scholarly journals Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Xiangyan Shi ◽  
Chinmayi Prasanna ◽  
Aghil Soman ◽  
Konstantin Pervushin ◽  
Lars Nordenskiöld
Keyword(s):  
Dynamic Networks ◽  
Structural Features ◽  
Epigenetic Changes ◽  
Internal Dynamics ◽  
Histone Tails ◽  
Multiple Timescales ◽  
Nucleosome Core ◽  
The Core ◽  
Nucleosome Core Particles ◽  
Core Particles

Abstract The dynamics of eukaryotic nucleosomes are essential in gene activity and well regulated by various factors. Here, we elucidated the internal dynamics at multiple timescales for the human histones hH3 and hH4 in the Widom 601 nucleosome core particles (NCP), suggesting that four dynamic networks are formed by the residues exhibiting larger-scale μs-ms motions that extend from the NCP core to the histone tails and DNA. Furthermore, despite possessing highly conserved structural features, histones in the telomeric NCP exhibit enhanced μs-ms dynamics in the globular sites residing at the identified dynamic networks and in a neighboring region. In addition, higher mobility was observed for the N-terminal tails of hH3 and hH4 in the telomeric NCP. The results demonstrate the existence of dynamic networks in nucleosomes, through which the center of the core regions could interactively communicate with histone tails and DNA to potentially propagate epigenetic changes.

Role of Histone Tails in the Conformation and Interactions of Nucleosome Core Particles†

Biochemistry ◽  
2004 ◽  
Vol 43 (16) ◽  
pp. 4773-4780 ◽  
Author(s):  
Aurélie Bertin ◽  
Amélie Leforestier ◽  
Dominique Durand ◽  
Françoise Livolant
Keyword(s):  
Histone Tails ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
Core Particles

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

1997 ◽  
Vol 328 (2) ◽  
pp. 409-414 ◽  
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.

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

2018 ◽  
Vol 115 (48) ◽  
pp. E11212-E11220 ◽  
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.

scholarly journals The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles

2016 ◽  
Vol 110 (8) ◽  
pp. 1720-1731 ◽  
Author(s):  
Nikolay V. Berezhnoy ◽  
Ying Liu ◽  
Abdollah Allahverdi ◽  
Renliang Yang ◽  
Chun-Jen Su ◽  
...  
Keyword(s):  
Histone Tails ◽  
Nucleosome Core ◽  
Ionic Environment ◽  
Nucleosome Core Particles ◽  
Core Particles

scholarly journals Localization of testis-variant histones in rat testis chromatin

1982 ◽  
Vol 205 (1) ◽  
pp. 15-21 ◽  
Author(s):  
M R S Rao ◽  
B J Rao ◽  
J Ganguly
Keyword(s):  
Sedimentation Coefficient ◽  
Soluble Proteins ◽  
Micrococcal Nuclease ◽  
Base Pairs ◽  
Rat Testis ◽  
Nucleosome Core ◽  
The Core ◽  
Nucleosome Core Particles ◽  
Acid Solubility ◽  
Core Particles

Nucleosome core particles and oligonucleosomes were isolated by digesting rat testis nuclei with micrococcal nuclease to 20% acid-solubility, followed by fractionation of the digest on a Bio-Gel A-5m column. The core particles thus isolated were characterized on the basis of their DNA length of 151 +/- 5 base-pairs and sedimentation coefficient of 11.4S. Analysis of the acid-soluble proteins of the core particles indicated that histones TH2B and X2 are constituents of the core particles, in addition to the somatic histones H2A, H2B, H3 and H4. The acid-soluble proteins of the oligonucleosomes comprised all the histones, including both the somatic (H1, H2A, H2B, H3, H4 and X2) and the testis-specific ones (TH1 and TH2B). It was also observed that histones TH1 and H1 are absent from the core particles and were readily extracted from the chromatin by 0.6 M-NaCl, which indicated that both of them are bound to the linker DNA.

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

Biochemistry ◽  
1987 ◽  
Vol 26 (12) ◽  
pp. 3643-3649 ◽  
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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