1
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Nagae F, Takada S, Terakawa T. Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome. Nucleic Acids Res 2023; 51:5351-5363. [PMID: 37177996 PMCID: PMC10287947 DOI: 10.1093/nar/gkad396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/22/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
DNA translocases, such as RNA polymerases, inevitably collide with nucleosomes on eukaryotic chromatin. Upon these collisions, histone chaperones are suggested to facilitate nucleosome disassembly and re-assembly. In this study, by performing in vitro transcription assays and molecular simulations, we found that partial unwrapping of a nucleosome by an RNA polymerase dramatically facilitates an H2A/H2B dimer dismantling from the nucleosome by Nucleosome Assembly Protein 1 (Nap1). Furthermore, the results uncovered molecular mechanisms of Nap1 functions in which the highly acidic C-terminal flexible tails of Nap1 contribute to the H2A/H2B binding by associating with the binding interface buried and not accessible to Nap1 globular domains, supporting the penetrating fuzzy binding mechanism seemingly shared across various histone chaperones. These findings have broad implications for the mechanisms by which histone chaperones process nucleosomes upon collisions with translocases in transcription, histone recycling and nucleosomal DNA repair.
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Affiliation(s)
- Fritz Nagae
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- PREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
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2
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Fan H. Single‐molecule tethered particle motion to study
protein‐DNA
interaction. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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3
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Efremov AK, Hovan L, Yan J. Nucleus size and its effect on nucleosome stability in living cells. Biophys J 2022; 121:4189-4204. [PMID: 36146936 PMCID: PMC9675033 DOI: 10.1016/j.bpj.2022.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/15/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
DNA architectural proteins play a major role in organization of chromosomal DNA in living cells by packaging it into chromatin, whose spatial conformation is determined by an intricate interplay between the DNA-binding properties of architectural proteins and physical constraints applied to the DNA by a tight nuclear space. Yet, the exact effects of the nucleus size on DNA-protein interactions and chromatin structure currently remain obscure. Furthermore, there is even no clear understanding of molecular mechanisms responsible for the nucleus size regulation in living cells. To find answers to these questions, we developed a general theoretical framework based on a combination of polymer field theory and transfer-matrix calculations, which showed that the nucleus size is mainly determined by the difference between the surface tensions of the nuclear envelope and the endoplasmic reticulum membrane as well as the osmotic pressure exerted by cytosolic macromolecules on the nucleus. In addition, the model demonstrated that the cell nucleus functions as a piezoelectric element, changing its electrostatic potential in a size-dependent manner. This effect has been found to have a profound impact on stability of nucleosomes, revealing a previously unknown link between the nucleus size and chromatin structure. Overall, our study provides new insights into the molecular mechanisms responsible for regulation of the nucleus size, as well as the potential role of nuclear organization in shaping the cell response to environmental cues.
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Affiliation(s)
- Artem K Efremov
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
| | - Ladislav Hovan
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
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4
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Ishida H, Kono H. Free Energy Landscape of H2A-H2B Displacement From Nucleosome. J Mol Biol 2022; 434:167707. [PMID: 35777463 DOI: 10.1016/j.jmb.2022.167707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 12/14/2022]
Abstract
Nucleosome reconstitution plays an important role in many cellular functions. As an initial step, H2A-H2B dimer displacement, which is accompanied by disruption of many of the interactions within the nucleosome, should occur. To understand how H2A-H2B dimer displacement occurs, an adaptively biased molecular dynamics (ABMD) simulation was carried out to generate a variety of displacements of the H2A-H2B dimer from the fully wrapped to partially unwrapped nucleosome structures. With regards to these structures, the free energy landscape of the dimer displacement was investigated using umbrella sampling simulations. We found that the main contributors to the free energy were the docking domain of H2A and the C-terminal of H4. There were various paths for the dimer displacement which were dependent on the extent of nucleosomal DNA wrapping, suggesting that modulation of the intra-nucleosomal interaction by external factors such as histone chaperons could control the path for the H2A-H2B dimer displacement. Key residues which contributed to the free energy have also been reported to be involved in the mutations and posttranslational modifications (PTMs) which are important for assembling and/or reassembling the nucleosome at the molecular level and are found in cancer cells at the phenotypic level. Our results give insight into how the H2A-H2B dimer displacement proceeds along various paths according to different interactions within the nucleosome.
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Affiliation(s)
- Hisashi Ishida
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 619-0215 Kizugawa, Kyoto, Japan.
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 619-0215 Kizugawa, Kyoto, Japan
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5
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Okimune K, Hataya S, Matsumoto K, Ushirogata K, Banko P, Takeda S, Takasuka TE. Histone chaperone-mediated co-expression assembly of tetrasomes and nucleosomes. FEBS Open Bio 2021; 11:2912-2920. [PMID: 34614293 PMCID: PMC8564334 DOI: 10.1002/2211-5463.13311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022] Open
Abstract
The nucleosome, a basic unit of chromatin found in all eukaryotes, is thought to be assembled through the orchestrated activity of several histone chaperones and chromatin assembly factors in a stepwise manner, proceeding from tetrasome assembly, to H2A/H2B deposition, and finally to formation of the mature nucleosome. In this study, we demonstrate chaperone-mediated assembly of both tetrasomes and nucleosomes on the well-defined Widom 601 positioning sequence using a co-expression/reconstitution wheat germ cell-free system. The purified tetrasomes and nucleosomes were positioned around the center of a given sequence. The heights and diameters were measured by atomic force microscopy. Together with the reported unmodified native histones produced by the wheat germ cell-free platform, our method is expected to be useful for downstream applications in the field of chromatin research.
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Affiliation(s)
- Kei‐ichi Okimune
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Shogo Hataya
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kazuki Matsumoto
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kanako Ushirogata
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Petra Banko
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | - Seiji Takeda
- Faculty of Pharmaceutical SciencesHokkaido University of ScienceSapporoJapan
| | - Taichi E. Takasuka
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
- Global Institute for Collaborative Research and EducationHokkaido UniversitySapporoJapan
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6
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You C, Zhang Y, Yang S, Wang X, Yao W, Jin W, Wang W, Hu X, Yang H. Proteomic Analysis of Generative and Vegetative Nuclei Reveals Molecular Characteristics of Pollen Cell Differentiation in Lily. FRONTIERS IN PLANT SCIENCE 2021; 12:641517. [PMID: 34163497 PMCID: PMC8215658 DOI: 10.3389/fpls.2021.641517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 06/13/2023]
Abstract
In plants, the cell fates of a vegetative cell (VC) and generative cell (GC) are determined after the asymmetric division of the haploid microspore. The VC exits the cell cycle and grows a pollen tube, while the GC undergoes further mitosis to produce two sperm cells for double fertilization. However, our understanding of the mechanisms underlying their fate differentiation remains limited. One major advantage of the nuclear proteome analysis is that it is the only method currently able to uncover the systemic differences between VC and GC due to GC being engulfed within the cytoplasm of VC, limiting the use of transcriptome. Here, we obtained pure preparations of the vegetative cell nuclei (VNs) and generative cell nuclei (GNs) from germinating lily pollens. Utilizing these high-purity VNs and GNs, we compared the differential nucleoproteins between them using state-of-the-art quantitative proteomic techniques. We identified 720 different amount proteins (DAPs) and grouped the results in 11 fate differentiation categories. Among them, we identified 29 transcription factors (TFs) and 10 cell fate determinants. Significant differences were found in the molecular activities of vegetative and reproductive nuclei. The TFs in VN mainly participate in pollen tube development. In comparison, the TFs in GN are mainly involved in cell differentiation and male gametogenesis. The identified novel TFs may play an important role in cell fate differentiation. Our data also indicate differences in nuclear pore complexes and epigenetic modifications: more nucleoporins synthesized in VN; more histone variants and chaperones; and structural maintenance of chromosome (SMC) proteins, chromatin remodelers, and DNA methylation-related proteins expressed in GN. The VC has active macromolecular metabolism and mRNA processing, while GC has active nucleic acid metabolism and translation. Moreover, the members of unfolded protein response (UPR) and programmed cell death accumulate in VN, and DNA damage repair is active in GN. Differences in the stress response of DAPs in VN vs. GN were also found. This study provides a further understanding of pollen cell differentiation mechanisms and also a sound basis for future studies of the molecular mechanisms behind cell fate differentiation.
