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Kuwayama N, Kujirai T, Kishi Y, Hirano R, Echigoya K, Fang L, Watanabe S, Nakao M, Suzuki Y, Ishiguro KI, Kurumizaka H, Gotoh Y. HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation. Nat Commun 2023; 14:6420. [PMID: 37828010 PMCID: PMC10570362 DOI: 10.1038/s41467-023-42094-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of factors that regulate chromatin condensation is important for understanding of gene regulation. High-mobility group AT-hook (HMGA) proteins 1 and 2 are abundant nonhistone chromatin proteins that play a role in many biological processes including tissue stem-progenitor cell regulation, but the nature of their protein function remains unclear. Here we show that HMGA2 mediates direct condensation of polynucleosomes and forms droplets with nucleosomes. Consistently, most endogenous HMGA2 localized to transposase 5- and DNase I-inaccessible chromatin regions, and its binding was mostly associated with gene repression, in mouse embryonic neocortical cells. The AT-hook 1 domain was necessary for chromatin condensation by HMGA2 in vitro and in cellulo, and an HMGA2 mutant lacking this domain was defective in the ability to maintain neuronal progenitors in vivo. Intrinsically disordered regions of other proteins could substitute for the AT-hook 1 domain in promoting this biological function of HMGA2. Taken together, HMGA2 may regulate neural cell fate by its chromatin condensation activity.
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Grants
- This research was supported by AMED-CREST and AMED-PRIME of the Japan Agency for Medical Research and Development (JP22gm1310004, JP22gm6110021), SECOM Science and Technology Foundation SECOM Science and Technology Foundation (for Y.K.), Platform Project for Supporting Drug Discovery and Life Science Research from AMED JP21am0101076 and (for H.K.), Research Support Project for Life Science and Drug Discovery from AMED JP22ama121009 (for H.K.), Japan Science and Technology Agency ERATO JPMJER1901 (for H.K.) and by KAKENHI grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan and the Japan Society for the Promotion of Science (JP21J14115 for N.K.; JP22K15033 for T.K.;16H06279, 20H03179, 21H00242 and 22H04687 for Y.K.; 20K07589 for S.W.; JP20H00449, JP18H05534 for H.K.; JP22H00431, JP16H06279 and JP22H04925 for Y.G.)
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Affiliation(s)
- Naohiro Kuwayama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Kishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rina Hirano
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Kenta Echigoya
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Lingyan Fang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Sugiko Watanabe
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Mitsuyoshi Nakao
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, 113-0033, Japan.
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2
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Yamaguchi K, Itakura M, Tsukamoto M, Lim SY, Uchida K. Natural polyphenols convert proteins into histone-binding ligands. J Biol Chem 2022; 298:102529. [PMID: 36162500 PMCID: PMC9589214 DOI: 10.1016/j.jbc.2022.102529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 12/01/2022] Open
Abstract
Antioxidants are sensitive to oxidation and are immediately converted into their oxidized forms that can react with proteins. We have recently found that proteins incubated with oxidized vitamin C (dehydroascorbate) gain a new function as a histone-binding ligand. This finding led us to predict that antioxidants, through conversion to their oxidized forms, may generally have similar functions. In the present study, we identified several natural polyphenols as a source of histone ligands and characterized the mechanism for the interaction of protein-bound polyphenols with histone. Through screening of 25 plant-derived polyphenols by assessing their ability to convert bovine serum albumin into histone ligands, we identified seven polyphenols, including (-)-epigallocatechin-3-O-gallate (EGCG). Additionally, we found that the histone tail domain, which is a highly charged and conformationally flexible region, is involved in the interaction with the polyphenol-modified proteins. Further mechanistic studies showed the involvement of a complex heterogeneous group of the polyphenol-derived compounds bound to proteins as histone-binding elements. We also determined that the interaction of polyphenol-modified proteins with histones formed aggregates and exerted a protective effect against histone-mediated cytotoxicity toward endothelial cells. These findings demonstrated that histones are one of the major targets of polyphenol-modified proteins and provide important insights into the chemoprotective functions of dietary polyphenols.
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Affiliation(s)
- Kosuke Yamaguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masanori Itakura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Mona Tsukamoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Sei-Young Lim
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Koji Uchida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; Japan Agency for Medical Research and Development, CREST, Tokyo, Japan.
