1
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Dhahri H, Saintilnord WN, Chandler D, Fondufe-Mittendorf YN. Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer. Int J Mol Sci 2024; 25:6788. [PMID: 38928493 PMCID: PMC11203562 DOI: 10.3390/ijms25126788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone-histone or histone-DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. These structural modifications alter chromatin compaction and accessibility of DNA by transcription factors and other regulatory proteins to influence gene regulatory processes such as DNA damage and repair, as well as transcriptional activation or repression. Histone variants can also generate a unique interactome composed of histone chaperones and chromatin remodeling complexes. Any of these perturbations can contribute to cellular plasticity and the progression of human diseases. Here, we focus on a frequently overlooked group of histone variants lying within the four human histone gene clusters and their contribution to breast cancer.
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Affiliation(s)
- Hejer Dhahri
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA or (H.D.); (W.N.S.)
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
| | - Wesley N. Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA or (H.D.); (W.N.S.)
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- The Edison Family Center of Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Darrell Chandler
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
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2
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Whiwon L, Salma S, Daniel A, Stephanie L, Marc C, Cherith S, Abby T, Angela S, Robin H, Yvonne B. Patient-facing digital tools for delivering genetic services: a systematic review. J Med Genet 2023; 60:1-10. [PMID: 36137613 DOI: 10.1136/jmg-2022-109085] [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: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 01/24/2023]
Abstract
This study systematically reviewed the literature on the impact of digital genetics tools on patient care and system efficiencies. MEDLINE and Embase were searched for articles published between January 2010 and March 2021. Studies evaluating the use of patient-facing digital tools in the context of genetic service delivery were included. Two reviewers screened and extracted patient-reported and system-focused outcomes from each study. Data were synthesised using a descriptive approach. Of 3226 unique studies identified, 87 were included. A total of 70 unique digital tools were identified. As a result of using digital tools, 84% of studies reported a positive outcome in at least one of the following patient outcomes: knowledge, psychosocial well-being, behavioural/management changes, family communication, decision-making or level of engagement. Digital tools improved workflow and efficiency for providers and reduced the amount of time they needed to spend with patients. However, we identified a misalignment between study purpose and patient-reported outcomes measured and a lack of tools that encompass the entire genetic counselling and testing trajectory. Given increased demand for genetic services and the shift towards virtual care, this review provides evidence that digital tools can be used to efficiently deliver patient-centred care. Future research should prioritise development, evaluation and implementation of digital tools that can support the entire patient trajectory across a range of clinical settings. PROSPERO registration numberCRD42020202862.
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Affiliation(s)
- Lee Whiwon
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shickh Salma
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Assamad Daniel
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Luca Stephanie
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Clausen Marc
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Somerville Cherith
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Tafler Abby
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Shaw Angela
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Hayeems Robin
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Bombard Yvonne
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
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3
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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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4
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Tessadori F, Duran K, Knapp K, Fellner M, Smithson S, Beleza Meireles A, Elting MW, Waisfisz Q, O’Donnell-Luria A, Nowak C, Douglas J, Ronan A, Brunet T, Kotzaeridou U, Svihovec S, Saenz MS, Thiffault I, Del Viso F, Devine P, Rego S, Tenney J, van Haeringen A, Ruivenkamp CA, Koene S, Robertson SP, Deshpande C, Pfundt R, Verbeek N, van de Kamp JM, Weiss JM, Ruiz A, Gabau E, Banne E, Pepler A, Bottani A, Laurent S, Guipponi M, Bijlsma E, Bruel AL, Sorlin A, Willis M, Powis Z, Smol T, Vincent-Delorme C, Baralle D, Colin E, Revencu N, Calpena E, Wilkie AO, Chopra M, Cormier-Daire V, Keren B, Afenjar A, Niceta M, Terracciano A, Specchio N, Tartaglia M, Rio M, Barcia G, Rondeau S, Colson C, Bakkers J, Mace PD, Bicknell LS, van Haaften G, van Haaften G. Recurrent de novo missense variants across multiple histone H4 genes underlie a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:750-758. [PMID: 35202563 PMCID: PMC9069069 DOI: 10.1016/j.ajhg.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Chromatin is essentially an array of nucleosomes, each of which consists of the DNA double-stranded fiber wrapped around a histone octamer. This organization supports cellular processes such as DNA replication, DNA transcription, and DNA repair in all eukaryotes. Human histone H4 is encoded by fourteen canonical histone H4 genes, all differing at the nucleotide level but encoding an invariant protein. Here, we present a cohort of 29 subjects with de novo missense variants in six H4 genes (H4C3, H4C4, H4C5, H4C6, H4C9, and H4C11) identified by whole-exome sequencing and matchmaking. All individuals present with neurodevelopmental features of intellectual disability and motor and/or gross developmental delay, while non-neurological features are more variable. Ten amino acids are affected, six recurrently, and are all located within the H4 core or C-terminal tail. These variants cluster to specific regions of the core H4 globular domain, where protein-protein interactions occur with either other histone subunits or histone chaperones. Functional consequences of the identified variants were evaluated in zebrafish embryos, which displayed abnormal general development, defective head organs, and reduced body axis length, providing compelling evidence for the causality of the reported disorder(s). While multiple developmental syndromes have been linked to chromatin-associated factors, missense-bearing histone variants (e.g., H3 oncohistones) are only recently emerging as a major cause of pathogenicity. Our findings establish a broader involvement of H4 variants in developmental syndromes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 Utrecht, the Netherlands.