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Affiliation(s)
- Chen You
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- College of Life Science, Henan Normal University, Xinxiang, China
| | - YuPing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - ShaoYu Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xu Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - WeiHuan Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiuLi Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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7
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Whitley MJ, Suwanpradid J, Lai C, Jiang SW, Cook JL, Zelac DE, Rudolph R, Corcoran DL, Degan S, Spasojevic I, Levinson H, Erdmann D, Reid C, Zhang JY, Robson SC, Healy E, Havran WL, MacLeod AS. ENTPD1 (CD39) Expression Inhibits UVR-Induced DNA Damage Repair through Purinergic Signaling and Is Associated with Metastasis in Human Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2021; 141:2509-2520. [PMID: 33848530 DOI: 10.1016/j.jid.2021.02.753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/21/2021] [Accepted: 02/07/2021] [Indexed: 12/24/2022]
Abstract
UVR and immunosuppression are major risk factors for cutaneous squamous cell carcinoma (cSCC). Regulatory T cells promote cSCC carcinogenesis, and in other solid tumors, infiltrating regulatory T cells and CD8+ T cells express ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1) (also known as CD39), an ectoenzyme that catalyzes the rate-limiting step in converting extracellular adenosine triphosphate (ATP) to extracellular adenosine (ADO). We previously showed that extracellular purine nucleotides influence DNA damage repair. In this study, we investigate whether DNA damage repair is modulated through purinergic signaling in cSCC. We found increased ENTPD1 expression on T cells within cSCCs when compared with the expression on T cells from blood or nonlesional skin, and accordingly, concentrations of derivative extracellular adenosine diphosphate (ADP), adenosine monophosphate (AMP), and ADO are increased in tumors compared with those in normal skin. Importantly, ENTPD1 expression is significantly higher in human cSCCs that metastasize than in those that are nonmetastatic. We also identify in a mouse model that ENTPD1 expression is induced by UVR in an IL-27-dependent manner. Finally, increased extracellular ADO is shown to downregulate the expression of NAP1L2, a nucleosome assembly protein we show to be important for DNA damage repair secondary to UVR. Together, these data suggest a role for ENTPD1 expression on skin-resident T cells to regulate DNA damage repair through purinergic signaling to promote skin carcinogenesis and metastasis.
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Affiliation(s)
- Melodi Javid Whitley
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jutamas Suwanpradid
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Chester Lai
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Simon W Jiang
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jonathan L Cook
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Daniel E Zelac
- Department of Dermatology and Mohs Surgery, Scripps Clinic, La Jolla, California, USA
| | - Ross Rudolph
- Division of Plastic Surgery, Scripps Clinic, San Diego, California, USA; Division of Plastic Surgery, University of California San Diego, San Diego, California, USA
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Simone Degan
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ivan Spasojevic
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA; PK/PD Core Lab, Duke Cancer Institute, Durham, North Carolina, USA
| | - Howard Levinson
- Division of Plastic, Maxillofacial, and Oral Surgery, Duke Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Detlev Erdmann
- Division of Plastic, Maxillofacial, and Oral Surgery, Duke Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Claire Reid
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jennifer Y Zhang
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Pinnell Center for Investigative Dermatology, Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Simon C Robson
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, Massachusetts, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts, USA
| | - Eugene Healy
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Wendy L Havran
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California, USA
| | - Amanda S MacLeod
- Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Pinnell Center for Investigative Dermatology, Department of Duke Dermatology, Duke University School of Medicine, Durham, North Carolina, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA; Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA.
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8
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Akishina AA, Kuvaeva EE, Vorontsova YE, Simonova OB. NAP Family Histone Chaperones: Characterization and Role in Ontogenesis. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420060028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Tan X, Ravasio A, Ong HT, Wu J, Hew CL. White spot syndrome viral protein VP9 alters the cellular higher-order chromatin structure. FASEB Bioadv 2020; 2:264-279. [PMID: 32259052 PMCID: PMC7133739 DOI: 10.1096/fba.2019-00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 10/26/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022] Open
Abstract
Viral protein 9 (VP9) is a non-structural protein of white spot syndrome virus (WSSV) highly expressed during the early stage of infection. The crystal structure of VP9 suggests that the polymers of VP9 dimers resemble a DNA mimic, but its function remains elusive. In this study, we demonstrated that VP9 impedes histones binding to DNA via single-molecule manipulation. We established VP9 expression in HeLa cells due to the lack of a WSSV-susceptible cell line, and observed abundant VP9 in the nucleus, which mirrors its distribution in the hemocytes of WSSV-infected shrimp. VP9 expression increased the dynamics and rotational mobility of histones in stable H3-GFP HeLa cells as revealed by fluorescent recovery after photobleaching and fluorescence anisotropy imaging, which suggested a loosened compaction of chromatin structure. Successive salt fractionation showed that a prominent population of histones was solubilized in high salt concentrations, which implies alterations of bulk chromatin structure. Southern blotting identified that VP9 alters juxtacentromeric chromatin structures to be more accessible to micrococcal nuclease digestion. RNA microarray revealed that VP9 expression also leads to significant changes of cellular gene expression. Our findings provide evidence that VP9 alters the cellular higher-order chromatin structure, uncovering a potential strategy adopted by WSSV to facilitate its replication.
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Affiliation(s)
- Xi Tan
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
- Present address:
School of Basic Medical SciencesGuizhou University of Traditional Chinese MedicineGuiyangGuizhou ProvinceChina
| | - Andrea Ravasio
- Institute for Biological and Medical EngineeringSchools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiago de ChileChile
| | - Hui T. Ong
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
| | - Jinlu Wu
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Choy L. Hew
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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10
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Ordu O, Lusser A, Dekker NH. DNA Sequence Is a Major Determinant of Tetrasome Dynamics. Biophys J 2019; 117:2217-2227. [PMID: 31521330 PMCID: PMC6895708 DOI: 10.1016/j.bpj.2019.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 10/26/2022] Open
Abstract
Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque buildup in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behavior. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.
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Affiliation(s)
- Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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11
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Liu Y, Xu L, Xie C, Hong J, Li F, Ruan K, Chen J, Wu J, Shi Y. Structural Insights into ceNAP1 Chaperoning Activity toward ceH2A-H2B. Structure 2019; 27:1798-1810.e3. [DOI: 10.1016/j.str.2019.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/11/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022]
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12
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Kameda T, Awazu A, Togashi Y. Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling. Front Mol Biosci 2019; 6:133. [PMID: 31850366 PMCID: PMC6896900 DOI: 10.3389/fmolb.2019.00133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/11/2019] [Indexed: 11/13/2022] Open
Abstract
Nucleosomes are structural units of the chromosome consisting of DNA wrapped around histone proteins, and play important roles in compaction and regulation of the chromatin structure. While the structure and dynamics of canonical nucleosomes have been studied extensively, those of nucleosomes in intermediate states, that occur when their structure or positioning is modulated, have been less understood. In particular, the dynamic features of partially disassembled nucleosomes have not been discussed in previous studies. Using all-atom molecular dynamics simulations, in this study, we investigated the dynamics and stability of nucleosome structures lacking a histone-dimer. DNA in nucleosomes lacking a histone H2A/H2B dimer was drastically deformed due to loss of local interactions between DNA and histones. In contrast, conformation of DNA in nucleosomes lacking H3/H4 was similar to the canonical nucleosome, as the H2A C-terminal domain infiltrated the space originally occupied by the dissociated H3/H4 histones and restricted DNA dynamics in close proximity. Our results suggest that, besides histone chaperones, the intrinsic dynamics of nucleosomes support the exchange of H2A/H2B, which is significantly more frequent than that of H3/H4.