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3
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Rad54L promotes bladder cancer progression by regulating cell cycle and cell senescence. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:185. [PMID: 36071250 DOI: 10.1007/s12032-022-01751-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/13/2022] [Indexed: 10/14/2022]
Abstract
Bladder cancer (BCa) is the most prevalent cancer of the urinary system, but its pathogenesis is still poorly understood. Several reports have suggested that gene damage repair is highly correlated with tumor development and drug resistance, in which homologous recombination repair gene Rad54L seems to play an important role, through yet unclear mechanisms. Therefore, this study stratified cancer patients by Rad54L expression in BCa tissue, and high Rad54L expression was associated with a poor prognosis. Mechanistically, we demonstrate that high Rad54L expression promotes abnormal bladder tumor cell proliferation by changing the cell cycle and cell senescence. In addition, this study also suggests that Rad54L may be associated with p53, p21, and pRB in BCa tissue. In summary, this study exposes Rad54L as potential a prognostic biomarker and precision treatment target in BCa.
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4
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Abstract
Reducing sugars can covalently react with proteins to generate a heterogeneous and complex group of compounds called advanced glycation end products (AGEs). AGEs are generally considered as pathogenic molecules, mediating a pro-inflammatory response and contributing to the development of a number of human diseases. However, the intrinsic function of AGEs remains to be elucidated. We now provide multiple lines of evidence showing that AGEs can specifically bind histone localized on the cell surface as an AGE-binding protein, regulate the function of histone as a plasminogen receptor, and result in the regulation of monocytes/macrophage recruitment to the site of inflammation. Our finding of histone as a cell-surface receptor for AGEs suggests that, beside our common concept of AGEs as danger-associated molecular patterns mediating a pro-inflammatory response, they may also be involved in the homeostatic response via binding to histone. Advanced glycation end products (AGEs) are believed to be pathogenic molecules that mediate pro-inflammatory responses. Here the authors identify histone as a cell-surface receptor for AGEs and show that AGEs may also be involved in the homeostatic response via binding to histone.
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5
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Ekstrom TL, Pathoulas NM, Huehls AM, Kanakkanthara A, Karnitz LM. VLX600 Disrupts Homologous Recombination and Synergizes with PARP Inhibitors and Cisplatin by Inhibiting Histone Lysine Demethylases. Mol Cancer Ther 2021; 20:1561-1571. [PMID: 34224364 DOI: 10.1158/1535-7163.mct-20-1099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022]
Abstract
Tumors with defective homologous recombination (HR) DNA repair are more sensitive to chemotherapies that induce lesions repaired by HR as well as PARP inhibitors (PARPis). However, these therapies have limited activity in HR-proficient cells. Accordingly, agents that disrupt HR may be a means to augment the activities of these therapies in HR-proficient tumors. Here we show that VLX600, a small molecule that has been in a phase I clinical trial, disrupts HR and synergizes with PARPis and platinum compounds in ovarian cancer cells. We further found that VLX600 and other iron chelators disrupt HR, in part, by inhibiting iron-dependent histone lysine demethylases (KDM) family members, thus blocking recruitment of HR repair proteins, including RAD51, to double-strand DNA breaks. Collectively, these findings suggest that pharmacologically targeting KDM family members with VLX600 may be a potential novel strategy to therapeutically induce HR defects in ovarian cancers and correspondingly sensitize them to platinum agents and PARPis, two standard-of-care therapies for ovarian cancer.