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5
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Zhou M, Malhan N, Ahkami AH, Engbrecht K, Myers G, Dahlberg J, Hollingsworth J, Sievert JA, Hutmacher R, Madera M, Lemaux PG, Hixson KK, Jansson C, Paša-Tolić L. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. Methods 2020; 184:29-39. [DOI: 10.1016/j.ymeth.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
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6
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Liu WH, Zheng J, Feldman JL, Klein MA, Kuznetsov VI, Peterson CL, Griffin PR, Denu JM. Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. Nat Commun 2020; 11:5244. [PMID: 33067423 PMCID: PMC7568541 DOI: 10.1038/s41467-020-19018-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022] Open
Abstract
The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity.
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Affiliation(s)
- Wallace H Liu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jie Zheng
- Department of Molecular Medicine, Scripps Research Florida, Jupiter, FL, 33458, USA
| | - Jessica L Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Mark A Klein
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Vyacheslav I Kuznetsov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Scripps Research Florida, Jupiter, FL, 33458, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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7
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Abstract
Histone proteins regulate cellular factors’ accessibility to DNA, and histone dosage has previously been linked with DNA damage susceptibility and efficiency of DNA repair pathways. Surplus histones are known to impede the DNA repair process by interfering with the homologous recombination-mediated DNA repair in Saccharomyces cerevisiae. Here, we discuss the recent finding of association of methyl methanesulfonate (MMS) resistance with the reduced histone H4 gene dosage in the pathogenic yeast Candida glabrata. We have earlier shown that while the low histone H3 gene dosage led to MMS susceptibility, the lack of two H4-encoding ORFs, CgHHF1 and CgHHF2, led to resistance to MMS-induced DNA damage. This resistance was linked with a higher rate of homologous recombination (HR). Taking these findings further, we review the interactome analysis of histones H3 and H4 in C. glabrata. We also report that the arginine residue present at the 95th position in the C-terminal tail of histone H4 protein is required for complementation of the MMS resistance in the Cghhf1Δhhf2Δ mutant, thereby pointing out a probable role of this residue in association with HR factors. Additionally, we present evidence that reduction in H4 protein levels may constitute an important part of varied stress responses in C. glabrata. Altogether, we present an overview of histone H4 dosage, HR-mediated repair of damaged DNA and stress resistance in this opportunistic human fungal pathogen.
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8
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Long M, Sun X, Shi W, Yanru A, Leung STC, Ding D, Cheema MS, MacPherson N, Nelson CJ, Ausio J, Yan Y, Ishibashi T. A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. Nucleic Acids Res 2019; 47:8399-8409. [PMID: 31219579 PMCID: PMC6895281 DOI: 10.1093/nar/gkz547] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Histone variants, present in various cell types and tissues, are known to exhibit different functions. For example, histone H3.3 and H2A.Z are both involved in gene expression regulation, whereas H2A.X is a specific variant that responds to DNA double-strand breaks. In this study, we characterized H4G, a novel hominidae-specific histone H4 variant. We found that H4G is expressed in a variety of human cell lines and exhibit tumor-stage dependent overexpression in tissues from breast cancer patients. We found that H4G localized primarily to the nucleoli of the cell nucleus. This localization was controlled by the interaction of the alpha-helix 3 of the histone fold motif with a histone chaperone, nucleophosmin 1. In addition, we found that modulating H4G expression affects rRNA expression levels, protein synthesis rates and cell-cycle progression. Our data suggest that H4G expression alters nucleolar chromatin in a way that enhances rDNA transcription in breast cancer tissues.