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Affiliation(s)
- Takeru Kameda
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuichi Togashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Japan.,RIKEN Center for Biosystems Dynamics Research (BDR), Higashi-Hiroshima, Japan
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13
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Rössler I, Embacher J, Pillet B, Murat G, Liesinger L, Hafner J, Unterluggauer JJ, Birner-Gruenberger R, Kressler D, Pertschy B. Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME. Nucleic Acids Res 2019; 47:6984-7002. [PMID: 31062022 PMCID: PMC6648895 DOI: 10.1093/nar/gkz317] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/12/2022] Open
Abstract
Dedicated chaperones protect newly synthesized ribosomal proteins (r-proteins) from aggregation and accompany them on their way to assembly into nascent ribosomes. Currently, only nine of the ∼80 eukaryotic r-proteins are known to be guarded by such chaperones. In search of new dedicated r-protein chaperones, we performed a tandem-affinity purification based screen and looked for factors co-enriched with individual small subunit r-proteins. We report the identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2, respectively. Both factors promote the solubility of their r-protein clients in vitro. While Tsr4 is specific for Rps2, Nap1 has several interaction partners including Rps6 and two other r-proteins. Tsr4 binds co-translationally to the essential, eukaryote-specific N-terminal extension of Rps2, whereas Nap1 interacts with a large, mostly eukaryote-specific binding surface of Rps6. Mutation of the essential Tsr4 and deletion of the non-essential Nap1 both enhance the 40S synthesis defects of the corresponding r-protein mutants. Our findings highlight that the acquisition of eukaryote-specific domains in r-proteins was accompanied by the co-evolution of proteins specialized to protect these domains and emphasize the critical role of r-protein chaperones for the synthesis of eukaryotic ribosomes.
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Affiliation(s)
- Ingrid Rössler
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Julia Embacher
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Laura Liesinger
- BioTechMed-Graz, Graz, Austria
- Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Julia Judith Unterluggauer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Ruth Birner-Gruenberger
- BioTechMed-Graz, Graz, Austria
- Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
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14
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Shimada M, Chen WY, Nakadai T, Onikubo T, Guermah M, Rhodes D, Roeder RG. Gene-Specific H1 Eviction through a Transcriptional Activator→p300→NAP1→H1 Pathway. Mol Cell 2019; 74:268-283.e5. [PMID: 30902546 DOI: 10.1016/j.molcel.2019.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/07/2019] [Accepted: 02/12/2019] [Indexed: 02/03/2023]
Abstract
Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by the H1 chaperone NAP1, which is recruited in a gene-specific manner through direct interactions with activator-bound p300 that facilitate core histone acetylation (by p300) and concomitant eviction of H1 and H2A-H2B. An analysis in B cells confirms the strong dependency on NAP1-mediated H1 eviction for induction of the silent CD40 gene and further demonstrates that H1 eviction, seeded by activator-p300-NAP1-H1 interactions, is propagated over a CCCTC-binding factor (CTCF)-demarcated region through a distinct mechanism that also involves NAP1. Our results confirm direct transcriptional inhibition by H1 and establish a gene-specific H1 eviction mechanism through an activator→p300→NAP1→H1 pathway.
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Affiliation(s)
- Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wei-Yi Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan; Cancer Progression Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Takashi Onikubo
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Mohamed Guermah
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Daniela Rhodes
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore 636921, Singapore
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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15
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van den Berg AA, Depken M. Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes. Nucleic Acids Res 2017; 45:7623-7632. [PMID: 28586463 PMCID: PMC5737439 DOI: 10.1093/nar/gkx513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/03/2017] [Indexed: 12/20/2022] Open
Abstract
During eukaryotic transcription, RNA polymerase (RNAP) translocates along DNA molecules covered with nucleosomes and other DNA binding proteins. Though the interactions between a single nucleosome and RNAP are by now fairly well understood, this understanding has not been synthesized into a description of transcription on crowded genes, where multiple RNAP transcribe through nucleosomes while preserving the nucleosome coverage. We here take a deductive modeling approach to establish the consequences of RNAP–nucleosome interactions for transcription in crowded environments. We show that under physiologically crowded conditions, the interactions of RNAP with nucleosomes induce a strong kinetic attraction between RNAP molecules, causing them to self-organize into stable and moving pelotons. The peloton formation quantitatively explains the observed nucleosome and RNAP depletion close to the initiation site on heavily transcribed genes. Pelotons further translate into short-timescale transcriptional bursts at termination, resulting in burst characteristics consistent with instances of bursty transcription observed in vivo. To facilitate experimental testing of our proposed mechanism, we present several analytic relations that make testable quantitative predictions.
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Affiliation(s)
- Aafke A van den Berg
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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16
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Chen X, Zhao E, Fu YV. Using single-molecule approach to visualize the nucleosome assembly in yeast nucleoplasmic extracts. Sci Bull (Beijing) 2017; 62:399-404. [PMID: 36659283 DOI: 10.1016/j.scib.2017.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In eukaryotic cells, the smallest subunit of chromatin is the nucleosome, which consists of a segment of DNA wound on histone protein cores. Despite many years of effort, the process of nucleosome assembly and disassembly is still not very clear. Here, we present a convenient method to investigate the process of nucleosome assembly at the single molecule level. We invented a novel system derived from the yeast nucleoplasmic extracts (YNPE), and demonstrated that the YNPE supports the nucleosome assembly under physiological condition. By combining the total internal reflection fluorescence microscopy with microfluidic flow-cell technique, the dynamic process of nucleosome assembly in YNPE was visualized at single-molecule level. Our system provides a novel in vitro single-molecule tool to investigate the dynamics of nucleosome assembly under physiological conditions.
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Affiliation(s)
- Xiuqiang Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ershuang Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu V Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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17
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Vlijm R, Kim SH, De Zwart PL, Dalal Y, Dekker C. The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes. NANOSCALE 2017; 9:1862-1870. [PMID: 28094382 PMCID: PMC7959483 DOI: 10.1039/c6nr06245h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.
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Affiliation(s)
- R Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - S H Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - P L De Zwart
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - Y Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - C Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
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18
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Levendosky RF, Sabantsev A, Deindl S, Bowman GD. The Chd1 chromatin remodeler shifts hexasomes unidirectionally. eLife 2016; 5. [PMID: 28032848 PMCID: PMC5226652 DOI: 10.7554/elife.21356] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022] Open
Abstract
Despite their canonical two-fold symmetry, nucleosomes in biological contexts are often asymmetric: functionalized with post-translational modifications (PTMs), substituted with histone variants, and even lacking H2A/H2B dimers. Here we show that the Widom 601 nucleosome positioning sequence can produce hexasomes in a specific orientation on DNA, providing a useful tool for interrogating chromatin enzymes and allowing for the generation of nucleosomes with precisely defined asymmetry. Using this methodology, we demonstrate that the Chd1 chromatin remodeler from Saccharomyces cerevisiae requires H2A/H2B on the entry side for sliding, and thus, unlike the back-and-forth sliding observed for nucleosomes, Chd1 shifts hexasomes unidirectionally. Chd1 takes part in chromatin reorganization surrounding transcribing RNA polymerase II (Pol II), and using asymmetric nucleosomes we show that ubiquitin-conjugated H2B on the entry side stimulates nucleosome sliding by Chd1. We speculate that biased nucleosome and hexasome sliding due to asymmetry contributes to the packing of arrays observed in vivo. DOI:http://dx.doi.org/10.7554/eLife.21356.001
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Affiliation(s)
- Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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19
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Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proc Natl Acad Sci U S A 2016; 114:334-339. [PMID: 28028239 DOI: 10.1073/pnas.1611118114] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during salt-induced disassembly of canonical NCPs. We find that H2A-H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.
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20
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CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly. PLoS One 2016; 11:e0165078. [PMID: 27820823 PMCID: PMC5098787 DOI: 10.1371/journal.pone.0165078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022] Open
Abstract
Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test this hypothesis by subjecting CENP-A and H3 octameric nucleosomes, assembled on random or on centromeric DNA sequences, to varying amounts of applied force by using single-molecule magnetic tweezers. We monitor individual disassembly events of CENP-A and H3 nucleosomes. Regardless of the DNA sequence, the force-mediated disassembly experiments for CENP-A and H3 nucleosomes demonstrate similar rupture forces, life time residency and disassembly steps. From these experiments, we conclude that CENP-A does not, by itself, contribute unique structural features to the nucleosome that lead to a significant resistance against force-mediated disruption. The data present insights into the mechanistic basis for how CENP-A nucleosomes might contribute to the structural foundation of the centromere in vivo.
