scholarly journals Regulation of ISW2 by Concerted Action of Histone H4 Tail and Extranucleosomal DNA

2006 ◽  
Vol 26 (20) ◽  
pp. 7388-7396 ◽  
Author(s):  
Weiwei Dang ◽  
Mohamedi N. Kagalwala ◽  
Blaine Bartholomew
Keyword(s):  
Incubation Time ◽  
Photoaffinity Labeling ◽  
Histone H4 ◽  
Concerted Action ◽  
Optimal Length ◽  
Nucleosome Remodeling ◽  
Dna Footprinting ◽  
Nucleosomal Dna ◽  
Histone Octamers

ABSTRACT The stable contact of ISW2 with nucleosomal DNA ∼20 bp from the dyad was shown by DNA footprinting and photoaffinity labeling using recombinant histone octamers to require the histone H4 N-terminal tail. Efficient ISW2 remodeling also required the H4 N-terminal tail, although the lack of the H4 tail can be mostly compensated for by increasing the incubation time or concentration of ISW2. Similarly, the length of extranucleosomal DNA affected the stable contact of ISW2 with this same internal nucleosomal site, with the optimal length being 70 to 85 bp. These data indicate the histone H4 tail, in concert with a favorable length of extranucleosomal DNA, recruits and properly orients ISW2 onto the nucleosome for efficient nucleosome remodeling. One consequence of this property of ISW2 is likely its previously observed nucleosome spacing activity.

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 Histone H4 H75E mutation attenuates global genomic and Rad26-independent transcription-coupled nucleotide excision repair

2019 ◽  
Vol 47 (14) ◽  
pp. 7392-7401 ◽  
Author(s):  
Kathiresan Selvam ◽  
Sheikh Arafatur Rahman ◽  
Shisheng Li
Keyword(s):  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Histone H3 ◽  
Chromatin Accessibility ◽  
Dna Lesions ◽  
Histone H4 ◽  
Uv Sensitivity ◽  
Nucleotide Excision ◽  
Histone Octamers ◽  
Dna Silencing

Abstract Nucleotide excision repair (NER) consists of global genomic NER (GG-NER) and transcription coupled NER (TC-NER) subpathways. In eukaryotic cells, genomic DNA is wrapped around histone octamers (an H3–H4 tetramer and two H2A–H2B dimers) to form nucleosomes, which are well known to profoundly inhibit the access of NER proteins. Through unbiased screening of histone H4 residues in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain, we identified 24 mutations that enhance or decrease UV sensitivity of Saccharomyces cerevisiae cells. The histone H4 H75E mutation, which is largely embedded in the nucleosome and interacts with histone H2B, significantly attenuates GG-NER and Rad26-independent TC-NER but does not affect TC-NER in the presence of Rad26. All the other histone H4 mutations, except for T73F and T73Y that mildly attenuate GG-NER, do not substantially affect GG-NER or TC-NER. The attenuation of GG-NER and Rad26-independent TC-NER by the H4H75E mutation is not due to decreased chromatin accessibility, impaired methylation of histone H3 K79 that is at the center of the LRS domain, or lowered expression of NER proteins. Instead, the attenuation is at least in part due to impaired recruitment of Rad4, the key lesion recognition and verification protein, to chromatin following induction of DNA lesions.

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 Nucleosome Remodeling by the Human SWI/SNF Complex Requires Transient Global Disruption of Histone-DNA Interactions

2002 ◽  
Vol 22 (11) ◽  
pp. 3653-3662 ◽  
Author(s):  
Sayura Aoyagi ◽  
Geeta Narlikar ◽  
Chunyang Zheng ◽  
Saïd Sif ◽  
Robert E. Kingston ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Atp Hydrolysis ◽  
Dnase I ◽  
Cross Linking ◽  
Dna Interactions ◽  
Nucleosome Remodeling ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Single Cross ◽  
A Site

