From DNA unwrapping to histone exchange

Science ◽  
2018 ◽  
Vol 362 (6411) ◽  
pp. 194.11-196
Author(s):  
Steve Mao
2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Rina Hirano ◽  
Yasuhiro Arimura ◽  
Tomoya Kujirai ◽  
Mikihiro Shibata ◽  
Aya Okuda ◽  
...  

AbstractH2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.


2021 ◽  
Author(s):  
Shuxiang Li ◽  
Yunhui Peng ◽  
David Landsman ◽  
Anna Panchenko

Cytosine methylation at the 5-carbon position is an essential DNA epigenetic mark in many eukaryotic organisms. Although countless structural and functional studies of cytosine methylation have been reported in both prokaryotes and eukaryotes, our understanding of how it influences the nucleosome assembly, structure, and dynamics remains obscure. Here we investigated the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. By applying long molecular dynamics simulations (five microsecond long trajectories, 60 microseconds in total), we generated extensive atomic level conformational full nucleosome ensembles. Our results revealed that methylation induces pronounced changes in geometry for both linker and nucleosomal DNA, leading to a more curved, under-twisted DNA, shifting the population equilibrium of sugar-phosphate backbone geometry. These conformational changes are associated with a considerable enhancement of interactions between methylated DNA and the histone octamer, doubling the number of contacts at some key arginines. H2A and H3 tails play important roles in these interactions, especially for DNA methylated nucleosomes. This, in turn, prevents a spontaneous DNA unwrapping of 3-4 helical turns for the methylated nucleosome with truncated histone tails, otherwise observed in the unmethylated system on several microsecond time scale.


Chromosoma ◽  
1985 ◽  
Vol 91 (5) ◽  
pp. 391-396 ◽  
Author(s):  
Nils R. Ringertz ◽  
Ulf Nyman ◽  
Mathias Bergman

Genetics ◽  
2020 ◽  
Vol 215 (3) ◽  
pp. 569-578
Author(s):  
William K. Storck ◽  
Sabrina Z. Abdulla ◽  
Michael R. Rountree ◽  
Vincent T. Bicocca ◽  
Eric U. Selker

In chromatin, nucleosomes are composed of ∼146 bp of DNA wrapped around a histone octamer, and are highly dynamic structures subject to remodeling and exchange. Histone turnover has previously been implicated in various processes including the regulation of chromatin accessibility, segregation of chromatin domains, and dilution of histone marks. Histones in different chromatin environments may turnover at different rates, possibly with functional consequences. Neurospora crassa sports a chromatin environment that is more similar to that of higher eukaryotes than yeasts, which have been utilized in the past to explore histone exchange. We constructed a simple light-inducible system to profile histone exchange in N. crassa on a 3xFLAG-tagged histone H3 under the control of the rapidly inducible vvd promoter. After induction with blue light, incorporation of tagged H3 into chromatin occurred within 20 min. Previous studies of histone turnover involved considerably longer incubation periods and relied on a potentially disruptive change of medium for induction. We used this reporter to explore replication-independent histone turnover at genes and examine changes in histone turnover at heterochromatin domains in different heterochromatin mutant strains. In euchromatin, H3-3xFLAG patterns were almost indistinguishable from that observed in wild-type in all mutant backgrounds tested, suggesting that loss of heterochromatin machinery has little effect on histone turnover in euchromatin. However, turnover at heterochromatin domains increased with loss of trimethylation of lysine 9 of histone H3 or HP1, but did not depend on DNA methylation. Our reporter strain provides a simple yet powerful tool to assess histone exchange across multiple chromatin contexts.


Biochemistry ◽  
1993 ◽  
Vol 32 (49) ◽  
pp. 13605-13614 ◽  
Author(s):  
Carolyn A. Perry ◽  
Christopher A. Dadd ◽  
C. David Allis ◽  
Anthony T. Annunziato

PLoS ONE ◽  
2019 ◽  
Vol 14 (3) ◽  
pp. e0212764 ◽  
Author(s):  
Randi M. Mackler ◽  
Nathan D. Jones ◽  
Anne M. Gardner ◽  
Miguel A. Lopez ◽  
Cecil J. Howard ◽  
...  

2006 ◽  
Vol 26 (18) ◽  
pp. 6890-6901 ◽  
Author(s):  
M. David Stewart ◽  
John Sommerville ◽  
Jiemin Wong

ABSTRACT Histone H3 lysine 9 (H3K9) methylation has broad roles in transcriptional repression, gene silencing, maintenance of heterochromatin, and epigenetic inheritance of heterochromatin. Using Xenopus laevis oocytes, we have previously shown that targeting G9a, an H3K9 histone methyltransferase, to chromatin increases H3K9 methylation and consequently represses transcription. Here we report that treatment with trichostatin A induces histone acetylation and is sufficient to activate transcription repressed by G9a, and this activation is accompanied by a reduction in dimethyl H3K9 (H3K9me2). We tested the possibility that the reduction in H3K9me2 was due to the replacement of methylated H3 with unmethylated H3.3. Surprisingly, we found that both free H3 and H3.3 are continually exchanged with chromatin-associated histones. This dynamic exchange of chromatin-associated H3 with free H3/H3.3 was not affected by alterations in transcriptional activity, elongation, acetylation, H3K9 methylation, or DNA replication. In support of this continual histone exchange model, we show that maintenance of H3K9 methylation at a specific site requires the continual presence of an H3K9 histone methyltransferase. Upon dissociation of the methyltransferase, H3K9 methylation decreases. Taken together, our data suggest that chromatin-associated and non-chromatin-associated histones are continually exchanged in the Xenopus oocyte, creating a highly dynamic chromatin environment.


2006 ◽  
Vol 5 (10) ◽  
pp. 1780-1787 ◽  
Author(s):  
Jeffrey Linger ◽  
Jessica K. Tyler

ABSTRACT The eukaryotic genome is packaged together with histone proteins into chromatin following DNA replication. Recent studies have shown that histones can also be assembled into chromatin independently of DNA replication and that this dynamic exchange of histones may be biased toward sites undergoing transcription. Here we show that epitope-tagged histone H4 can be incorporated into nucleosomes throughout the budding yeast (Saccharomyces cerevisiae) genome regardless of the phase of the cell cycle, the transcriptional status, or silencing of the region. Direct comparisons reveal that the amount of histone incorporation that occurs in G1-arrested cells is similar to that occurring in cells undergoing DNA replication. Additionally, we show that this histone incorporation is not dependent on the histone H3/H4 chaperones CAF-1, Asf1, and Hir1 individually. This study demonstrates that DNA replication and transcription are not necessary prerequisites for histone exchange in budding yeast, indicating that chromatin is more dynamic than previously thought.


2017 ◽  
Vol 45 (12) ◽  
pp. 7249-7260 ◽  
Author(s):  
Chia-Liang Lin ◽  
Yuriy Chaban ◽  
David M. Rees ◽  
Elizabeth A. McCormack ◽  
Lorraine Ocloo ◽  
...  

2017 ◽  
Vol 112 (3) ◽  
pp. 370a-371a
Author(s):  
Yujie Chen ◽  
Joshua Tokuda ◽  
Traci Topping ◽  
Steve Meisburger ◽  
Suzette Pabit ◽  
...  
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