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21
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Pedersen HL, Horvei KD, Thiyagarajan D, Seredkina N, Rekvig OP. Murine and Human Lupus Nephritis: Pathogenic Mechanisms and Theoretical Strategies for Therapy. Semin Nephrol 2016; 35:427-38. [PMID: 26573545 DOI: 10.1016/j.semnephrol.2015.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lupus nephritis is one of the most serious manifestations of systemic lupus erythematosus, and represents one of the criteria implemented to classify systemic lupus erythematosus. Although studied for decades, no consensus has been reached related to the basic cellular, molecular, and immunologic mechanism(s) responsible for lupus nephritis. No causal treatments have been developed; therapy is approached mainly with nonspecific immunosuppressive medications. More detailed insight into disease mechanisms therefore is indispensable to develop new therapeutic strategies. In this review, contemporary knowledge on the pathogenic mechanisms of lupus nephritis is discussed based on recent data in murine and human lupus nephritis. Specific focus is given to the effect of anti-double-stranded DNA/antinucleosome antibodies in the kidneys and whether they bind exposed chromatin fragments in glomeruli or whether they bind inherent glomerular structures by cross-recognition. Overall, the data presented here favor the exposed chromatin model because we did not find any indication to substantiate the anti-double-stranded DNA antibody cross-reacting model. At the end of this review we present data on why chromatin fragments are expressed in the glomeruli of patients with lupus nephritis, and discuss how this knowledge can be used to direct the development of future therapies.
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Affiliation(s)
- Hege Lynum Pedersen
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
| | - Kjersti Daae Horvei
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Dhivya Thiyagarajan
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Natalya Seredkina
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ole Petter Rekvig
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway; Department of Radiology, University Hospital of North Norway, Tromsø, Norway
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22
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Aizawa M, Sugimoto N, Watanabe S, Yoshida K, Fujita M. Nucleosome assembly and disassembly activity of GRWD1, a novel Cdt1-binding protein that promotes pre-replication complex formation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2739-2748. [PMID: 27552915 DOI: 10.1016/j.bbamcr.2016.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023]
Abstract
GRWD1 was previously identified as a novel Cdt1-binding protein that possesses histone-binding and nucleosome assembly activities and promotes MCM loading, probably by maintaining chromatin openness at replication origins. However, the molecular mechanisms underlying these activities remain unknown. We prepared reconstituted mononucleosomes from recombinant histones and a DNA fragment containing a nucleosome positioning sequence, and investigated the effects of GRWD1 on them. GRWD1 could disassemble these preformed mononucleosomes in vitro in an ATP-independent manner. Thus, our data suggest that GRWD1 facilitates removal of H2A-H2B dimers from nucleosomes, resulting in formation of hexasomes. The activity was compromised by deletion of the acidic domain, which is required for efficient histone binding. In contrast, nucleosome assembly activity of GRWD1 was not affected by deletion of the acidic domain. In HeLa cells, the acidic domain of GRWD1 was necessary to maintain chromatin openness and promote MCM loading at replication origins. Taken together, our results suggest that GRWD1 promotes chromatin fluidity by influencing nucleosome structures, e.g., by transient eviction of H2A-H2B, and thereby promotes efficient MCM loading at replication origins.
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Affiliation(s)
- Masahiro Aizawa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Shinya Watanabe
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan.
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23
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Coordinated Action of Nap1 and RSC in Disassembly of Tandem Nucleosomes. Mol Cell Biol 2016; 36:2262-71. [PMID: 27273866 DOI: 10.1128/mcb.00195-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
The SWI/SNF and RSC family of ATP-dependent chromatin remodelers disassembles nucleosomes by moving nucleosomes into the vicinity of adjoining nucleosomes. We found that the histone chaperone Nap1 efficiently promotes disassembly of adjacent nucleosomes with which RSC collides and not the disassembly of nucleosomes mobilized by RSC. Nap1 is specific to RSC, as it does not target SWI/SNF, its paralog in Saccharomyces cerevisiae Extensive mutational analysis of Nap1 has revealed that Nap1 affinity for histones H2A-H2B and H3-H4 and its ability to displace histones from DNA are required for Nap1 to enhance RSC-mediated disassembly. Other histone chaperones, such as Vps75, that also bind histones are not able to enhance RSC-mediated disassembly. Our study suggests a mechanism by which Nap1 is recruited to actively transcribed regions and assists in the passage of the transcription complex through chromatin, and it provides a novel mechanism for the coordinated action of RSC and Nap1.
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24
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Aguilar-Gurrieri C, Larabi A, Vinayachandran V, Patel NA, Yen K, Reja R, Ebong IO, Schoehn G, Robinson CV, Pugh BF, Panne D. Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly. EMBO J 2016; 35:1465-82. [PMID: 27225933 PMCID: PMC4931181 DOI: 10.15252/embj.201694105] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/21/2016] [Indexed: 11/25/2022] Open
Abstract
Nap1 is a histone chaperone involved in the nuclear import of H2A–H2B and nucleosome assembly. Here, we report the crystal structure of Nap1 bound to H2A–H2B together with in vitro and in vivo functional studies that elucidate the principles underlying Nap1‐mediated H2A–H2B chaperoning and nucleosome assembly. A Nap1 dimer provides an acidic binding surface and asymmetrically engages a single H2A–H2B heterodimer. Oligomerization of the Nap1–H2A–H2B complex results in burial of surfaces required for deposition of H2A–H2B into nucleosomes. Chromatin immunoprecipitation‐exonuclease (ChIP‐exo) analysis shows that Nap1 is required for H2A–H2B deposition across the genome. Mutants that interfere with Nap1 oligomerization exhibit severe nucleosome assembly defects showing that oligomerization is essential for the chaperone function. These findings establish the molecular basis for Nap1‐mediated H2A–H2B deposition and nucleosome assembly.
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Affiliation(s)
- Carmen Aguilar-Gurrieri
- European Molecular Biology Laboratory, Grenoble, France Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Amédé Larabi
- European Molecular Biology Laboratory, Grenoble, France Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Vinesh Vinayachandran
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Nisha A Patel
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Kuangyu Yen
- Department of Cell Biology, Southern Medical University, Guangzhou, China
| | - Rohit Reja
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Ima-O Ebong
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Guy Schoehn
- Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France Université Grenoble-Alpes, Grenoble, France Centre National de la Recherche Scientifique (CNRS) IBS, Grenoble, France CEA, IBS, Grenoble, France
| | | | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
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25
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Yamamoto T, Schiessel H. Transcription Driven Phase Separation in Chromatin Brush. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3036-3044. [PMID: 26974855 DOI: 10.1021/acs.langmuir.6b00442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We theoretically predict the local density of nucleosomes on DNA brushes in a solution of molecules, which are necessary for transcription and the assembly of nucleosomes. Our theory predicts that in a confined space, DNA brushes show phase separation, where a region of relatively large nucleosomal occupancy coexists with a region of smaller nucleosomal occupancy. This phase separation is driven by an instability arising from the fact that the rate of transcription increases as the nucleosomal occupancy decreases due to the excluded volume interactions between nucleosomes and RNA polymerase during thermal diffusion and, in turn, nucleosomes are (in some cases) desorbed from DNA when RNA polymerase collides with nucleosomes during transcription. The miscibility phase diagram shows critical points, which are sensitive to the rate constants involved in transcription, the changes of interactions of DNA chain segments by assembling nucleosomes, and pressures that are applied to the brushes.
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Affiliation(s)
- Tetsuya Yamamoto
- National Composite Center, Nagoya University Furo-cho , Chikusa-ku, Nagoya 464-8603, Japan
| | - Helmut Schiessel
- Instituut-Lorentz for Theoretical Physics , Niels Bohrweg 2, Leiden, NL-2333 CA, The Netherlands
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26
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Vlijm R, Lee M, Ordu O, Boltengagen A, Lusser A, Dekker NH, Dekker C. Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes. PLoS One 2015; 10:e0141267. [PMID: 26506534 PMCID: PMC4623960 DOI: 10.1371/journal.pone.0141267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 01/18/2023] Open
Abstract
Eukaryotic nucleosomes consists of an (H3-H4)2 tetramer and two H2A-H2B dimers, around which 147 bp of DNA are wrapped in 1.7 left-handed helical turns. During chromatin assembly, the (H3-H4)2 tetramer binds first, forming a tetrasome that likely constitutes an important intermediate during ongoing transcription. We recently showed that (H3-H4)2 tetrasomes spontaneously switch between a left- and right-handed wrapped state of the DNA, a phenomenon that may serve to buffer changes in DNA torque induced by RNA polymerase in transcription. Within nucleosomes of actively transcribed genes, however, canonical H3 is progressively replaced by its variant H3.3. Consequently, one may ask if and how the DNA chirality dynamics of tetrasomes is altered by H3.3. Recent findings that H3.3-containing nucleosomes result in less stable and less condensed chromatin further underline the need to study the microscopic underpinnings of H3.3-containing tetrasomes and nucleosomes. Here we report real-time single-molecule studies of (H3.3-H4)2 tetrasome dynamics using Freely Orbiting Magnetic Tweezers and Electromagnetic Torque Tweezers. We find that the assembly of H3.3-containing tetrasomes and nucleosomes by the histone chaperone Nucleosome Assembly Protein 1 (NAP1) occurs in an identical manner to that of H3-containing tetrasomes and nucleosomes. Likewise, the flipping behavior of DNA handedness in tetrasomes is not impacted by the presence of H3.3. We also examine the effect of free NAP1, H3.3, and H4 in solution on flipping behavior and conclude that the probability for a tetrasome to occupy the left-handed state is only slightly enhanced by the presence of free protein. These data demonstrate that the incorporation of H3.3 does not alter the structural dynamics of tetrasomes, and hence that the preferred incorporation of this histone variant in transcriptionally active regions does not result from its enhanced ability to accommodate torsional stress, but rather may be linked to specific chaperone or remodeler requirements or communication with the nuclear environment.
