the wake of RNA polymerase.
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Affiliation(s)
- Shoudeng Chen
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anne Rufiange
- Groupe St-Patrick de Recherche en Oncologie Fondamentale, L'Hôtel-Dieu de Québec (Université Laval), Québec G1R 2J6, Canada
| | - Hongda Huang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Kanagalaghatta R Rajashankar
- Northeastern Collaborative Access Team (NE-CAT), Advanced Photon Source, Argonne National Laboratory, Chicago, Illinois 60439, USA; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amine Nourani
- Groupe St-Patrick de Recherche en Oncologie Fondamentale, L'Hôtel-Dieu de Québec (Université Laval), Québec G1R 2J6, Canada
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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Kulminski AM, Culminskaya I, Arbeev KG, Arbeeva L, Ukraintseva SV, Stallard E, Wu D, Yashin AI. Birth Cohort, Age, and Sex Strongly Modulate Effects of Lipid Risk Alleles Identified in Genome-Wide Association Studies. PLoS One 2015; 10:e0136319. [PMID: 26295473 PMCID: PMC4546650 DOI: 10.1371/journal.pone.0136319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/02/2015] [Indexed: 02/07/2023] Open
Abstract
Insights into genetic origin of diseases and related traits could substantially impact strategies for improving human health. The results of genome-wide association studies (GWAS) are often positioned as discoveries of unconditional risk alleles of complex health traits. We re-analyzed the associations of single nucleotide polymorphisms (SNPs) associated with total cholesterol (TC) in a large-scale GWAS meta-analysis. We focused on three generations of genotyped participants of the Framingham Heart Study (FHS). We show that the effects of all ten directly-genotyped SNPs were clustered in different FHS generations and/or birth cohorts in a sex-specific or sex-unspecific manner. The sample size and procedure-therapeutic issues play, at most, a minor role in this clustering. An important result was clustering of significant associations with the strongest effects in the youngest, or 3rd Generation, cohort. These results imply that an assumption of unconditional connections of these SNPs with TC is generally implausible and that a demographic perspective can substantially improve GWAS efficiency. The analyses of genetic effects in age-matched samples suggest a role of environmental and age-related mechanisms in the associations of different SNPs with TC. Analysis of the literature supports systemic roles for genes for these SNPs beyond those related to lipid metabolism. Our analyses reveal strong antagonistic effects of rs2479409 (the PCSK9 gene) that cautions strategies aimed at targeting this gene in the next generation of lipid drugs. Our results suggest that standard GWAS strategies need to be advanced in order to appropriately address the problem of genetic susceptibility to complex traits that is imperative for translation to health care.
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Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
- * E-mail:
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Liubov Arbeeva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Svetlana V. Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Eric Stallard
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Deqing Wu
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27708–0408, United States of America
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Abstract
An extreme case of chromatin remodelling is the genome-wide exchange of histones with basic non-histone DNA-packaging proteins that occurs in post-meiotic male germ cells. The scale of this genome reorganization is such that chromatin needs to undergo a prior "preparation" for a facilitated action of the factors involved. Stage-specific incorporation of specialized histone variants, affecting large domains of chromatin, combined with histone post-translational modifications accompany the successive steps of the male genome reorganization. Recently, it has been shown that a testis-specific H2B variant, TH2B, one of the first identified core histone variants, replaces H2B at the time of cells' commitment into meiotic divisions and contributes to the process of global histone removal. These investigations also revealed a previously unknown histone dosage compensation mechanism that also ensures a functional interconnection between histone variant expression and histone post-translational modifications and will be further discussed here.
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Affiliation(s)
- Jérôme Govin
- CEA, iRTSV; Biologie à Grande Echelle; Grenoble, France; INSERM, U1038; Grenoble, France; Université Grenoble-Alpes; Grenoble, France; INSERM, U823; Institut Albert Bonniot; Grenoble, France
| | - Saadi Khochbin
- Université Grenoble-Alpes; Grenoble, France; INSERM, U823; Institut Albert Bonniot; Grenoble, France
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