Assembly and Disassembly of Nucleosome Core Particles Containing Histone Variants by Human Nucleosome Assembly Protein I

ABSTRACT Histone variants play important roles in the maintenance and regulation of the chromatin structure. In order to characterize the biochemical properties of the chromatin structure containing histone variants, we investigated the dynamic status of nucleosome core particles (NCPs) that were assembled with recombinant histones. We found that in the presence of nucleosome assembly protein I (NAP-I), a histone chaperone, H2A-Barr body deficient (H2A.Bbd) confers the most flexible nucleosome structure among the mammalian histone H2A variants known thus far. NAP-I mediated the efficient assembly and disassembly of the H2A.Bbd-H2B dimers from NCPs. This reaction was accomplished more efficiently when the NCPs contained H3.3, a histone H3 variant known to be localized in the active chromatin, than when the NCPs contained the canonical H3. These observations indicate that the histone variants H2A.Bbd and H3.3 are involved in the formation and maintenance of the active chromatin structure. We also observed that acidic histone binding proteins, TAF-I/SET and B23.1, demonstrated dimer assembly and disassembly activity, but the efficiency of their activity was considerably lower than that of NAP-I. Thus, both the acidic nature of NAP-I and its other functional structure(s) may be essential to mediate the assembly and disassembly of the dimers in NCPs.

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Reconstitution of native-like nucleosome core particles from reversed-phase-HPLC-fractionated histones

Biochemical Journal ◽

10.1042/bj3280409 ◽

1997 ◽

Vol 328 (2) ◽

pp. 409-414 ◽

Cited By ~ 8

Author(s):

C. Susan MOORE ◽

Philip RICE ◽

Maya ISKANDAR ◽

Juan AUSIÓ

Keyword(s):

Random Sequence ◽

Histone Variants ◽

Structural Features ◽

Reversed Phase ◽

Reversed Phase Hplc ◽

Nucleosome Core ◽

Biological Source ◽

Nucleosome Core Particles ◽

Core Histones ◽

Core Particles

We have reconstituted nucleosome core particles from reversed-phase-HPLC-purified chicken erythrocyte core histones and 145 bp random-sequence DNA fragments. Characterization of the resulting nucleoprotein complexes by sedimentation velocity, CD and DNase I footprinting showed that they are structurally indistinguishable from native nucleosome core particles. Furthermore, we have shown that the ability to reproduce these native-like structural features in these reconstituted nucleosome core particles is basically independent of the biological source or the method used (i.e. salt versus acid) for the extraction of histones before their HPLC fractionation. The usefulness and relevance of this approach for the reconstitution of native-like chromatin structures from histone types (histone variants/post-translationally modified histones), which are usually available only in relatively small amounts, is discussed.

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Histone tails decrease N7-methyl-2′-deoxyguanosine depurination and yield DNA–protein cross-links in nucleosome core particles and cells

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1813338115 ◽

2018 ◽

Vol 115 (48) ◽

pp. E11212-E11220 ◽

Cited By ~ 12

Author(s):

Kun Yang ◽

Daeyoon Park ◽

Natalia Y. Tretyakova ◽

Marc M. Greenberg

Keyword(s):