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Affiliation(s)
- Thomas L Ekstrom
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Nicholas M Pathoulas
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amelia M Huehls
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Arun Kanakkanthara
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Larry M Karnitz
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
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6
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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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7
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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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8
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Shibata T, Iwasaki W, Hirota K. The intrinsic ability of double-stranded DNA to carry out D-loop and R-loop formation. Comput Struct Biotechnol J 2020; 18:3350-3360. [PMID: 33294131 PMCID: PMC7677664 DOI: 10.1016/j.csbj.2020.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/03/2022] Open
Abstract
Double-stranded (ds)DNA, not dsRNA, has an ability to form a homologous complex with single-stranded (ss)DNA or ssRNA of homologous sequence. D-loops and homologous triplexes are homologous complexes formed with ssDNA by RecA/Rad51-family homologous-pairing proteins, and are a key intermediate of homologous (genetic/DNA) recombination. R-loop formation independent of transcription (R-loop formation in trans) was recently found to play roles in gene regulation and development of mammals and plants. In addition, the crRNA-Cas effector complex in CRISPR-Cas systems also relies on R-loop formation to recognize specific target. In homologous complex formation, ssDNA/ssRNA finds a homologous sequence in dsDNA by Watson-Crick base-pairing. crRNA-Cas effector complexes appear to actively melt dsDNA to make its bases available for annealing to crRNA. On the other hand, in D-loop formation and homologous-triplex formation, it is likely that dsDNA recognizes the homologous sequence before the melting of its double helix by using its intrinsic molecular function depending on CH2 at the 2'-position of the deoxyribose, and that the major role of RecA is the extension of ssDNA and the holding dsDNA at a position suitable for homology search. This intrinsic dsDNA function would also play a role in R-loop formation. The dependency of homologous-complex formation on 2'-CH2 of the deoxyribose would explain the absence of homologous complex formation by dsRNA, and dsDNA as sole genome molecule in all cellular organisms.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi, Yokohama, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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9
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Nucleosome binding by the pioneer transcription factor OCT4. Sci Rep 2020; 10:11832. [PMID: 32678275 PMCID: PMC7367260 DOI: 10.1038/s41598-020-68850-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/24/2020] [Indexed: 11/22/2022] Open
Abstract
Transcription factor binding to genomic DNA is generally prevented by nucleosome formation, in which the DNA is tightly wrapped around the histone octamer. In contrast, pioneer transcription factors efficiently bind their target DNA sequences within the nucleosome. OCT4 has been identified as a pioneer transcription factor required for stem cell pluripotency. To study the nucleosome binding by OCT4, we prepared human OCT4 as a recombinant protein, and biochemically analyzed its interactions with the nucleosome containing a natural OCT4 target, the LIN28B distal enhancer DNA sequence, which contains three potential OCT4 target sequences. By a combination of chemical mapping and cryo-electron microscopy single-particle analysis, we mapped the positions of the three target sequences within the nucleosome. A mutational analysis revealed that OCT4 preferentially binds its target DNA sequence located near the entry/exit site of the nucleosome. Crosslinking mass spectrometry consistently showed that OCT4 binds the nucleosome in the proximity of the histone H3 N-terminal region, which is close to the entry/exit site of the nucleosome. We also found that the linker histone H1 competes with OCT4 for the nucleosome binding. These findings provide important information for understanding the molecular mechanism by which OCT4 binds its target DNA in chromatin.
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10
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Shi L, Sun J, Kinomura A, Fukuto A, Horikoshi Y, Tashiro S. Matrin3 promotes homologous recombinational repair by regulation of RAD51. J Biochem 2019; 166:343-351. [PMID: 31119278 DOI: 10.1093/jb/mvz041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/15/2019] [Indexed: 01/19/2023] Open
Abstract
Matrin3 is a highly conserved inner nuclear matrix protein involved in multiple stages of RNA metabolism. Although Matrin3 may also play a role in DNA repair, its precise roles have remained unclear. In this study, we showed that the depletion of Matrin3 led to decreased homologous recombination (HR) efficiency and increased radiation sensitivity of cells. Matrin3-depleted cells showed impaired DNA damage-dependent focus formation of RAD51, a key protein in HR. These findings suggest that Matrin3 promotes HR by regulating RAD51.