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Affiliation(s)
- Mengping Long
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Xulun Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Wenjin Shi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - An Yanru
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Sophia T C Leung
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Dongbo Ding
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Nicol MacPherson
- Department of Medical Oncology, BC Cancer Vancouver Island Centre, Victoria, BC V8R 6V5, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Yan Yan
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
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9
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Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H. Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Nucleic Acids Res 2019; 46:10007-10018. [PMID: 30053102 PMCID: PMC6212774 DOI: 10.1093/nar/gky661] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/11/2018] [Indexed: 01/09/2023] Open
Abstract
Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.
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Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Masae Ikura
- Laboratory of Chromatin Regulatory Network, Department of Genome Biology, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Risa Fujita
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mamiko Noda
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Wataru Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,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
| | - 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
| | - Lin Shi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Masayuki Kusakabe
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, 468-1 Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, 468-1 Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, 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
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Genome Biology, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,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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10
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Abstract
The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes. Instead of discrete multimers, in vivo data suggest assembly of “nucleosomes” of variable size, consisting of multiples of dimers, which are able to induce repression of transcription. Based on these data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into “endless” hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, which are expected to be unable to assemble into hypernucleosomes. Finally, we identify atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar to the tails of eukaryotic histones, which are subject to post-translational modification. Based on the expected characteristics of these archaeal histones, we discuss possibilities of involvement of histones in archaeal transcription regulation. Both Archaea and eukaryotes express histones, but whereas the tertiary structure of histones is conserved, the quaternary structure of histone–DNA complexes is very different. In a recent study, the crystal structure of the archaeal hypernucleosome was revealed to be an “endless” core of interacting histones that wraps the DNA around it in a left-handed manner. The ability to form a hypernucleosome is likely determined by dimer–dimer interactions as well as stacking interactions between individual layers of the hypernucleosome. We analyzed a wide variety of archaeal histones and found that most but not all histones possess residues able to facilitate hypernucleosome formation. Among these are histones with truncated termini or extended histone tails. Based on our analysis, we propose several possibilities of archaeal histone involvement in transcription regulation.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Clara van Emmerik
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Hugo van Ingen
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- * E-mail:
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11
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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12
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018; 57:9734-9738. [DOI: 10.1002/anie.201804707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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13
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Perišić O, Schlick T. Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment. J Phys Chem B 2017; 121:7823-7832. [PMID: 28732449 DOI: 10.1021/acs.jpcb.7b04917] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The linker histone (LH), an auxiliary protein that can bind to chromatin and interact with the linker DNA to form stem motifs, is a key element of chromatin compaction. By affecting the chromatin condensation level, it also plays an active role in gene expression. However, the presence and variable concentration of LH in chromatin fibers with different DNA linker lengths indicate that its folding and condensation are highly adaptable and dependent on the immediate nucleosome environment. Recent experimental studies revealed that the behavior of LH in mononucleosomes markedly differs from that in small nucleosome arrays, but the associated mechanism is unknown. Here we report a structural analysis of the behavior of LH in mononucleosomes and oligonucleosomes (2-6 nucleosomes) using mesoscale chromatin simulations. We show that the adapted stem configuration heavily depends on the strength of electrostatic interactions between LH and its parental DNA linkers, and that those interactions tend to be asymmetric in small oligonucleosome systems. Namely, LH in oligonucleosomes dominantly interacts with one DNA linker only, as opposed to mononucleosomes where LH has similar interactions with both linkers and forms a highly stable nucleosome stem. Although we show that the LH condensation depends sensitively on the electrostatic interactions with entering and exiting DNA linkers, other interactions, especially by nonparental cores and nonparental linkers, modulate the structural condensation by softening LH and thus making oligonucleosomes more flexible, in comparison to to mono- and dinucleosomes. We also find that the overall LH/chromatin interactions sensitively depend on the linker length because the linker length determines the maximal nucleosome stem length. For mononucleosomes with DNA linkers shorter than LH, LH condenses fully, while for DNA linkers comparable or longer than LH, the LH extension in mononucleosomes strongly follows the length of DNA linkers, unhampered by neighboring linker histones. Thus, LH is more condensed for mononucleosomes with short linkers, compared to oligonucleosomes, and its orientation is variable and highly environment-dependent. More generally, the work underscores the agility of LH whose folding dynamics critically controls genomic packaging and gene expression.
