scholarly journals The SWI/SNF Complex Creates Loop Domains in DNA and Polynucleosome Arrays and Can Disrupt DNA-Histone Contacts within These Domains

1999 ◽  
Vol 19 (2) ◽  
pp. 1470-1478 ◽  
Author(s):  
David P. Bazett-Jones ◽  
Jacques Côté ◽  
Carolyn C. Landel ◽  
Craig L. Peterson ◽  
Jerry L. Workman
Keyword(s):  
Chromatin Remodeling ◽  
Dna Content ◽  
Naked Dna ◽  
Nucleosome Organization ◽  
Nucleosomal Dna ◽  
Close Proximity ◽  
Loop Domains

ABSTRACT To understand the mechanisms by which the chromatin-remodeling SWI/SNF complex interacts with DNA and alters nucleosome organization, we have imaged the SWI/SNF complex with both naked DNA and nucleosomal arrays by using energy-filtered microscopy. By making ATP-independent contacts with DNA at multiple sites on its surface, SWI/SNF creates loops, bringing otherwise-distant sites into close proximity. In the presence of ATP, SWI/SNF action leads to the disruption of nucleosomes within domains that appear to be topologically constrained by the complex. The data indicate that the action of one SWI/SNF complex on an array of nucleosomes can lead to the formation of a region where multiple nucleosomes are disrupted. Importantly, nucleosome disruption by SWI/SNF results in a loss of DNA content from the nucleosomes. This indicates a mechanism by which SWI/SNF unwraps part of the nucleosomal DNA.

Models for chromatin remodeling: a critical comparison

2003 ◽  
Vol 81 (3) ◽  
pp. 169-172 ◽  
Author(s):  
K van Holde ◽  
T Yager
Keyword(s):  
Diffusion Model ◽  
Chromatin Remodeling ◽  
Experimental Studies ◽  
Nucleosome Remodeling ◽  
Defect Generation ◽  
Critical Comparison ◽  
Nucleosomal Dna ◽  
Reptation Model ◽  
Cast Doubt ◽  
Random Diffusion

Nucleosome remodeling has been shown, in many cases, to involve cis displacement of nucleosomes on the DNA. This process seems similar to the long-recognized random diffusion of nucleosomes along DNA, but the remodeling process is unidirectional and ATP dependent. Several years ago, we developed a model for nucleosome migration, based on the diffusion of "twist-defects" within the nucleosomal DNA. This has been modified into a model that incorporates ATP-dependent defect generation, and can account for many observations concerning remodeling. However, certain experimental studies in recent years have cast doubt on the applicability of the twist-diffusion model for remodeling, and seem to favor instead a "reptation" model. We discuss herein these problems and propose a resolution.Key words: nucleosome, remodeling, chromatin.

scholarly journals Functional Role of Extranucleosomal DNA and the Entry Site of the Nucleosome in Chromatin Remodeling by ISW2

2004 ◽  
Vol 24 (22) ◽  
pp. 10047-10057 ◽  
Author(s):  
Martin Zofall ◽  
Jim Persinger ◽  
Blaine Bartholomew
Keyword(s):  
Chromatin Remodeling ◽  
Functional Role ◽  
Minimal Amount ◽  
Dna Fragments ◽  
Entry Site ◽  
Torsional Strain ◽  
Mapping Approach ◽  
Nucleosomal Dna ◽  
Initial Stage

ABSTRACT A minimal amount of extranucleosomal DNA was required for nucleosome mobilization by ISW2 as shown by using a photochemical histone mapping approach to analyze nucleosome movement on a set of nucleosomes with varied lengths of extranucleosomal DNA. ISW2 was ineffective in repositioning or mobilizing nucleosomes with ≤20 bp of extranucleosomal DNA. In addition, ISW2 was able to slide nucleosomes to within only 10 to 13 bp of the edge of DNA fragments. The nucleosome mobilization was promoted by extranucleosomal single-stranded DNA with modest strand preference. Gaps (10 bp) just inside the nucleosome and in the extranucleosomal DNA showed that the transfer of torsional strain (twist) into the nucleosomal DNA region was not required for mobilizing nucleosomes. However, indications are that the extranucleosomal DNA immediately adjacent to the nucleosome has an important role in the initial stage of nucleosome movement by ISW2.

