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Li Y, Zhang H, Li X, Wu W, Zhu P. Cryo-ET study from in vitro to in vivo revealed a general folding mode of chromatin with two-start helical architecture. Cell Rep 2023; 42:113134. [PMID: 37708029 DOI: 10.1016/j.celrep.2023.113134] [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: 07/07/2022] [Revised: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
The organization and dynamics of chromatin fiber play crucial roles in regulating DNA accessibility for gene expression. Here we combine cryoelectron tomography (cryo-ET), sub-volume averaging, and 3D segmentation to visualize the in vitro and in vivo chromatin fibers folding by linker histone. We discover that an increased nucleosome repeat length and prolonged fiber length do not change the two-start helical architecture in reconstituted chromatin of homogeneous composition. Additionally, an isolated chromatin fiber with heterogeneous composition was observed, which includes short-range regions compatible with two-start helix. In vivo, sub-volume averaging reveals similar subunits of two-start helical architecture in transcriptionally inactive chromatin in frog erythrocyte nuclei. Strikingly, unambiguous DNA trajectories that displayed a zigzag pattern universally between alternate N/N+2 nucleosomes were further determined by cryo-ET with voltage phase plate. Therefore, these structural similarities suggest a general folding mode of chromatin induced by linker histone, and heterogeneous compositions mainly affect local conformation rather than changing the overall architecture.
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Affiliation(s)
- Yan Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China
| | - Haonan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyu Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Chromatin, stacked at the centromere. Nat Struct Mol Biol 2022; 29:288-290. [PMID: 35422518 DOI: 10.1038/s41594-022-00759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Role of Linker Histones in Chromatin Structural Organization. 2. Interaction with DNA and Nuclear Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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4
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Wu C, Travers A. Modelling and DNA topology of compact 2-start and 1-start chromatin fibres. Nucleic Acids Res 2019; 47:9902-9924. [PMID: 31219588 PMCID: PMC6765122 DOI: 10.1093/nar/gkz495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/15/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023] Open
Abstract
We have investigated the structure of the most compact 30-nm chromatin fibres by modelling those with 2-start or 1-start crossed-linker organisations. Using an iterative procedure we obtained possible structural solutions for fibres of the highest possible compaction permitted by physical constraints, including the helical repeat of linker DNA. We find that this procedure predicts a quantized nucleosome repeat length (NRL) and that only fibres with longer NRLs (≥197 bp) can more likely adopt the 1-start organisation. The transition from 2-start to 1-start fibres is consistent with reported differing binding modes of the linker histone. We also calculate that in 1-start fibres the DNA constrains more torsion (as writhe) than 2-start fibres with the same NRL and that the maximum constraint obtained is in accord with previous experimental results. We posit that the coiling of the fibre is driven by overtwisting of linker DNA which, in the most compact forms - for example, in echinoderm sperm and avian erythrocytes - could adopt a helical repeat of ∼10 bp/turn. We argue that in vivo the total twist of linker DNA could be modulated by interaction with other abundant chromatin-associated proteins and by epigenetic modifications of the C-terminal tail of linker histones.
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Affiliation(s)
- Chenyi Wu
- Molecular Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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5
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Starkova TY, Artamonova TO, Ermakova VV, Chikhirzhina EV, Khodorkovskii MA, Tomilin AN. The Profile of Post-translational Modifications of Histone H1 in Chromatin of Mouse Embryonic Stem Cells. Acta Naturae 2019; 11:82-91. [PMID: 31413884 PMCID: PMC6643340 DOI: 10.32607/20758251-2019-11-2-82-91] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 01/10/2023] Open
Abstract
Linker histone H1 is one of the main chromatin proteins which plays an important role in organizing eukaryotic DNA into a compact structure. There is data indicating that cell type-specific post-translational modifications of H1 modulate chromatin activity. Here, we compared histone H1 variants from NIH/3T3, mouse embryonic fibroblasts (MEFs), and mouse embryonic stem (ES) cells using matrix-assisted laser desorption/ ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS). We found significant differences in the nature and positions of the post-translational modifications (PTMs) of H1.3-H1.5 variants in ES cells compared to differentiated cells. For instance, methylation of K75 in the H1.2-1.4 variants; methylation of K108, K148, K151, K152 K154, K155, K160, K161, K179, and K185 in H1.1, as well as of K168 in H1.2; phosphorylation of S129, T146, T149, S159, S163, and S180 in H1.1, T180 in H1.2, and T155 in H1.3 were identified exclusively in ES cells. The H1.0 and H1.2 variants in ES cells were characterized by an enhanced acetylation and overall reduced expression levels. Most of the acetylation sites of the H1.0 and H1.2 variants from ES cells were located within their C-terminal tails known to be involved in the stabilization of the condensed chromatin. These data may be used for further studies aimed at analyzing the functional role played by the revealed histone H1 PTMs in the self-renewal and differentiation of pluripotent stem cells.