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Affiliation(s)
- Lin Shi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Atsuhiko Fukuto
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
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11
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Jiang H, Xue X, Panda S, Kawale A, Hooy RM, Liang F, Sohn J, Sung P, Gekara NO. Chromatin-bound cGAS is an inhibitor of DNA repair and hence accelerates genome destabilization and cell death. EMBO J 2019; 38:e102718. [PMID: 31544964 PMCID: PMC6826206 DOI: 10.15252/embj.2019102718] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/19/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022] Open
Abstract
DNA repair via homologous recombination (HR) is indispensable for genome integrity and cell survival but if unrestrained can result in undesired chromosomal rearrangements. The regulatory mechanisms of HR are not fully understood. Cyclic GMP-AMP synthase (cGAS) is best known as a cytosolic innate immune sensor critical for the outcome of infections, inflammatory diseases, and cancer. Here, we report that cGAS is primarily a chromatin-bound protein that inhibits DNA repair by HR, thereby accelerating genome destabilization, micronucleus generation, and cell death under conditions of genomic stress. This function is independent of the canonical STING-dependent innate immune activation and is physiologically relevant for irradiation-induced depletion of bone marrow cells in mice. Mechanistically, we demonstrate that inhibition of HR repair by cGAS is linked to its ability to self-oligomerize, causing compaction of bound template dsDNA into a higher-ordered state less amenable to strand invasion by RAD51-coated ssDNA filaments. This previously unknown role of cGAS has implications for understanding its involvement in genome instability-associated disorders including cancer.
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Affiliation(s)
- Hui Jiang
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA.,Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Swarupa Panda
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Ajinkya Kawale
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Richard M Hooy
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengshan Liang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA.,Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Nelson O Gekara
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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12
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Dilworth D, Gong F, Miller K, Nelson CJ. FKBP25 participates in DNA double-strand break repair. Biochem Cell Biol 2019; 98:42-49. [PMID: 30620620 PMCID: PMC7457334 DOI: 10.1139/bcb-2018-0328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
FK506-binding proteins (FKBPs) alter the conformation of proteins via cis-trans isomerization of prolyl-peptide bonds. While this activity can be demonstrated in vitro, the intractability of detecting prolyl isomerization events in cells has limited our understanding of the biological processes regulated by FKBPs. Here we report that FKBP25 is an active participant in the repair of DNA double-strand breaks (DSBs). FKBP25 influences DSB repair pathway choice by promoting homologous recombination (HR) and suppressing single-strand annealing (SSA). Consistent with this observation, cells depleted of FKBP25 form fewer Rad51 repair foci in response to etoposide and ionizing radiation, and they are reliant on the SSA repair factor Rad52 for viability. We find that FKBP25’s catalytic activity is required for promoting DNA repair, which is the first description of a biological function for this enzyme activity. Consistent with the importance of the FKBP catalytic site in HR, rapamycin treatment also impairs homologous recombination, and this effect is at least in part independent of mTor. Taken together these results identify FKBP25 as a component of the DNA DSB repair pathway.
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Affiliation(s)
- David Dilworth
- The Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Fade Gong
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712 USA
| | - Kyle Miller
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712 USA
| | - Christopher J Nelson
- The Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
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13
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The histone chaperone NAP1L3 is required for haematopoietic stem cell maintenance and differentiation. Sci Rep 2018; 8:11202. [PMID: 30046127 PMCID: PMC6060140 DOI: 10.1038/s41598-018-29518-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 07/12/2018] [Indexed: 01/04/2023] Open
Abstract
Nucleosome assembly proteins (NAPs) are histone chaperones with an important role in chromatin structure and epigenetic regulation of gene expression. We find that high gene expression levels of mouse Nap1l3 are restricted to haematopoietic stem cells (HSCs) in mice. Importantly, with shRNA or CRISPR-Cas9 mediated loss of function of mouse Nap1l3 and with overexpression of the gene, the number of colony-forming cells and myeloid progenitor cells in vitro are reduced. This manifests as a striking decrease in the number of HSCs, which reduces their reconstituting activities in vivo. Downregulation of human NAP1L3 in umbilical cord blood (UCB) HSCs impairs the maintenance and proliferation of HSCs both in vitro and in vivo. NAP1L3 downregulation in UCB HSCs causes an arrest in the G0 phase of cell cycle progression and induces gene expression signatures that significantly correlate with downregulation of gene sets involved in cell cycle regulation, including E2F and MYC target genes. Moreover, we demonstrate that HOXA3 and HOXA5 genes are markedly upregulated when NAP1L3 is suppressed in UCB HSCs. Taken together, our findings establish an important role for NAP1L3 in HSC homeostasis and haematopoietic differentiation.