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Affiliation(s)
- Rifka Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Mina Lee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Anastasiya Boltengagen
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Nynke H. Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- * E-mail: (NHD); (CD)
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- * E-mail: (NHD); (CD)
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Zhou W, Zhu Y, Dong A, Shen WH. Histone H2A/H2B chaperones: from molecules to chromatin-based functions in plant growth and development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:78-95. [PMID: 25781491 DOI: 10.1111/tpj.12830] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 05/06/2023]
Abstract
Nucleosomal core histones (H2A, H2B, H3 and H4) must be assembled, replaced or exchanged to preserve or modify chromatin organization and function according to cellular needs. Histone chaperones escort histones, and play key functions during nucleosome assembly/disassembly and in nucleosome structure configuration. Because of their location at the periphery of nucleosome, histone H2A-H2B dimers are remarkably dynamic. Here we focus on plant histone H2A/H2B chaperones, particularly members of the NUCLEOSOME ASSEMBLY PROTEIN-1 (NAP1) and FACILITATES CHROMATIN TRANSCRIPTION (FACT) families, discussing their molecular features, properties, regulation and function. Covalent histone modifications (e.g. ubiquitination, phosphorylation, methylation, acetylation) and H2A variants (H2A.Z, H2A.X and H2A.W) are also discussed in view of their crucial importance in modulating nucleosome organization and function. We further discuss roles of NAP1 and FACT in chromatin-based processes, such as transcription, DNA replication and repair. Specific functions of NAP1 and FACT are evident when their roles are considered with respect to regulation of plant growth and development and in plant responses to environmental stresses. Future major challenges remain in order to define in more detail the overlapping and specific roles of various members of the NAP1 family as well as differences and similarities between NAP1 and FACT family members, and to identify and characterize their partners as well as new families of chaperones to understand histone variant incorporation and chromatin target specificity.
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Affiliation(s)
- Wangbin Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
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Katan AJ, Vlijm R, Lusser A, Dekker C. Dynamics of nucleosomal structures measured by high-speed atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:976-984. [PMID: 25336288 DOI: 10.1002/smll.201401318] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 09/05/2014] [Indexed: 06/04/2023]
Abstract
The accessibility of DNA is determined by the number, position, and stability of nucleosomes, complexes consisting of a core of 8 histone proteins with DNA wrapped around it. Since the structure and dynamics of nucleosomes affects essential cellular processes, they are the subject of many current studies. Here, high-speed atomic force microscopy is used to visualize dynamic processes in nucleosomes and tetrasomes (subnucleosomal structures that contain 4 rather than 8 histones in the protein core). Nucleosomes can spontaneously disassemble in a process (at a 1 second timescale). For tetrasomes, multiple dynamic phenomena are observed. For example, during disassembly the formation of a DNA loop (∼25 nm in length) is seen, which remains stable for several minutes. For intact tetrasomes, dynamics in the form of sliding and reversible hopping between stable positions along the DNA are observed. The data emphasize that tetrasomes are not merely static objects but highly dynamic. Since tetrasomes (in contrast to nucleosomes) can stay on the DNA during transcription, the observed tetrasome dynamics is relevant for an understanding of the nucleosomal dynamics during transcription. These results illustrate the diversity of nucleosome dynamics and demonstrate the ability of high speed AFM to characterize protein-DNA interactions.
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Affiliation(s)
- Allard J Katan
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628, CJ, The Netherlands
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29
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Abstract
A huge amount of information is stored in genomic DNA and this stored information resides inside the nucleus with the aid of chromosomal condensation factors. It has been reported that the repeat nucleosome core particle (NCP) consists of 147-bp of DNA and two copies of H2A, H2B, H3 and H4. Regulation of chromosomal structure is important to many processes inside the cell. In vivo, a group of histone chaperones facilitate and regulate nucleosome assembly. How NCPs are constructed with the aid of histone chaperones remains unclear. In this study, the histone chaperone-mediated nucleosome assembly process was investigated using single-molecule tethered particle motion (TPM) experiments. It was found that Asf1 is able to exert more influence than Nap1 and poly glutamate acid (PGA) on the nucleosome formation process, which highlights Asf1’s specific role in tetrasome formation. Thermodynamic parameters supported a model whereby energetically favored nucleosomal complexes compete with non-nucleosomal complexes. In addition, our kinetic findings propose the model that histone chaperones mediate nucleosome assembly along a path that leads to enthalpy-favored products with free histones as reaction substrates.
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30
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Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes. Cell Rep 2015; 10:216-25. [DOI: 10.1016/j.celrep.2014.12.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/04/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022] Open
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31
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Lee JY, Lee J, Yue H, Lee TH. Dynamics of nucleosome assembly and effects of DNA methylation. J Biol Chem 2014; 290:4291-303. [PMID: 25550164 DOI: 10.1074/jbc.m114.619213] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleosome is the fundamental packing unit of the eukaryotic genome, and CpG methylation is an epigenetic modification associated with gene repression and silencing. We investigated nucleosome assembly mediated by histone chaperone Nap1 and the effects of CpG methylation based on three-color single molecule FRET measurements, which enabled direct monitoring of histone binding in the context of DNA wrapping. According to our observation, (H3-H4)2 tetramer incorporation must precede H2A-H2B dimer binding, which is independent of DNA termini wrapping. Upon CpG methylation, (H3-H4)2 tetramer incorporation and DNA termini wrapping are facilitated, whereas proper incorporation of H2A-H2B dimers is inhibited. We suggest that these changes are due to rigidified DNA and increased random binding of histones to DNA. According to the results, CpG methylation expedites nucleosome assembly in the presence of abundant DNA and histones, which may help facilitate gene packaging in chromatin. The results also indicate that the slowest steps in nucleosome assembly are DNA termini wrapping and tetramer positioning, both of which are affected heavily by changes in the physical properties of DNA.
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Affiliation(s)
- Ju Yeon Lee
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jaehyoun Lee
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hongjun Yue
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Tae-Hee Lee
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
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32
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Osberg B, Nuebler J, Korber P, Gerland U. Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays. Nucleic Acids Res 2014; 42:13633-45. [PMID: 25428353 PMCID: PMC4267636 DOI: 10.1093/nar/gku1190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 11/13/2022] Open
Abstract
The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches high density extremely slowly, due to a jamming phenomenon. The nucleosome-shifting action of remodeling enzymes has been proposed as a mechanism to resolve such jams. Here, we suggest two biophysical mechanisms which assist rapid filling of DNA with nucleosomes, and we quantitatively characterize these mechanisms within mathematical models. First, we show that the 'softness' of nucleosomes, due to nucleosome breathing and stepwise nucleosome assembly, significantly alters the filling behavior, speeding up the process relative to 'hard' particles with fixed, mutually exclusive DNA footprints. Second, we explore model scenarios in which the progression of the replication fork could eliminate nucleosome jamming, either by rapid filling in its wake or via memory of the parental nucleosome positions. Taken together, our results suggest that biophysical effects promote rapid nucleosome filling, making the reassembly of densely packed nucleosomes after DNA replication a simpler task for cells than was previously thought.