Alkylating Agents ◽

Histone Variants ◽

Site Formation ◽

Abasic Site ◽

Histone Tails ◽

Nucleosome Core ◽

Nucleosome Core Particles ◽

Cross Links ◽

Positively Charged ◽

Core Particles

Monofunctional alkylating agents preferentially react at the N7 position of 2′-deoxyguanosine in duplex DNA. Methylated DNA, such as that produced by methyl methanesulfonate (MMS) and temozolomide, exists for days in organisms. The predominant consequence of N7-methyl-2′-deoxyguanosine (MdG) is widely believed to be abasic site (AP) formation via hydrolysis, a process that is slow in free DNA. Examination of MdG reactivity within nucleosome core particles (NCPs) provided two general observations. MdG depurination rate constants are reduced in NCPs compared with when the identical DNA sequence is free in solution. The magnitude of the decrease correlates with proximity to the positively charged histone tails, and experiments in NCPs containing histone variants reveal that positively charged amino acids are responsible for the decreased rate of abasic site formation from MdG. In addition, the lysine-rich histone tails form DNA–protein cross-links (DPCs) with MdG. Cross-link formation is reversible and is ascribed to nucleophilic attack at the C8 position of MdG. DPC and retarded abasic site formation are observed in NCPs randomly damaged by MMS, indicating that these are general processes. Histone–MdG cross-links were also detected by mass spectrometry in chromatin isolated from V79 Chinese hamster lung cells treated with MMS. The formation of DPCs following damage by a monofunctional alkylating agent has not been reported previously. These observations reveal the possibility that such DPCs may contribute to the cytotoxicity of monofunctional alkylating agents, such as MMS, N-methyl-N-nitrosourea, and temozolomide.

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Binding of C-reactive protein to chromatin and nucleosome core particles. A possible physiological role of C-reactive protein.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)39873-3 ◽

1984 ◽

Vol 259 (11) ◽

pp. 7311-7316 ◽

Cited By ~ 13

Author(s):

F A Robey ◽

K D Jones ◽

T Tanaka ◽

T Y Liu

Keyword(s):

Physiological Role ◽

C Reactive Protein ◽

Nucleosome Core ◽

Reactive Protein ◽

Nucleosome Core Particles ◽

Core Particles

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Phosphorylation within Intrinsic Disordered Region Discriminates Histone Variant macroH2A1 Splicing Isoforms—macroH2A1.1 and macroH2A1.2

Biology ◽

10.3390/biology10070659 ◽

2021 ◽

Vol 10 (7) ◽

pp. 659

Author(s):

Sebastiano Giallongo ◽

Oriana Lo Re ◽

Gabriela Lochmanová ◽

Luca Parca ◽

Francesco Petrizzelli ◽

...

Keyword(s):

Fluorescent Protein ◽

Regulatory Element ◽

Histone Variants ◽

Histone H2a ◽

Human Hepatoma Cells ◽

Nucleosome Core ◽

Intrinsically Disordered ◽

Splicing Isoforms ◽

The Impact

Background: Gene expression in eukaryotic cells can be governed by histone variants, which replace replication-coupled histones, conferring unique chromatin properties. MacroH2A1 is a histone H2A variant containing a domain highly similar to H2A and a large non-histone (macro) domain. MacroH2A1, in turn, is present in two alternatively exon-spliced isoforms: macroH2A1.1 and macroH2A1.2, which regulate cell plasticity and proliferation in a remarkably distinct manner. The N-terminal and the C-terminal tails of H2A histones stem from the nucleosome core structure and can be target sites for several post-translational modifications (PTMs). MacroH2A1.1 and macroH2A1.2 isoforms differ only in a few amino acids and their ability to bind NAD-derived metabolites, a property allegedly conferring their different functions in vivo. Some of the modifications on the macroH2A1 variant have been identified, such as phosphorylation (T129, S138) and methylation (K18, K123, K239). However, no study to our knowledge has analyzed extensively, and in parallel, the PTM pattern of macroH2A1.1 and macroH2A1.2 in the same experimental setting, which could facilitate the understanding of their distinct biological functions in health and disease. Methods: We used a mass spectrometry-based approach to identify the sites for phosphorylation, acetylation, and methylation in green fluorescent protein (GFP)-tagged macroH2A1.1 and macroH2A1.2 expressed in human hepatoma cells. The impact of selected PTMs on macroH2A1.1 and macroH2A1.2 structure and function are demonstrated using computational analyses. Results: We identified K7 as a new acetylation site in both macroH2A1 isoforms. Quantitative comparison of histone marks between the two isoforms revealed significant differences in the levels of phosphorylated T129 and S170. Our computational analysis provided evidence that the phosphorylation status in the intrinsically disordered linker region in macroH2A1 isoforms might represent a key regulatory element contributing to their distinct biological responses. Conclusions: Taken together, our results report different PTMs on the two macroH2A1 splicing isoforms as responsible for their distinct features and distribution in the cell.