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Charbonnel C, Rymarenko O, Da Ines O, Benyahya F, White CI, Butter F, Amiard S. The Linker Histone GH1-HMGA1 Is Involved in Telomere Stability and DNA Damage Repair. PLANT PHYSIOLOGY 2018; 177:311-327. [PMID: 29622687 PMCID: PMC5933147 DOI: 10.1104/pp.17.01789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/28/2018] [Indexed: 05/19/2023]
Abstract
Despite intensive searches, few proteins involved in telomere homeostasis have been identified in plants. Here, we used pull-down assays to identify potential telomeric interactors in the model plant species Arabidopsis (Arabidopsis thaliana). We identified the candidate protein GH1-HMGA1 (also known as HON4), an uncharacterized linker histone protein of the High Mobility Group Protein A (HMGA) family in plants. HMGAs are architectural transcription factors and have been suggested to function in DNA damage repair, but their precise biological roles remain unclear. Here, we show that GH1-HMGA1 is required for efficient DNA damage repair and telomere integrity in Arabidopsis. GH1-HMGA1 mutants exhibit developmental and growth defects, accompanied by ploidy defects, increased telomere dysfunction-induced foci, mitotic anaphase bridges, and degraded telomeres. Furthermore, mutants have a higher sensitivity to genotoxic agents such as mitomycin C and γ-irradiation. Our work also suggests that GH1-HMGA1 is involved directly in the repair process by allowing the completion of homologous recombination.
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Affiliation(s)
- Cyril Charbonnel
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | | | - Olivier Da Ines
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | - Fatiha Benyahya
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | - Falk Butter
- Institute of Molecular Biology, 455128 Mainz, Germany
| | - Simon Amiard
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
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15
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Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H. Crystal structure of the overlapping dinucleosome composed of hexasome and octasome. Science 2017; 356:205-208. [PMID: 28408607 DOI: 10.1126/science.aak9867] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/17/2017] [Indexed: 12/19/2022]
Abstract
Nucleosomes are dynamic entities that are repositioned along DNA by chromatin remodeling processes. A nucleosome repositioned by the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms the intermediate "overlapping dinucleosome." Here, we report the crystal structure of the overlapping dinucleosome, in which two nucleosomes are associated, at 3.14-angstrom resolution. In the overlapping dinucleosome structure, the unusual "hexasome" nucleosome, composed of the histone hexamer lacking one H2A-H2B dimer from the conventional histone octamer, contacts the canonical "octasome" nucleosome, and they intimately associate. Consequently, about 250 base pairs of DNA are left-handedly wrapped in three turns, without a linker DNA segment between the hexasome and octasome moieties. The overlapping dinucleosome structure may provide important information to understand how nucleosome repositioning occurs during the chromatin remodeling process.
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Affiliation(s)
- Daiki Kato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, 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
| | - 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
| | - Yuka Mizukami
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumi Saikusa
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Sam-Yong Park
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Atsushi Matsumoto
- National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Rintaro Inoue
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Osaka 590-0494, 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. .,Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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16
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Kobayashi W, Hosoya N, Machida S, Miyagawa K, Kurumizaka H. SYCP3 regulates strand invasion activities of RAD51 and DMC1. Genes Cells 2017; 22:799-809. [DOI: 10.1111/gtc.12513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/14/2017] [Indexed: 01/26/2023]
Affiliation(s)
- 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
| | - Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine; Graduate School of Medicine, The University of Tokyo; Tokyo 113-8655 Japan
| | - 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
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine; Graduate School of Medicine, The University of Tokyo; Tokyo 113-8655 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
- Institute for Medical-oriented Structural Biology; Waseda University; 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo 162-8480 Japan
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17
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Abstract
Eukaryotic genomes are packaged in chromatin. The higher-order organization of nucleosome core particles is controlled by the association of the intervening linker DNA with either the linker histone H1 or high mobility group box (HMGB) proteins. While H1 is thought to stabilize the nucleosome by preventing DNA unwrapping, the DNA bending imposed by HMGB may propagate to the nucleosome to destabilize chromatin. For metazoan H1, chromatin compaction requires its lysine-rich C-terminal domain, a domain that is buried between globular domains in the previously characterized yeast Saccharomyces cerevisiae linker histone Hho1p. Here, we discuss the functions of S. cerevisiae HMO1, an HMGB family protein unique in containing a terminal lysine-rich domain and in stabilizing genomic DNA. On ribosomal DNA (rDNA) and genes encoding ribosomal proteins, HMO1 appears to exert its role primarily by stabilizing nucleosome-free regions or "fragile" nucleosomes. During replication, HMO1 likewise appears to ensure low nucleosome density at DNA junctions associated with the DNA damage response or the need for topoisomerases to resolve catenanes. Notably, HMO1 shares with the mammalian linker histone H1 the ability to stabilize chromatin, as evidenced by the absence of HMO1 creating a more dynamic chromatin environment that is more sensitive to nuclease digestion and in which chromatin-remodeling events associated with DNA double-strand break repair occur faster; such chromatin stabilization requires the lysine-rich extension of HMO1. Thus, HMO1 appears to have evolved a unique linker histone-like function involving the ability to stabilize both conventional nucleosome arrays as well as DNA regions characterized by low nucleosome density or the presence of noncanonical nucleosomes.