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Affiliation(s)
- Brendan Osberg
- Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
| | - Johannes Nuebler
- Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
| | - Philipp Korber
- Adolf-Butenandt-Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany
| | - Ulrich Gerland
- Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
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33
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Chen Y, Tokuda JM, Topping T, Sutton JL, Meisburger SP, Pabit SA, Gloss LM, Pollack L. Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Res 2014; 42:8767-76. [PMID: 24990379 PMCID: PMC4117781 DOI: 10.1093/nar/gku562] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.
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Affiliation(s)
- Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Joshua M Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Traci Topping
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Julie L Sutton
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Steve P Meisburger
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Lisa M Gloss
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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34
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Machida S, Takaku M, Ikura M, Sun J, Suzuki H, Kobayashi W, Kinomura A, Osakabe A, Tachiwana H, Horikoshi Y, Fukuto A, Matsuda R, Ura K, Tashiro S, Ikura T, Kurumizaka H. Nap1 stimulates homologous recombination by RAD51 and RAD54 in higher-ordered chromatin containing histone H1. Sci Rep 2014; 4:4863. [PMID: 24798879 PMCID: PMC4010968 DOI: 10.1038/srep04863] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/15/2014] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination plays essential roles in mitotic DNA double strand break (DSB) repair and meiotic genetic recombination. In eukaryotes, RAD51 promotes the central homologous-pairing step during homologous recombination, but is not sufficient to overcome the reaction barrier imposed by nucleosomes. RAD54, a member of the ATP-dependent nucleosome remodeling factor family, is required to promote the RAD51-mediated homologous pairing in nucleosomal DNA. In higher eukaryotes, most nucleosomes form higher-ordered chromatin containing the linker histone H1. However, the mechanism by which RAD51/RAD54-mediated homologous pairing occurs in higher-ordered chromatin has not been elucidated. In this study, we found that a histone chaperone, Nap1, accumulates on DSB sites in human cells, and DSB repair is substantially decreased in Nap1-knockdown cells. We determined that Nap1 binds to RAD54, enhances the RAD54-mediated nucleosome remodeling by evicting histone H1, and eventually stimulates the RAD51-mediated homologous pairing in higher-ordered chromatin containing histone H1.
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Affiliation(s)
- Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- These authors contributed equally to this work
| | - Motoki Takaku
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- These authors contributed equally to this work
| | - Masae Ikura
- Department of Mutagenesis, Division of Chromatin Regulatory Network, Radiation Biology Center, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hidekazu Suzuki
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Atsuhiko Fukuto
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Ryo Matsuda
- Department of Mutagenesis, Division of Chromatin Regulatory Network, Radiation Biology Center, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kiyoe Ura
- Division of Gene Therapy Science, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Tsuyoshi Ikura
- Department of Mutagenesis, Division of Chromatin Regulatory Network, Radiation Biology Center, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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35
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Towards a mechanism for histone chaperones. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:211-221. [PMID: 24459723 DOI: 10.1016/j.bbagrm.2011.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Histone chaperones can be broadly defined as histone-binding proteins that influence chromatin dynamics in an ATP-independent manner. Their existence reflects the importance of chromatin homeostasis and the unique and unusual biochemistry of the histone proteins. Histone supply and demand at chromatin is regulated by a network of structurally and functionally diverse histone chaperones. At the core of this network is a mechanistic variability that is only beginning to be appreciated. In this review, we highlight the challenges in determining histone chaperone mechanism and discuss possible mechanisms in the context of nucleosome thermodynamics. We discuss how histone chaperones prevent promiscuous histone interactions, and consider if this activity represents the full extent of histone chaperone function in governing chromatin dynamics. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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36
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Parikh RY, Kim HD. The effect of an intervening promoter nucleosome on gene expression. PLoS One 2013; 8:e63072. [PMID: 23700413 PMCID: PMC3659125 DOI: 10.1371/journal.pone.0063072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 03/27/2013] [Indexed: 12/02/2022] Open
Abstract
Nucleosomes, which are the basic packaging units of chromatin, are stably positioned in promoters upstream of most stress-inducible genes. These promoter nucleosomes are generally thought to repress gene expression due to exclusion; they prevent transcription factors from accessing their target sites on the DNA. However, the role of promoter nucleosomes that do not directly occlude transcription factor binding sites is not obvious. Here, we varied the stability of a non-occluding nucleosome positioned between a transcription factor binding site and the TATA box region in an inducible yeast promoter and measured downstream gene expression level. We found that gene expression level depends on the occupancy of the non-occluding nucleosome in a non-monotonic manner. We postulated that a non-occluding nucleosome can serve both as a vehicle of and a barrier to chromatin remodeling activity and built a quantitative, nonequilibrium model to explain the observed nontrivial effect of the intervening nucleosome. Our work sheds light on the dual role of nucleosome as a repressor and an activator and expands the standard model of gene expression to include irreversible promoter chromatin transitions.
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Affiliation(s)
- Rasesh Y. Parikh
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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37
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The carboxyl terminus of Rtt109 functions in chaperone control of histone acetylation. EUKARYOTIC CELL 2013; 12:654-64. [PMID: 23457193 DOI: 10.1128/ec.00291-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Rtt109 is a fungal histone acetyltransferase (HAT) that catalyzes histone H3 acetylation functionally associated with chromatin assembly. Rtt109-mediated H3 acetylation involves two histone chaperones, Asf1 and Vps75. In vivo, Rtt109 requires both chaperones for histone H3 lysine 9 acetylation (H3K9ac) but only Asf1 for full H3K56ac. In vitro, Rtt109-Vps75 catalyzes both H3K9ac and H3K56ac, whereas Rtt109-Asf1 catalyzes only H3K56ac. In this study, we extend the in vitro chaperone-associated substrate specificity of Rtt109 by showing that it acetylates vertebrate linker histone in the presence of Vps75 but not Asf1. In addition, we demonstrate that in Saccharomyces cerevisiae a short basic sequence at the carboxyl terminus of Rtt109 (Rtt109C) is required for H3K9ac in vivo. Furthermore, through in vitro and in vivo studies, we demonstrate that Rtt109C is required for optimal H3K56ac by the HAT in the presence of full-length Asf1. When Rtt109C is absent, Vps75 becomes important for H3K56ac by Rtt109 in vivo. In addition, we show that lysine 290 (K290) in Rtt109 is required in vivo for Vps75 to enhance the activity of the HAT. This is the first in vivo evidence for a role for Vps75 in H3K56ac. Taken together, our results contribute to a better understanding of chaperone control of Rtt109-mediated H3 acetylation.
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38
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Tachiwana H, Miya Y, Shono N, Ohzeki JI, Osakabe A, Otake K, Larionov V, Earnshaw WC, Kimura H, Masumoto H, Kurumizaka H. Nap1 regulates proper CENP-B binding to nucleosomes. Nucleic Acids Res 2013; 41:2869-80. [PMID: 23325853 PMCID: PMC3597661 DOI: 10.1093/nar/gks1464] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CENP-B is a widely conserved centromeric satellite DNA-binding protein, which specifically binds to a 17-bp DNA sequence known as the CENP-B box. CENP-B functions positively in the de novo assembly of centromeric nucleosomes, containing the centromere-specific histone H3 variant, CENP-A. At the same time, CENP-B also prevents undesired assembly of the CENP-A nucleosome through heterochromatin formation on satellite DNA integrated into ectopic sites. Therefore, improper CENP-B binding to chromosomes could be harmful. However, no CENP-B eviction mechanism has yet been reported. In the present study, we found that human Nap1, an acidic histone chaperone, inhibited the non-specific binding of CENP-B to nucleosomes and apparently stimulated CENP-B binding to its cognate CENP-B box DNA in nucleosomes. In human cells, the CENP-B eviction activity of Nap1 was confirmed in model experiments, in which the CENP-B binding to a human artificial chromosome or an ectopic chromosome locus bearing CENP-B boxes was significantly decreased when Nap1 was tethered near the CENP-B box sequence. In contrast, another acidic histone chaperone, sNASP, did not promote CENP-B eviction in vitro and in vivo and did not stimulate specific CENP-B binding to CENP-A nucleosomes in vitro. We therefore propose a novel mechanism of CENP-B regulation by Nap1.