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Affiliation(s)
- Ognjen Perišić
- Big Blue Genomics , Vojvode Brane 32, 11000 Belgrade, Serbia
| | - Tamar Schlick
- Department of Chemistry, New York University , 1001 Silver, 100 Washington Square East, New York, New York 10003, United States.,Courant Institute of Mathematical Sciences, New York University , 251 Mercer Street, New York, New York 10012, United States
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14
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Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 2017; 18:141-158. [PMID: 28053344 DOI: 10.1038/nrm.2016.159] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The association of histones with specific chaperone complexes is important for their folding, oligomerization, post-translational modification, nuclear import, stability, assembly and genomic localization. In this way, the chaperoning of soluble histones is a key determinant of histone availability and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin.
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Affiliation(s)
- Colin M Hammond
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Caroline B Strømme
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Hongda Huang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
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15
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Cureau N, AlJahdali N, Vo N, Carbonero F. Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives. Epigenomics 2016; 8:1259-73. [DOI: 10.2217/epi-2016-0057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human microbiota and epigenetic processes have both been shown to play a crucial role in health and disease. However, there is extremely scarce information on epigenetic modulation of microbiota members except for a few pathogens. Mainly DNA adenine methylation has been described extensively in modulating the virulence of pathogenic bacteria in particular. It would thus appear likely that such mechanisms are widespread for most bacterial members of the microbiota. This review will present briefly the current knowledge on epigenetic processes in bacteria, give examples of known methylation processes in microbial members of the human microbiota and summarize the knowledge on regulation of host epigenetic processes by the human microbiota.
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Affiliation(s)
- Natacha Cureau
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
| | - Nesreen AlJahdali
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
| | - Nguyen Vo
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
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16
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Zhou Q, Abraham AD, Li L, Babalmorad A, Bagby S, Arcaroli JJ, Hansen RJ, Valeriote FA, Gustafson DL, Schaack J, Messersmith WA, LaBarbera DV. Topoisomerase IIα mediates TCF-dependent epithelial-mesenchymal transition in colon cancer. Oncogene 2016; 35:4990-9. [PMID: 26947016 PMCID: PMC5036162 DOI: 10.1038/onc.2016.29] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/16/2015] [Accepted: 01/06/2016] [Indexed: 12/23/2022]
Abstract
Aberrant T-cell factor (TCF) transcription is implicated in the majority of colorectal cancers (CRCs). TCF transcription induces epithelial–mesenchymal transition (EMT), promoting a tumor-initiating cell (TIC) phenotype characterized by increased proliferation, multidrug resistance (MDR), invasion and metastasis. The data presented herein characterize topoisomerase IIα (TopoIIα) as a required component of TCF transcription promoting EMT. Using chromatin immunoprecipitation (ChIP) and protein co-immunoprecipitation (co-IP) studies, we show that TopoIIα forms protein–protein interactions with β-catentin and TCF4 and interacts with Wnt response elements (WREs) and promoters of direct target genes of TCF transcription, including: MYC, vimentin, AXIN2 and LEF1. Moreover, both TopoIIα and TCF4 ChIP with the N-cadherin promoter, which is a new discovery indicating that TCF transcription may directly regulate N-cadherin expression. TopoIIα N-terminal ATP-competitive inhibitors, exemplified by the marine alkaloid neoamphimedine (neo), block TCF activity in vitro and in vivo. Neo effectively inhibits TopoIIα and TCF4 from binding WREs/promoter sites, whereas protein–protein interactions remain intact. Neo inhibition of TopoIIα-dependent TCF transcription also correlates with significant antitumor effects in vitro and in vivo, including the reversion of EMT, the loss of TIC-mediated clonogenic colony formation, and the loss of cell motility and invasion. Interestingly, non-ATP-competitive inhibitors of TopoIIα, etoposide and merbarone, were ineffective at preventing TopoIIα-dependent TCF transcription. Thus, we propose that TopoIIα participation in TCF transcription may convey a mechanism of MDR to conventional TopoIIα inhibitors. However, our results indicate that TopoIIα N-terminal ATP-binding sites remain conserved and available for drug targeting. This article defines a new strategy for targeted inhibition of TCF transcription that may lead to effective therapies for the treatment of CRC and potentially other Wnt-dependent cancers.