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Affiliation(s)
- T. Yu. Starkova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - T. O. Artamonova
- Peter the Great St.Petersburg Polytechnic University, Politekhnicheskaya Str. 29, St. Petersburg, 195251 , Russia
| | - V. V. Ermakova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - E. V. Chikhirzhina
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - M. A. Khodorkovskii
- Peter the Great St.Petersburg Polytechnic University, Politekhnicheskaya Str. 29, St. Petersburg, 195251 , Russia
| | - A. N. Tomilin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
- Saint Petersburg State University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
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6
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Chikhirzhina E, Starkova T, Polyanichko A. The Role of Linker Histones in Chromatin Structural Organization. 1. H1 Family Histones. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918060064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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7
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Arhondakis S, Varriale A. Distribution of Nucleosome-enriched Sequences of Human Sperm Chromatin Along Isochores. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2018; 3:54-60. [DOI: 10.14218/erhm.2018.00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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On possible role of DNA electrodynamics in chromatin regulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 134:50-54. [DOI: 10.1016/j.pbiomolbio.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022]
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9
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Cutter AR, Hayes JJ. Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochem Cell Biol 2016; 95:171-178. [PMID: 28177778 DOI: 10.1139/bcb-2016-0097] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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10
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Liquid-like behavior of chromatin. Curr Opin Genet Dev 2016; 37:36-45. [DOI: 10.1016/j.gde.2015.11.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022]
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11
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Flanagan TW, Files JK, Casano KR, George EM, Brown DT. Photobleaching studies reveal that a single amino acid polymorphism is responsible for the differential binding affinities of linker histone subtypes H1.1 and H1.5. Biol Open 2016; 5:372-80. [PMID: 26912777 PMCID: PMC4810752 DOI: 10.1242/bio.016733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mammals express six major somatic linker histone subtypes, all of which display dynamic binding to chromatin, characterized by transient binding at a given location followed by rapid translocation to a new site. Using photobleaching techniques, we systematically measured the exchange rate of all six mouse H1 subtypes to determine their relative chromatin-binding affinity. Two subtypes, H1.1 and H1.2, display binding affinities that are significantly lower than all other subtypes. Using in vitro mutagenesis, the differences in chromatin-binding affinities between H1.1 (lower binding affinity) and H1.5 (higher binding affinity) were mapped to a single amino acid polymorphism near the junction of the globular and C-terminal domains. Overexpression of H1.5 in density arrested fibroblasts did not affect cell cycle progression after release. By contrast, overexpression of H1.1 resulted in a more rapid progression through G1/S relative to control cells. These results provide structural insights into the proposed functional significance of linker histone heterogeneity. Summary: Mouse linker histone subtypes H1.1 and H1.5 bind to chromatin with different affinities due to a single amino acid polymorphism. Overexpression of H1.1 in fibroblasts accelerates cell cycle progression.
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Affiliation(s)
- Thomas W Flanagan
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jacob K Files
- Clinton High School, Clinton, MS 39056, USA Spring Hill College, Mobile, AL 36608, USA
| | | | - Eric M George
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA Department of Physiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David T Brown
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
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12
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Krajewski WA. On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function. Biochem Biophys Rep 2016; 5:492-501. [PMID: 28955857 PMCID: PMC5600426 DOI: 10.1016/j.bbrep.2016.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 01/10/2023] Open
Abstract
Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is 'translated' to the particular 'activating' or 'repressing' chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content - such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products) of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a 'polymer' of individual 'canonical' nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.