Dinoflagellates have a eukaryotic nuclear matrix with lamin-like proteins and topoisomerase II

1994 ◽  
Vol 107 (10) ◽  
pp. 2861-2873
Author(s):  
A. Minguez ◽  
S. Franca ◽  
S. Moreno Diaz de la Espina
Keyword(s):  
Nuclear Matrix ◽  
Topoisomerase Ii ◽  
Higher Plants ◽  
Supramolecular Organization ◽  
Free Living ◽  
Eukaryotic Nucleus ◽  
Nucleosomal Dna ◽  
Eukaryotic Chromatin ◽  
Early Acquisition ◽  
Loop Domains

Unicellular Dinoflagellates represent the only eukaryotic Phylum lacking histones and nucleosomes. To investigate whether Dinoflagellates do have a nuclear matrix that would modulate the supramolecular organization of their non-nucleosomal DNA and chromosomes, cells of the free-living unarmored Dinoflagellate Amphidinium carterae were encapsulated in agarose microbeads and submitted to sequential extraction with non-ionic detergents, nucleases and 2 M NaCl. Our results demonstrate that this species has a residual nuclear matrix similar to that of vertebrates and higher plants. The cytoskeleton-nuclear matrix complex of A. carterae shows a relatively intricate polypeptide pattern. Immunoblots with different antibodies reveal several intermediate filament types of proteins, one of which is immunologically related to vertebrate lamins, confirming that these proteins are ancestral members of the IF family, which is highly conserved in eukaryotes. A topoisomerase II homologue has also been identified in the nuclear matrix, suggesting that these structures could play a role in organizing the Dinoflagellate DNA in loop domains. Taken together our results demonstrate that the nuclear matrix is an early acquisition of the eukaryotic nucleus, independent of histones and nucleosomes in such a way that the mechanisms controlling the two levels of organization in eukaryotic chromatin would be molecularly and evolutionarily independent.

scholarly journals Dependency of ISW1a Chromatin Remodeling on Extranucleosomal DNA

2007 ◽  
Vol 27 (8) ◽  
pp. 3217-3225 ◽  
Author(s):  
Vamsi K. Gangaraju ◽  
Blaine Bartholomew
Keyword(s):  
Atpase Activity ◽  
Chromatin Remodeling ◽  
Molecular Basis ◽  
The Other ◽  
Entry And Exit ◽  
Exit Site ◽  
Optimal Length ◽  
Nucleosome Remodeling ◽  
Dna Footprinting ◽  
Nucleosomal Dna

ABSTRACT The nucleosome remodeling activity of ISW1a was dependent on whether ISW1a was bound to one or both extranucleosomal DNAs. ISW1a preferentially bound nucleosomes with an optimal length of ∼33 to 35 bp of extranucleosomal DNA at both the entry and exit sites over nucleosomes with extranucleosomal DNA at only one entry or exit site. Nucleosomes with extranucleosomal DNA at one of the entry/exit sites were readily remodeled by ISW1a and stimulated the ATPase activity of ISW1a, while conversely, nucleosomes with extranucleosomal DNA at both entry/exit sites were unable either to stimulate the ATPase activity of ISW1a or to be mobilized. DNA footprinting revealed that a major conformational difference between the nucleosomes was the lack of ISW1a binding to nucleosomal DNA two helical turns from the dyad axis in nucleosomes with extranucleosomal DNA at both entry/exit sites. The Ioc3 subunit of ISW1a was found to be the predominant subunit associated with extranucleosomal DNA when ISW1a is bound either to one or to both extranucleosomal DNAs. These two conformations of the ISW1a-nucleosome complex are suggested to be the molecular basis for the nucleosome spacing activity of ISW1a on nucleosomal arrays. ISW1b, the other isoform of ISW1, does not have the same dependency for extranucleosomal DNA as ISW1a and, likewise, is not able to space nucleosomes.