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18
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Zhou W, Gao J, Ma J, Cao L, Zhang C, Zhu Y, Dong A, Shen WH. Distinct roles of the histone chaperones NAP1 and NRP and the chromatin-remodeling factor INO80 in somatic homologous recombination in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:397-410. [PMID: 27352805 DOI: 10.1111/tpj.13256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/24/2016] [Indexed: 05/10/2023]
Abstract
Homologous recombination (HR) of nuclear DNA occurs within the context of a highly complex chromatin structure. Despite extensive studies of HR in diverse organisms, mechanisms regulating HR within the chromatin context remain poorly elucidated. Here we investigate the role and interplay of the histone chaperones NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) and NAP1-RELATED PROTEIN (NRP) and the ATP-dependent chromatin-remodeling factor INOSITOL AUXOTROPHY80 (INO80) in regulating somatic HR in Arabidopsis thaliana. We show that simultaneous knockout of the four AtNAP1 genes and the two NRP genes in the sextuple mutant m123456-1 barely affects normal plant growth and development. Interestingly, compared with the respective AtNAP1 (m123-1 and m1234-1) or NRP (m56-1) loss-of-function mutants, the sextuple mutant m123456-1 displays an enhanced plant hypersensitivity to UV or bleomycin treatments. Using HR reporter constructs, we show that AtNAP1 and NRP act in parallel to synergistically promote somatic HR. Distinctively, the AtINO80 loss-of-function mutation (atino80-5) is epistatic to m56-1 in plant phenotype and telomere length but hypostatic to m56-1 in HR determinacy. Further analyses show that expression of HR machinery genes and phosphorylation of H2A.X (γ-H2A.X) are not impaired in the mutants. Collectively, our study indicates that NRP and AtNAP1 synergistically promote HR upstream of AtINO80-mediated chromatin remodeling after the formation of γ-H2A.X foci during DNA damage repair.
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Affiliation(s)
- Wangbin Zhou
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Juan Gao
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
- School of Life Sciences, Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Lin Cao
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Chi Zhang
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Yan Zhu
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Aiwu Dong
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Wen-Hui Shen
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
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19
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Panday A, Grove A. The high mobility group protein HMO1 functions as a linker histone in yeast. Epigenetics Chromatin 2016; 9:13. [PMID: 27030801 PMCID: PMC4812653 DOI: 10.1186/s13072-016-0062-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/16/2016] [Indexed: 12/18/2022] Open
Abstract
Background Eukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length. Histone H1 associates with the linker DNA to stabilize the higher-order chromatin structure and to modulate the ability of regulatory factors to access their nucleosomal targets. In Saccharomyces cerevisiae, the protein with greatest sequence similarity to H1 is Hho1p. However, during vegetative growth, hho1∆ cells do not show any discernible cell growth defects or the changes in bulk chromatin structure that are characteristic of chromatin from multicellular eukaryotes in which H1 is depleted. In contrast, the yeast high mobility group (HMGB) protein HMO1 has been reported to compact chromatin, as evidenced by increased nuclease sensitivity in hmo1∆ cells. HMO1 has an unusual domain architecture compared to vertebrate HMGB proteins in that the HMG domains are followed by a lysine-rich extension instead of an acidic domain. We address here the hypothesis that HMO1 serves the role of H1 in terms of chromatin compaction and that this function requires the lysine-rich extension. Results We show here that HMO1 fulfills this function of a linker histone. For histone H1, chromatin compaction requires its basic C-terminal domain, and we find that the same pertains to HMO1, as deletion of its C-terminal lysine-rich extension renders chromatin nuclease sensitive. On rDNA, deletion of both HMO1 and Hho1p is required for significantly increased nuclease sensitivity. Expression of human histone H1 completely reverses the nuclease sensitivity characteristic of chromatin isolated from hmo1∆ cells. While chromatin remodeling events associated with repair of DNA double-strand breaks occur faster in the more dynamic chromatin environment created by the hmo1 deletion, expression of human histone H1 results in chromatin remodeling and double-strand break repair similar to that observed in wild-type cells. Conclusion Our data suggest that S. cerevisiae HMO1 protects linker DNA from nuclease digestion, a property also characteristic of mammalian linker histone H1. Notably, association with HMO1 creates a less dynamic chromatin environment that depends on its lysine-rich domain. That HMO1 has linker histone function has implications for investigations of chromatin structure and function as well as for evolution of proteins with roles in chromatin compaction.