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Affiliation(s)
- Wladyslaw A Krajewski
- Institute of Developmental Biology of Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334 Russia
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13
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Nazarov I, Chekliarova I, Rychkov G, Ilatovskiy AV, Crane-Robinson C, Tomilin A. AFM studies in diverse ionic environments of nucleosomes reconstituted on the 601 positioning sequence. Biochimie 2015; 121:5-12. [PMID: 26586109 DOI: 10.1016/j.biochi.2015.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/09/2015] [Indexed: 01/02/2023]
Abstract
Atomic force microscopy (AFM) was used to study mononucleosomes reconstituted from a DNA duplex of 353 bp containing the strong 601 octamer positioning sequence, together with recombinant human core histone octamers. Three parameters were measured: 1) the length of DNA wrapped around the core histones; 2) the number of superhelical turns, calculated from the total angle through which the DNA is bent, and 3) the volume of the DNA-histone core. This approach allowed us to define in detail the structural diversity of nucleosomes caused by disassembly of the octasome to form subnucleosomal structures containing hexasomes, tetrasomes and disomes. At low ionic strength (TE buffer) and in the presence of physiological concentrations of monovalent cations, the majority of the particles were subnucleosomal, but physiological concentrations of bivalent cations resulted in about half of the nucleosomes being canonical octasomes in which the exiting DNA duplexes cross orthogonally. The dominance of this last species explains why bivalent but not monovalent cations can induce the initial step towards compaction and convergence of neighboring nucleosomes in nucleosomal arrays to form the chromatin fiber in the absence of linker histone. The observed nucleosome structural diversity may reflect the functional plasticity of nucleosomes under physiological conditions.
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Affiliation(s)
- Igor Nazarov
- Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia.
| | - Iana Chekliarova
- Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia
| | - Georgy Rychkov
- Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St.Petersburg Polytechnic University, Polytechnicheskaya 29, Saint-Petersburg, RF, 195251, Russia; Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, 188300, Russia
| | - Andrey V Ilatovskiy
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, 188300, Russia; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Colyn Crane-Robinson
- Biophysics Laboratories, St. Michael's Building, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Alexey Tomilin
- Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia
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14
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Abstract
Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.
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Affiliation(s)
- Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
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15
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Interaction of chromatin with a histone H1 containing swapped N- and C-terminal domains. Biosci Rep 2015; 35:BSR20150087. [PMID: 26182371 PMCID: PMC4613717 DOI: 10.1042/bsr20150087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/27/2015] [Indexed: 12/12/2022] Open
Abstract
The present study was to understand whether the globular or C-terminal linker histone domain is more important for its binding to chromatin. Using histone H1, with swapped domain orientation,
we found that both domains are equally important for nucleosome binding. Although the details of the structural involvement of histone H1 in the organization of the nucleosome are quite well understood, the sequential events involved in the recognition of its binding site are not as well known. We have used a recombinant human histone H1 (H1.1) in which the N- and C-terminal domains (NTD/CTD) have been swapped and we have reconstituted it on to a 208-bp nucleosome. We have shown that the swapped version of the protein is still able to bind to nucleosomes through its structurally folded wing helix domain (WHD); however, analytical ultracentrifuge analysis demonstrates its ability to properly fold the chromatin fibre is impaired. Furthermore, FRAP analysis shows that the highly dynamic binding association of histone H1 with the chromatin fibre is altered, with a severely decreased half time of residence. All of this suggests that proper binding of histone H1 to chromatin is determined by the simultaneous and synergistic binding of its WHD–CTD to the nucleosome.
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16
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Li G, Zhu P. Structure and organization of chromatin fiber in the nucleus. FEBS Lett 2015; 589:2893-904. [PMID: 25913782 DOI: 10.1016/j.febslet.2015.04.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 12/30/2022]
Abstract
Eukaryotic genomes are organized hierarchically into chromatin structures by histones. Despite extensive research for over 30 years, not only the fundamental structure of the 30-nm chromatin fiber is being debated, but the actual existence of such fiber remains hotly contested. In this review, we focus on the most recent progress in elucidating the structure of the 30-nm fiber upon in vitro reconstitution, and its possible organization inside the nucleus. In addition, we discuss the roles of linker histone H1 as well as the importance of specific nucleosome-nucleosome interactions in the formation of the 30-nm fiber. Finally, we discuss the involvement of structural variations and epigenetic mechanisms available for the regulation of this chromatin form.
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Affiliation(s)
- Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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