scholarly journals Ikaros and GATA-1 Combinatorial Effect Is Required for Silencing of Human γ-Globin Genes

2008 ◽  
Vol 29 (6) ◽  
pp. 1526-1537 ◽  
Author(s):  
Stefania Bottardi ◽  
Julie Ross ◽  
Vincent Bourgoin ◽  
Nasser Fotouhi-Ardakani ◽  
El Bachir Affar ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Globin Gene ◽  
Gene Promoters ◽  
Globin Genes ◽  
Close Proximity ◽  
Transcriptional Switch ◽  
Globin Gene Regulation ◽  
First Time ◽  
Globin Gene Expression

ABSTRACT During development and erythropoiesis, globin gene expression is finely modulated through an important network of transcription factors and chromatin modifying activities. In this report we provide in vivo evidence that endogenous Ikaros is recruited to the human β-globin locus and targets the histone deacetylase HDAC1 and the chromatin remodeling protein Mi-2 to the human γ-gene promoters, thereby contributing to γ-globin gene silencing at the time of the γ- to β-globin gene transcriptional switch. We show for the first time that Ikaros interacts with GATA-1 and enhances the binding of the latter to different regulatory regions across the locus. Consistent with these results, we show that the combinatorial effect of Ikaros and GATA-1 impairs close proximity between the locus control region and the human γ-globin genes. Since the absence of Ikaros also affects GATA-1 recruitment to GATA-2 promoter, we propose that the combinatorial effect of Ikaros and GATA-1 is not restricted to globin gene regulation.

scholarly journals Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
R Stefan Isaac ◽  
Fuguo Jiang ◽  
Jennifer A Doudna ◽  
Wendell A Lim ◽  
Geeta J Narlikar ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Dna Sequences ◽  
Surveillance System ◽  
Dynamic Properties ◽  
Eukaryotic Cells ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Eukaryotic Chromatin ◽  
Versatile Tool

The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo.

scholarly journals Nucleosome-CHD4 chromatin remodeler structure maps human disease mutations

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Lucas Farnung ◽  
Moritz Ochmann ◽  
Patrick Cramer
Keyword(s):  
Chromatin Remodeling ◽  
Homo Sapiens ◽  
Human Cancer ◽  
Gene Activation ◽  
Nucleosome Core Particle ◽  
Defect Model ◽  
Nucleosome Core ◽  
Cryo Electron Microscopy ◽  
Nucleosomal Dna ◽  
Disease Mutations

Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here, we report the cryo-electron microscopy (cryo-EM) structure of Homo sapiens CHD4 engaged with a nucleosome core particle in the presence of the non-hydrolysable ATP analogue AMP-PNP at an overall resolution of 3.1 Å. The ATPase motor of CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the ‘twist defect’ model of chromatin remodeling. CHD4 does not induce unwrapping of terminal DNA, in contrast to its homologue Chd1, which functions in gene activation. Our structure also maps CHD4 mutations that are associated with human cancer or the intellectual disability disorder Sifrim-Hitz-Weiss syndrome.

scholarly journals The mechanistic basis for chromatin invasion and remodeling by the yeast pioneer transcription factor Rap1

2019 ◽  
Author(s):  
Maxime Mivelaz ◽  
Anne-Marinette Cao ◽  
Slawomir Kubik ◽  
Sevil Zencir ◽  
Ruud Hovius ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Bound States ◽  
Chromatin Fiber ◽  
Naked Dna ◽  
Promoter Architecture ◽  
Nucleosomal Dna ◽  
Pioneer Transcription Factor ◽  
Mechanistic Basis ◽  
Active Promoter