ABSTRACT We utilized a site-specific cross-linking technique to investigate the mechanism of nucleosome remodeling by hSWI/SNF. We found that a single cross-link between H2B and DNA virtually eliminates the accumulation of stably remodeled species as measured by restriction enzyme accessibility assays. However, cross-linking the histone octamer to nucleosomal DNA does not inhibit remodeling as monitored by DNase I digestion assays. Importantly, we found that the restriction enzyme-accessible species can be efficiently cross-linked after remodeling and that the accessible state does not require continued ATP hydrolysis. These results imply that the generation of stable remodeled states requires at least transient disruption of histone-DNA interactions throughout the nucleosome, while hSWI/SNF-catalyzed disruption of just local histone-DNA interactions yields less-stable remodeled states that still display an altered DNase I cleavage pattern. The implications of these results for models of the mechanism of SWI/SNF-catalyzed nucleosome remodeling are discussed.

A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA

Nature ◽  
1988 ◽  
Vol 331 (6154) ◽  
pp. 365-367 ◽  
Author(s):  
Konstantin K. Ebralidse ◽  
Sergei A. Grachev ◽  
Andrei D. Mirzabekov
Keyword(s):  
Histone H4 ◽  
Nucleosomal Dna

scholarly journals Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer

2010 ◽  
Vol 107 (5) ◽  
pp. 1936-1941 ◽  
Author(s):  
Manu Shubhdarshan Shukla ◽  
Sajad Hussain Syed ◽  
Fabien Montel ◽  
Cendrine Faivre-Moskalenko ◽  
Jan Bednar ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Dna Interactions ◽  
One Pot ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Force Microscopy ◽  
Histone Octamer ◽  
Distinct Variable ◽  
Nucleosomal Dna ◽  
Dnase I Footprinting

Chromatin remodelers are sophisticated nano-machines that are able to alter histone-DNA interactions and to mobilize nucleosomes. Neither the mechanism of their action nor the conformation of the remodeled nucleosomes are, however, yet well understood. We have studied the mechanism of Remodels Structure of Chromatin (RSC)-nucleosome mobilization by using high-resolution microscopy and biochemical techniques. Atomic force microscopy and electron cryomicroscopy (EC-M) analyses show that two types of products are generated during the RSC remodeling: (i) stable non-mobilized particles, termed remosomes that contain about 180 bp of DNA associated with the histone octamer and, (ii) mobilized particles located at the end of DNA. EC-M reveals that individual remosomes exhibit a distinct, variable, highly-irregular DNA trajectory. The use of the unique “one pot assays” for studying the accessibility of nucleosomal DNA towards restriction enzymes, DNase I footprinting and ExoIII mapping demonstrate that the histone-DNA interactions within the remosomes are strongly perturbed, particularly in the vicinity of the nucleosome dyad. The data suggest a two-step mechanism of RSC-nucleosome remodeling consisting of an initial formation of a remosome followed by mobilization. In agreement with this model, we show experimentally that the remosomes are intermediate products generated during the first step of the remodeling reaction that are further efficiently mobilized by RSC.

scholarly journals Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Johanna Ludwigsen ◽  
Sabrina Pfennig ◽  
Ashish K Singh ◽  
Christina Schindler ◽  
Nadine Harrer ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Docking Site ◽  
Atpase Domain ◽  
Histone H4 ◽  
Regulatory Motif ◽  
Nucleosome Remodeling ◽  
Autoinhibitory Domain ◽  
Functional Regulation ◽  
Shed Light

ISWI-family nucleosome remodeling enzymes need the histone H4 N-terminal tail to mobilize nucleosomes. Here we mapped the H4-tail binding pocket of ISWI. Surprisingly the binding site was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the N-terminal region (NTR) of ISWI, indicating that AutoN does not act as a simple pseudosubstrate as suggested previously. Rather, AutoN cooperated with a hitherto uncharacterized motif, termed AcidicN, to confer H4-tail sensitivity and discriminate between DNA and nucleosomes. A third motif in the NTR, ppHSA, was functionally required in vivo and provided structural stability by clamping the NTR to Lobe 2 of the ATPase domain. This configuration is reminiscent of Chd1 even though Chd1 contains an unrelated NTR. Our results shed light on the intricate structural and functional regulation of ISWI by the NTR and uncover surprising parallels with Chd1.