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Affiliation(s)
- Q Zhou
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - A D Abraham
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L Li
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - A Babalmorad
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - S Bagby
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J J Arcaroli
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R J Hansen
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - F A Valeriote
- Colorado State University, Flint Animal Cancer Center, Fort Collins, CO, USA
| | - D L Gustafson
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Schaack
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Josephine Ford Cancer Center, Henry Ford Health Systems, Detroit, MI, USA
| | - W A Messersmith
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - D V LaBarbera
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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17
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Dahlin JL, Chen X, Walters MA, Zhang Z. Histone-modifying enzymes, histone modifications and histone chaperones in nucleosome assembly: Lessons learned from Rtt109 histone acetyltransferases. Crit Rev Biochem Mol Biol 2014; 50:31-53. [PMID: 25365782 DOI: 10.3109/10409238.2014.978975] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During DNA replication, nucleosomes ahead of replication forks are disassembled to accommodate replication machinery. Following DNA replication, nucleosomes are then reassembled onto replicated DNA using both parental and newly synthesized histones. This process, termed DNA replication-coupled nucleosome assembly (RCNA), is critical for maintaining genome integrity and for the propagation of epigenetic information, dysfunctions of which have been implicated in cancers and aging. In recent years, it has been shown that RCNA is carefully orchestrated by a series of histone modifications, histone chaperones and histone-modifying enzymes. Interestingly, many features of RCNA are also found in processes involving DNA replication-independent nucleosome assembly like histone exchange and gene transcription. In yeast, histone H3 lysine K56 acetylation (H3K56ac) is found in newly synthesized histone H3 and is critical for proper nucleosome assembly and for maintaining genomic stability. The histone acetyltransferase (HAT) regulator of Ty1 transposition 109 (Rtt109) is the sole enzyme responsible for H3K56ac in yeast. Much research has centered on this particular histone modification and histone-modifying enzyme. This Critical Review summarizes much of our current understanding of nucleosome assembly and highlights many important insights learned from studying Rtt109 HATs in fungi. We highlight some seminal features in nucleosome assembly conserved in mammalian systems and describe some of the lingering questions in the field. Further studying fungal and mammalian chromatin assembly may have important public health implications, including deeper understandings of human cancers and aging as well as the pursuit of novel anti-fungal therapies.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine , Rochester, MN , USA
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18
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The C terminus of the histone chaperone Asf1 cross-links to histone H3 in yeast and promotes interaction with histones H3 and H4. Mol Cell Biol 2012. [PMID: 23184661 DOI: 10.1128/mcb.01053-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The central histone H3/H4 chaperone Asf1 comprises a highly conserved globular core and a divergent C-terminal tail. While the function and structure of the Asf1 core are well known, the function of the tail is less well understood. Here, we have explored the role of the yeast (yAsf1) and human (hAsf1a and hAsf1b) Asf1 tails in Saccharomyces cerevisiae. We show, using a photoreactive, unnatural amino acid, that Asf1 tail residue 210 cross-links to histone H3 in vivo and, further, that loss of C-terminal tail residues 211 to 279 weakens yAsf1-histone binding affinity in vitro nearly 200-fold. Via several yAsf1 C-terminal truncations and yeast-human chimeric proteins, we found that truncations at residue 210 increase transcriptional silencing and that the hAsf1a tail partially substitutes for full-length yAsf1 with respect to silencing but that full-length hAsf1b is a better overall substitute for full-length yAsf1. In addition, we show that the C-terminal tail of Asf1 is phosphorylated at T270 in yeast. Loss of this phosphorylation site does not prevent coimmunoprecipitation of yAsf1 and Rad53 from yeast extracts, whereas amino acid residue substitutions at the Asf1-histone H3/H4 interface do. Finally, we show that residue substitutions in yAsf1 near the CAF-1/HIRA interface also influence yAsf1's function in silencing.
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19
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Liu WH, Roemer SC, Port AM, Churchill MEA. CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA. Nucleic Acids Res 2012; 40:11229-39. [PMID: 23034810 PMCID: PMC3526290 DOI: 10.1093/nar/gks906] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approaches using full-length proteins in the budding yeast system. We find that the C-terminal tail of Asf1 enhances the interaction of Asf1 with CAF-1. Surprisingly, although H3/H4 also enhances the interaction of Asf1 with the CAF-1 subunit Cac2, H3/H4 forms a tight complex with CAF-1 exclusive of Asf1, with an affinity weaker than Asf1–H3/H4 or H3/H4–DNA interactions. Unlike Asf1, monomeric CAF-1 binds to multiple H3/H4 dimers, which ultimately promotes the formation of (H3/H4)2 tetramers on DNA. Thus, transition of H3/H4 from the Asf1-associated dimer to the DNA-associated tetramer is promoted by CAF-1-induced H3/H4 oligomerization.
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Affiliation(s)
- Wallace H Liu
- Department of Pharmacology, University of Colorado School of Medicine, Mail Stop 8303, PO Box 6511, Aurora, CO 80045, USA
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