ABSTRACTPioneer transcription factors (pTFs) bind to target sites within compact chromatin initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here we reveal, using single-molecule fluorescence approaches, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber, but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting nucleosome-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to destabilize promoter nucleosomes, paving the way to form long-lived bound states on now exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.

scholarly journals Novel trans-Tail Regulation of H2B Ubiquitylation and H3K4 Methylation by the N Terminus of Histone H2A

2010 ◽  
Vol 30 (14) ◽  
pp. 3635-3645 ◽  
Author(s):  
Suting Zheng ◽  
John J. Wyrick ◽  
Joseph C. Reese
Keyword(s):  
Histone Modifications ◽  
Cross Talk ◽  
Docking Site ◽  
Histone H2a ◽  
H3k4 Methylation ◽  
Nucleosomal Dna ◽  
Close Proximity ◽  
N Terminus ◽  
Partially Occluded

ABSTRACT Chromatin is regulated by cross talk among different histone modifications, which can occur between residues within the same tail or different tails in the nucleosome. The latter is referred to as trans-tail regulation, and the best-characterized example of this is the dependence of H3 methylation on H2B ubiquitylation. Here we describe a novel form of trans-tail regulation of histone modifications involving the N-terminal tail of histone H2A. Mutating or deleting residues in the N-terminal tail of H2A reduces H2B ubiquitylation and H3K4 methylation but does not affect the recruitment of the modifying enzymes, Rad6/Bre1 and COMPASS, to genes. The H2A tail is required for the incorporation of Cps35 into COMPASS, and increasing the level of ubiquitylated H2B in H2A tail mutants suppresses the H3K4 methylation defect, suggesting that the H2A tail regulates H2B-H3 cross talk. We mapped the region primarily responsible for this regulation to the H 2 A r epression domain, HAR. The HAR and K123 of H2B are in close proximity to each other on the nucleosome, suggesting that they form a docking site for the ubiquitylation machinery. Interestingly, the HAR is partially occluded by nucleosomal DNA, suggesting that the function of the H2A cross talk pathway is to restrict histone modifications to nucleosomes altered by transcription.

scholarly journals Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH, to nucleosome cores.

1994 ◽  
Vol 14 (2) ◽  
pp. 970-981 ◽  
Author(s):  
M Vettese-Dadey ◽  
P Walter ◽  
H Chen ◽  
L J Juan ◽  
J L Workman
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Core Histone ◽  
Nucleosome Core ◽  
Naked Dna ◽  
The Core ◽  
Nucleosomal Dna ◽  
Multiple Binding Sites ◽  
Multiple Binding

Facilitated, "cooperative" binding of GAL4-AH to nucleosomal DNA occurred in response to inhibition from the core histone amino termini. The binding of GAL4-AH (which contains the DNA-binding and dimerization domains of GAL4) to nucleosome cores containing multiple binding sites initiated at the end of a nucleosome core and proceeded in a cooperative manner until all sites were occupied. However, following tryptic removal of the core histone amino termini, GAL4-AH binding appeared to be noncooperative, similar to binding naked DNA. Binding of GAL4-AH to nucleosomes bearing a single GAL4 site at different positions indicated that inhibition of GAL4 binding was largely mediated by the histone amino termini and primarily occurred at sites well within the core and not near the end. When the histone amino termini were intact, binding of GAL4-AH to sites near the center of a nucleosome core was greatly enhanced by the presence of additional GAL4 dimers bound to more-accessible positions. These data illustrate that the binding of a factor to more-accessible sites, near the end of a nucleosome, allows facilitated binding of additional factors to the center of the nucleosome, thereby overcoming repression from the core histone amino termini. This mechanism may contribute to the binding of multiple factors to complex promoter and enhancer elements in cellular chromatin.

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