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Damage Control of DNA in Nucleosome Core Particles

Chemistry & Biology ◽

10.1016/s1074-5521(02)00128-x ◽

2002 ◽

Vol 9 (4) ◽

pp. 399 ◽

Cited By ~ 5

Author(s):

Nicholas J Turro

Keyword(s):

Damage Control ◽

Nucleosome Core ◽

Nucleosome Core Particles ◽

Core Particles

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Computer Modeling Reveals that Modifications of the Histone Tail Charges Define Salt-Dependent Interaction of the Nucleosome Core Particles

Biophysical Journal ◽

10.1016/j.bpj.2008.10.073 ◽

2009 ◽

Vol 96 (6) ◽

pp. 2082-2094 ◽

Cited By ~ 25

Author(s):

Ye Yang ◽

Alexander P. Lyubartsev ◽

Nikolay Korolev ◽

Lars Nordenskiöld

Keyword(s):

Computer Modeling ◽

Histone Tail ◽

Nucleosome Core ◽

Nucleosome Core Particles ◽

Dependent Interaction ◽

Core Particles

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Polyamines and acetylpolyamines increase the stability and alter the conformation of nucleosome core particles

Biochemistry ◽

10.1021/bi00386a058 ◽

1987 ◽

Vol 26 (12) ◽

pp. 3643-3649 ◽

Cited By ~ 54

Author(s):

James E. Morgan ◽

James W. Blankenship ◽

Harry R. Matthews

Keyword(s):

Nucleosome Core ◽

Nucleosome Core Particles ◽

The Stability ◽

Core Particles

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Assembly states of the nucleosome assembly protein 1 (NAP-1) revealed by sedimentation velocity and non-denaturing MS

Biochemical Journal ◽

10.1042/bj20102063 ◽

2011 ◽

Vol 436 (1) ◽

pp. 101-112 ◽

Cited By ~ 15

Author(s):

Masanori Noda ◽

Susumu Uchiyama ◽

Adam R. McKay ◽

Akihiro Morimoto ◽

Shigeki Misawa ◽

...

Keyword(s):

Protein Interactions ◽

Electrostatic Interactions ◽

Analytical Ultracentrifugation ◽

Three Dimensional ◽

Sedimentation Velocity ◽

Dimensional Structure ◽

Histone H2a ◽

Nucleosome Assembly ◽

Nucleosome Assembly Protein ◽

Nucleosome Assembly Protein 1

Proteins often exist as ensembles of interconverting states in solution which are often difficult to quantify. In the present manuscript we show that the combination of MS under nondenaturing conditions and AUC-SV (analytical ultracentrifugation sedimentation velocity) unambiguously clarifies a distribution of states and hydrodynamic shapes of assembled oligomers for the NAP-1 (nucleosome assembly protein 1). MS established the number of associated units, which was utilized as input for the numerical analysis of AUC-SV profiles. The AUC-SV analysis revealed that less than 1% of NAP-1 monomer exists at the micromolar concentration range and that the basic assembly unit consists of dimers of yeast or human NAP-1. These dimers interact non-covalently to form even-numbered higher-assembly states, such as tetramers, hexamers, octamers and decamers. MS and AUC-SV consistently showed that the formation of the higher oligomers was suppressed with increasing ionic strength, implicating electrostatic interactions in the formation of higher oligomers. The hydrodynamic shapes of the NAP-1 tetramer estimated from AUC-SV agreed with the previously proposed assembly models built using the known three-dimensional structure of yeast NAP-1. Those of the hexamer and octamer could be represented by new models shown in the present study. Additionally, MS was used to measure the stoichiometry of the interaction between the human NAP-1 dimer and the histone H2A–H2B dimer or H3–H4 tetramer. The present study illustrates a rigorous procedure for the analysis of protein assembly and protein–protein interactions in solution.

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