scholarly journals Chromatin Condensation Fluctuations Rather than Steady-State Predict Chromatin Accessibility

2018 ◽  
Author(s):  
Nicolas Audugé ◽  
Sergi Padilla-Parra ◽  
Marc Tramier ◽  
Nicolas Borghi ◽  
Maïté Coppey-Moisan
Keyword(s):  
Cell Biology ◽  
Dynamic Properties ◽  
Chromatin Condensation ◽  
Direct Interaction ◽  
Chromatin Accessibility ◽  
Live Cells ◽  
Histone H4 ◽  
Epigenetic Marks ◽  
Nucleosomal Dna ◽  
Acetylated Histone H4

AbstractChromatin accessibility to protein factors is critical for genome activities. Dynamic changes in nucleosomal DNA compaction and higher order chromatin structures are expected to allow specific sites to be accessible to regulatory factors and the transcriptional machinery. However, the dynamic properties of chromatin that regulate its accessibility are poorly understood. Here, we took advantage of the microenvironment sensitivity of the fluorescence lifetime of EGFP-H4 histone incorporated in chromatin to map in the nucleus of live cells the dynamics of chromatin condensation and its direct interaction with a tail acetylation recognition domain (the double bromodomain module of human TAFII250, dBD). We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation. Fluctuations are spontaneous, yet their amplitudes are affected by their sub-nuclear localization and by distinct and competing mechanisms dependent on histone acetylation, ATP, and both. Moreover, we show that accessibility of acetylated histone H4 to dBD is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.SignificanceIn higher eukaryotes, the structure and compaction of chromatin are considered as barriers to genome activities. Epigenetic marks such as post-translational modifications of histones can modify the structure and compaction of chromatin. The accessibility of protein factors to these epigenetic marks is therefore of paramount importance for genome activities. We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation itself. We show that accessibility of acetylated histone H4 to double bromodomains is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.ClassificationBiological Sciences, Cell Biology

scholarly journals Architecture of the SWI/SNF-Nucleosome Complex

2008 ◽  
Vol 28 (19) ◽  
pp. 6010-6021 ◽  
Author(s):  
Mekonnen Lemma Dechassa ◽  
Bei Zhang ◽  
Rachel Horowitz-Scherer ◽  
Jim Persinger ◽  
Christopher L. Woodcock ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Catalytic Subunit ◽  
Cross Linking ◽  
Dependent Manner ◽  
Transcription Activator ◽  
Entry Site ◽  
Dna Footprinting ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Protein Cross Linking

ABSTRACT The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a transcription activator. SWI/SNF was found by DNA footprinting to contact tightly around one gyre of DNA spanning ∼50 bp from the nucleosomal entry site to near the dyad axis. The DNA footprint is consistent with nucleosomes binding to an asymmetric trough of SWI/SNF that was revealed by the improved imaging of free SWI/SNF. The DNA site-directed cross-linking revealed that the catalytic subunit Swi2/Snf2 is associated with nucleosomes two helical turns from the dyad axis and that the Snf6 subunit is proximal to the transcription factor recruiting SWI/SNF. The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound.

scholarly journals Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro.

1996 ◽  
Vol 15 (10) ◽  
pp. 2508-2518 ◽  
Author(s):  
M. Vettese-Dadey ◽  
P. A. Grant ◽  
T. R. Hebbes ◽  
C. Crane- Robinson ◽  
C. D. Allis ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Primary Role ◽  
Histone H4 ◽  
Factor Binding ◽  
Nucleosomal Dna
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