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Affiliation(s)
- Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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39
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Fierz B, Kilic S, Hieb AR, Luger K, Muir TW. Stability of nucleosomes containing homogenously ubiquitylated H2A and H2B prepared using semisynthesis. J Am Chem Soc 2012; 134:19548-51. [PMID: 23163596 DOI: 10.1021/ja308908p] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Post-translational modifications (PTMs) of histones are an essential feature in the dynamic regulation of chromatin. One of these modifications, ubiquitylation, has been speculated to directly influence the stability of the nucleosome, which represents the basic building block of chromatin. Here we report a strategy for the semisynthesis of site-specifically ubiquitylated histone H2A (uH2A). This branched protein was generated through a three-piece expressed protein ligation approach including a traceless ligation at valine. uH2A could be efficiently incorporated into nucleosomes, thereby opening the way to detailed biochemical and biophysical studies on the function of this PTM. Accordingly, we used uH2A, as well as a previously generated ubiquitylated H2B, in chaperone-coupled nucleosome stability assays to demonstrate that the direct effect of ubiquitylated histones on nucleosomal stability is in fact modest.
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Affiliation(s)
- Beat Fierz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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40
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White RH, Keberlein M, Jackson V. A mutational mimic analysis of histone H3 post-translational modifications: specific sites influence the conformational state of H3/H4, causing either positive or negative supercoiling of DNA. Biochemistry 2012; 51:8173-88. [PMID: 23003102 DOI: 10.1021/bi300872t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Histone H3 has specific sites of post-translational modifications that serve as epigenetic signals to cellular machinery to direct various processes. Mutational mimics of these modifications (glutamine for acetylation, methionine and leucine for methylation, and glutamic acid for phosphorylation) were constructed at the relevant sites of the major histone variant, H3.2, and their effects on the conformational equilibrium of the H3/H4 tetramer at physiological ionic strength were determined when bound to or free of DNA. The deposition vehicle used for this analysis was NAP1, nucleosome assembly protein 1. Acetylation mimics in the N-terminus preferentially stabilized the left-handed conformer (DNA negatively supercoiled), and mutations within the globular region preferred the right-handed conformer (DNA positively supercoiled). The methylation mimics in the N-terminus tended to maintain characteristics similar to those of wild-type H3/H4; i.e., the conformational equilibrium maintains similar levels of both left- and right-handed conformers. Phosphorylation mimics facilitated a mixed effect, i.e., when at serines, the left-handed conformer, and at threonines, a mixture of both conformers. When double mutations were present, the conformational equilibrium was shifted dramatically, either leftward or rightward depending on the specific sites. In contrast, these mutations tended not to affect the direction and extent of supercoiling for variants H3.1 and H3.3. Variant H3.3 promoted only the left-handed conformer, and H3.1 tended to maintain both conformers. Additional experiments indicate the importance of a propagation mechanism for ensuring the formation of a particular superhelical state over an extended region of the DNA. The potential relevance of these results to the maintenance of epigenetic information on a gene is discussed.
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Affiliation(s)
- Rachel H White
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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41
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Vlijm R, Smitshuijzen JSJ, Lusser A, Dekker C. NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers. PLoS One 2012; 7:e46306. [PMID: 23050009 PMCID: PMC3457989 DOI: 10.1371/journal.pone.0046306] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/30/2012] [Indexed: 11/19/2022] Open
Abstract
While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching force and supercoiling density to a single DNA molecule, and to study in real time the change in linking number, stiffness and length of the DNA during nucleosome formation. We observe a decrease in end-to-end length when NAP1 and core histones (CH) are added to the dsDNA. We characterize the formation of complete nucleosomes by measuring the change in linking number of DNA, which is induced by the NAP1-assisted nucleosome assembly, and which does not occur for non-nucleosomal bound histones H3 and H4. By rotating the magnets, the supercoils formed upon nucleosome assembly are removed and the number of assembled nucleosomes can be counted. We find that the compaction of DNA at low force is about 56 nm per assembled nucleosome. The number of compaction steps and associated change in linking number indicate that NAP1-assisted nucleosome assembly is a two-step process.
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Affiliation(s)
- Rifka Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
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Arimura Y, Tachiwana H, Oda T, Sato M, Kurumizaka H. Structural Analysis of the Hexasome, Lacking One Histone H2A/H2B Dimer from the Conventional Nucleosome. Biochemistry 2012; 51:3302-9. [DOI: 10.1021/bi300129b] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Structural Biology,
Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku,
Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology,
Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku,
Tokyo 162-8480, Japan
| | - Takashi Oda
- Division
of Macromolecular Crystallography,
Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi,
Yokohama 230-0045, Japan
| | - Mamoru Sato
- Division
of Macromolecular Crystallography,
Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi,
Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo,
Hyogo 679-5148, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology,
Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku,
Tokyo 162-8480, Japan
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Huang YC, Saito S, Yokoyama KK. Histone chaperone Jun dimerization protein 2 (JDP2): role in cellular senescence and aging. Kaohsiung J Med Sci 2012; 26:515-31. [PMID: 20950777 DOI: 10.1016/s1607-551x(10)70081-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/22/2010] [Indexed: 01/12/2023] Open
Abstract
Transcription factor Jun dimerization protein 2 (JDP2) binds directly to histones and DNA, and inhibits p300-mediated acetylation of core histones and reconstituted nucleosomes that contain JDP2-recognition DNA sequences. The region of JDP2 that encompasses its histone-binding domain and DNA-binding region is essential to inhibit histone acetylation by histone acetyltransferases. Moreover, assays of nucleosome assembly in vitro demonstrate that JDP2 also has histone-chaperone activity. The mutation of the region responsible for inhibition of histone acetyltransferase activity within JDP2 eliminates repression of transcription from the c-jun promoter by JDP2, as well as JDP2-mediated inhibition of retinoic-acid-induced differentiation. Thus JDP2 plays a key role as a repressor of cell differentiation by regulating the expression of genes with an activator protein 1 (AP-1) site via inhibition of histone acetylation and/or assembly and disassembly of nucleosomes. Senescent cells show a series of alterations, including flatten and enlarged morphology, increase in nonspecific acidic β-galactosidase activity, chromatin condensation, and changes in gene expression patterns. The onset and maintenance of senescence are regulated by two tumor suppressors, p53 and retinoblastoma proteins. The expression of p53 and retinoblastoma proteins is regulated by two distinct proteins, p16(Ink4a) and Arf, respectively, which are encoded by cdkn2a. JDP2 inhibits recruitment of the polycomb repressive complexes 1 and 2 (PRC-1 and PRC-2) to the promoter of the gene that encodes p16(Ink4a) and inhibits the methylation of lysine 27 of histone H3 (H3K27). The PRCs associate with the p16(Ink4a)/Arf locus in young proliferating cells and dissociate from it in senescent cells. Therefore, it seems that chromatin-remodeling factors that regulate association and dissociation of PRCs, and are controlled by JDP2, might play an important role in the senescence program. The molecular mechanisms that underlie the action of JDP2 in cellular aging and replicative senescence by mediating the dissociation of PRCs from the p16(Ink4a)/Arf locus are discussed.
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Affiliation(s)
- Yu-Chang Huang
- Center of Excellence for Environmental Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Ettig R, Kepper N, Stehr R, Wedemann G, Rippe K. Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping. Biophys J 2012; 101:1999-2008. [PMID: 22004754 DOI: 10.1016/j.bpj.2011.07.057] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 07/17/2011] [Accepted: 07/27/2011] [Indexed: 11/25/2022] Open
Abstract
The nucleosome complex of DNA wrapped around a histone protein octamer organizes the genome of eukaryotes and regulates the access of protein factors to the DNA. We performed molecular dynamics simulations of the nucleosome in explicit water to study the dynamics of its histone-DNA interactions. A high-resolution histone-DNA interaction map was derived that revealed a five-nucleotide periodicity, in which the two DNA strands of the double helix made alternating contacts. On the 100-ns timescale, the histone tails mostly maintained their initial positions relative to the DNA, and the spontaneous unwrapping of DNA was limited to 1-2 basepairs. In steered molecular dynamics simulations, external forces were applied to the linker DNA to investigate the unwrapping pathway of the nucleosomal DNA. In comparison with a nucleosome without the unstructured N-terminal histone tails, the following findings were obtained: 1), Two main barriers during unwrapping were identified at DNA position ±70 and ±45 basepairs relative to the central DNA basepair at the dyad axis. 2), DNA interactions of the histone H3 N-terminus and the histone H2A C-terminus opposed the initiation of unwrapping. 3), The N-terminal tails of H2A, H2B, and H4 counteracted the unwrapping process at later stages and were essential determinants of nucleosome dynamics. Our detailed analysis of DNA-histone interactions revealed molecular mechanisms for modulating access to nucleosomal DNA via conformational rearrangements of its structure.