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Affiliation(s)
- Arvind Panday
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
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20
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Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H. Structure and function of human histone H3.Y nucleosome. Nucleic Acids Res 2016; 44:6127-41. [PMID: 27016736 PMCID: PMC5291245 DOI: 10.1093/nar/gkw202] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stable in vitro and in vivo. Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes.
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Affiliation(s)
- Tomoya Kujirai
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - 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
| | - 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
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, 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 Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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21
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RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat Commun 2016; 7:10548. [PMID: 26817820 PMCID: PMC4738357 DOI: 10.1038/ncomms10548] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 12/25/2015] [Indexed: 01/20/2023] Open
Abstract
Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells.
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22
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Machida S, Hayashida R, Takaku M, Fukuto A, Sun J, Kinomura A, Tashiro S, Kurumizaka H. Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T. Biochemistry 2016; 55:637-46. [DOI: 10.1021/acs.biochem.5b01126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Ryota Hayashida
- Laboratory
of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
- Institute
for Medical-oriented Structural Biology, Waseda University, 2-2
Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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23
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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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24
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Miller KE, Heald R. Glutamylation of Nap1 modulates histone H1 dynamics and chromosome condensation in Xenopus. ACTA ACUST UNITED AC 2015; 209:211-20. [PMID: 25897082 PMCID: PMC4411273 DOI: 10.1083/jcb.201412097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/25/2015] [Indexed: 01/05/2023]
Abstract
Nap1 is required for linker histone H1M-mediated mitotic chromosome condensation in Xenopus egg extracts, and glutamylation of Nap1 is required for proper deposition and turnover of H1M on chromatin during both interphase and mitosis. Linker histone H1 is required for mitotic chromosome architecture in Xenopus laevis egg extracts and, unlike core histones, exhibits rapid turnover on chromatin. Mechanisms regulating the recruitment, deposition, and dynamics of linker histones in mitosis are largely unknown. We found that the cytoplasmic histone chaperone nucleosome assembly protein 1 (Nap1) associates with the embryonic isoform of linker histone H1 (H1M) in egg extracts. Immunodepletion of Nap1 decreased H1M binding to mitotic chromosomes by nearly 50%, reduced H1M dynamics as measured by fluorescence recovery after photobleaching and caused chromosome decondensation similar to the effects of H1M depletion. Defects in H1M dynamics and chromosome condensation were rescued by adding back wild-type Nap1 but not a mutant lacking sites subject to posttranslational modification by glutamylation. Nap1 glutamylation increased the deposition of H1M on sperm nuclei and chromatin-coated beads, indicating that charge-shifting posttranslational modification of Nap1 contributes to H1M dynamics that are essential for higher order chromosome architecture.
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Affiliation(s)
- Kelly E Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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Kato D, Osakabe A, Tachiwana H, Tanaka H, Kurumizaka H. Human tNASP Promotes in Vitro Nucleosome Assembly with Histone H3.3. Biochemistry 2015; 54:1171-9. [DOI: 10.1021/bi501307g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daiki Kato
- Laboratory of Structural
Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, 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
| | - Hiroki Tanaka
- Laboratory of Structural
Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, 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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