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Affiliation(s)
- Ramona Ettig
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
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Hondele M, Ladurner AG. The chaperone-histone partnership: for the greater good of histone traffic and chromatin plasticity. Curr Opin Struct Biol 2011; 21:698-708. [PMID: 22054910 DOI: 10.1016/j.sbi.2011.10.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/11/2011] [Accepted: 10/11/2011] [Indexed: 01/25/2023]
Abstract
Histones are highly positively charged proteins that wrap our genome. Their surface properties also make them prone to nonspecific interactions and aggregation. A class of proteins known as histone chaperones is dedicated to safeguard histones by aiding their proper incorporation into nucleosomes. Histone chaperones facilitate ordered nucleosome assembly and disassembly reactions through the formation of semi-stable histone-chaperone intermediates without requiring ATP, but merely providing a complementary protein surface for histones to dynamically interact with. Recurrent 'chaperoning' mechanisms involve the masking of the histone's positive charge and the direct blocking of crucial histone surface sites, including those required for H3-H4 tetramerization or the binding of nucleosomal DNA. This shielding prevents histones from engaging in premature or unwanted interactions with nucleic acids and other cellular components. In this review, we analyze recent structural studies on chaperone-histone interactions and discuss the implications of this vital partnership for nucleosome assembly and disassembly pathways.
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Affiliation(s)
- Maria Hondele
- Department of Physiological Chemistry, Butenandt Institute of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377 Munich, Germany
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Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga JT. Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF. Mol Cell 2011; 43:638-48. [PMID: 21855802 DOI: 10.1016/j.molcel.2011.07.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/27/2011] [Accepted: 07/15/2011] [Indexed: 10/17/2022]
Abstract
Chromatin assembly involves the combined action of histone chaperones and ATP-dependent motor proteins. Here, we investigate the mechanism of nucleosome assembly with a purified chromatin assembly system containing the histone chaperone NAP1 and the ATP-dependent motor protein ACF. These studies revealed the rapid formation of a stable nonnucleosomal histone-DNA intermediate that is converted into canonical nucleosomes by ACF. The histone-DNA intermediate does not supercoil DNA like a canonical nucleosome, but has a nucleosome-like appearance by atomic force microscopy. This intermediate contains all four core histones, lacks NAP1, and is formed by the initial deposition of histones H3-H4. Conversion of the intermediate into histone H1-containing chromatin results in increased resistance to micrococcal nuclease digestion. These findings suggest that the histone-DNA intermediate corresponds to nascent nucleosome-like structures, such as those observed at DNA replication forks. Related complexes might be formed during other chromatin-directed processes such as transcription, DNA repair, and histone exchange.
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Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0347, USA
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Abstract
Chromatin is a highly regulated, modular nucleoprotein complex that is central to many processes in eukaryotes. The organization of DNA into nucleosomes and higher-order structures has profound implications for DNA accessibility. Alternative structural states of the nucleosome, and the thermodynamic parameters governing its assembly and disassembly, need to be considered in order to understand how access to nucleosomal DNA is regulated. In this review, we provide a brief historical account of how the overriding perception regarding aspects of nucleosome structure has changed over the past thirty years. We discuss recent technical advances regarding nucleosome structure and its physical characterization and review the evidence for alternative nucleosome conformations and their implications for nucleosome and chromatin dynamics.
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Affiliation(s)
- Andrew J Andrews
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
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Hedberg A, Fismen S, Fenton KA, Fenton C, Osterud B, Mortensen ES, Rekvig OP. Heparin exerts a dual effect on murine lupus nephritis by enhancing enzymatic chromatin degradation and preventing chromatin binding in glomerular membranes. ACTA ACUST UNITED AC 2011; 63:1065-75. [PMID: 21190297 DOI: 10.1002/art.30211] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Association of nucleosome-IgG immune complexes with glomerular basement membranes (GBMs) is an important event in the development of lupus nephritis. Preventing this binding and/or increasing nuclease sensitivity of nucleosomes may be viable strategies for the prevention of the disease. Theoretically, heparin may alter nucleosomal structure and increase sensitivity to proteinases and nucleases, and may also inhibit binding of nucleosomes and nucleosome-IgG complexes to basement membrane structures. The aim of this study was to investigate whether and eventually how heparin prevents murine lupus nephritis. METHODS Surface plasmon resonance was used to analyze if heparin inhibits binding of nucleosomes to laminin and collagen. The effect of heparin on nuclease- and proteinase-mediated degradation of nucleosomes was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and agarose gel electrophoresis. In vitro results were compared with analyses in vivo in heparin-treated (NZB × NZW)F(1) mice. Anti-double-stranded DNA antibody production, deposition of nucleosome-IgG complexes in GBMs, and development of proteinuria were monitored, and circulating chromatin fragments were quantified using quantitative polymerase chain reaction. RESULTS In vitro studies demonstrated that heparin increased enzymatic degradation of nucleosomes and almost completely inhibited binding of nucleosomes to laminin and collagen. (NZB × NZW)F(1) mice treated with heparin demonstrated delayed or no antibody production and higher variation of circulating chromatin levels compared with untreated control mice. This effect was accompanied by highly reduced nucleosome-IgG complexes in GBMs and delayed development of nephritis. CONCLUSION Increasing the degradation of nucleosomes, reducing their immunogenicity, and preventing binding of nucleosome-IgG complexes in glomeruli together provide an alternative basis for the treatment of lupus nephritis.
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Hedberg A, Mortensen ES, Rekvig OP. Chromatin as a target antigen in human and murine lupus nephritis. Arthritis Res Ther 2011; 13:214. [PMID: 21542875 PMCID: PMC3132027 DOI: 10.1186/ar3281] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The present review focuses on pathogenic molecular and transcriptional events in patients with lupus nephritis. These factors are renal DNaseI, exposed chromatin fragments and the corresponding chromatin-reactive autoantibodies. Lupus nephritis is the most serious complication in human systemic lupus erythematosus, and is characterised by deposition of chromatin fragment-IgG complexes in the mesangial matrix and glomerular basement membranes. The latter deposition defines end-stage disease. This event is stringently linked to a renal-restricted shutdown of expression of the DNaseI gene, as determined by loss of DNaseI mRNA level and DNaseI enzyme activity. The major aim of the present review is to generate new therapeutic strategies based on new insight into the disease pathogenesis.
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Affiliation(s)
- Annica Hedberg
- Molecular Pathology Research Group, Institute of Medical Biology, Faculty of Health Science, University of Tromsø, N-9037 Tromsø, Norway
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Wang J, Onoshima D, Aki M, Okamoto Y, Kaji N, Tokeshi M, Baba Y. Label-free detection of DNA-binding proteins based on microfluidic solid-state molecular beacon sensor. Anal Chem 2011; 83:3528-32. [PMID: 21476599 DOI: 10.1021/ac200236r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A solid-state molecular beacon using a gold support as a fluorescence quencher is combined with a polydimethylsiloxane (PDMS) microfluidic channel to construct an optical sensor for detecting single-stranded DNA binding protein (SSBP) and histone protein. The single-stranded DNA-Cy3 probe or double-stranded DNA-Cy3 probe immobilized on the gold surface is prepared for the detection of SSBP or histone, respectively. Due to the different quenching ability of gold to the immobilized single-stranded DNA-Cy3 probe and the immobilized double-stranded DNA-Cy3 probe, low fluorescence intensity of the attached single-stranded DNA-Cy3 is obtained in SSBP detection, whereas high fluorescence intensity of the attached double-stranded DNA-Cy3 is obtained in histone detection. The amounts of SSBP in sample solutions are determined from the degree of fluorescence recovery of the immobilized single-stranded DNA-Cy3 probe, whereas that of histone in sample solutions is determined from the degree of fluorescence quenching of the immobilized double-stranded DNA-Cy3 probe. Using this approach, label-free detection of target proteins at nanomolar concentrations is achieved in a convenient, general, continuous flow format. Our approach has high potential for the highly sensitive label-free detection of various proteins based on binding-induced conformation changes of immobilized DNA probes.
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Affiliation(s)
- Jun Wang
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Japan.
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