scholarly journals Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

2018 ◽  
Vol 14 (11) ◽  
pp. e1006512 ◽  
Author(s):  
Giovanni B. Brandani ◽  
Shoji Takada
Keyword(s):  
Defect Formation ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna

scholarly journals Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

2018 ◽  
Author(s):  
Giovanni B. Brandani ◽  
Shoji Takada
Keyword(s):  
Genome Organization ◽  
Electrostatic Interactions ◽  
Defect Formation ◽  
Energy Landscape ◽  
Molecular Machines ◽  
Biological Processes ◽  
Complete Understanding ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Dynamics Simulations

ABSTRACTATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the remodeler overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally. The sliding is initiated at the remodeler binding location via the generation of twist defects, which then spontaneously propagate to complete sliding throughout the entire nucleosome. We also reveal how remodeler mutations and DNA sequence control active nucleosome repositioning, explaining several past experimental observations. These results offer a detailed mechanistic picture of remodeling important for the complete understanding of these important biological processes.

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 Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome

2021 ◽  
Vol 118 (4) ◽  
pp. e2014498118
Author(s):  
Ilana M. Nodelman ◽  
Zhongtian Shen ◽  
Robert F. Levendosky ◽  
Gregory D. Bowman
Keyword(s):  
Bound States ◽  
Atp Binding ◽  
Dna Binding Domain ◽  
Dna Translocation ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Nucleosome Sliding ◽  
Underlying Mechanisms ◽  
Histone Core ◽  
Block Sliding

Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements that control the direction of nucleosome sliding, but underlying mechanisms of inhibition have been unclear. Here, we show that autoinhibitory elements of the yeast Chd1 remodeler block nucleosome sliding by preventing initiation of twist defects. We show that two autoinhibitory elements—the chromodomains and bridge—reinforce each other to block sliding when the DNA-binding domain is not bound to entry-side DNA. Our data support a model where the chromodomains and bridge target nucleotide-free and ADP-bound states of the ATPase motor, favoring a partially disengaged state of the ATPase motor on the nucleosome. By bypassing distortions of nucleosomal DNA prior to ATP binding, we propose that autoinhibitory elements uncouple the ATP binding/hydrolysis cycle from DNA translocation around the histone core.

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 A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Jessica Winger ◽  
Ilana M Nodelman ◽  
Robert F Levendosky ◽  
Gregory D Bowman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transition State ◽  
Base Pair ◽  
Bound States ◽  
Chromatin Remodelers ◽  
Transition State Analogs ◽  
Nucleosomal Dna ◽  
Defect Mechanism ◽  
Histone Core ◽  
Dna Twist

As superfamily 2 (SF2)-type translocases, chromatin remodelers are expected to use an inchworm-type mechanism to walk along DNA. Yet how they move DNA around the histone core has not been clear. Here we show that a remodeler ATPase motor can shift large segments of DNA by changing the twist and length of nucleosomal DNA at superhelix location 2 (SHL2). Using canonical and variant 601 nucleosomes, we find that the Saccharomyces cerevisiae Chd1 remodeler decreased DNA twist at SHL2 in nucleotide-free and ADP-bound states, and increased twist with transition state analogs. These differences in DNA twist allow the open state of the ATPase to pull in ~1 base pair (bp) by stabilizing a small DNA bulge, and closure of the ATPase to shift the DNA bulge toward the dyad. We propose that such formation and elimination of twist defects underlie the mechanism of nucleosome sliding by CHD-, ISWI-, and SWI/SNF-type remodelers.

scholarly journals Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Manu Shubhdarshan Shukla ◽  
Sajad Hussain Syed ◽  
Ramachandran Boopathi ◽  
Elsa Ben Simon ◽  
Sunil Nahata ◽  
...  
Keyword(s):  
Dna Repair ◽  
High Resolution ◽  
Restriction Enzymes ◽  
Dna Interactions ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Dna Accessibility ◽  
Nucleosomal Dna ◽  
Dnase I Footprinting ◽  
High Resolution Microscopy

Abstract Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and structure of the products of nucleosome remodeling by SWI/SNF and ACF complexes using high-resolution microscopy combined with novel biochemical approaches. We find that SWI/SNF generates a multitude of nucleosome-like metastable particles termed “remosomes”. Restriction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histone-DNA interactions within these particles. Electron cryo-microscopy shows that remosomes adopt a variety of different structures with variable irregular DNA path, similar to those described upon RSC remodeling. Remosome DNA accessibility to restriction enzymes is also markedly increased. We suggest that the generation of remosomes is a common feature of the SWI/SNF family remodelers. In contrast, the ACF remodeler, belonging to ISWI family, only produces repositioned nucleosomes and no evidence for particles associated with extra DNA, or perturbed DNA paths was found. The remosome generation by the SWI/SNF type of remodelers may represent a novel mechanism involved in processes where nucleosomal DNA accessibility is required, such as DNA repair or transcription regulation.

Structure of nucleosome-bound human BAF complex

Science ◽  
2020 ◽  
Vol 367 (6480) ◽  
pp. 875-881 ◽  
Author(s):  
Shuang He ◽  
Zihan Wu ◽  
Yuan Tian ◽  
Zishuo Yu ◽  
Jiali Yu ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Chromatin Remodelers ◽  
Baf Complex ◽  
Cryo Electron Microscopy ◽  
Nucleosomal Dna ◽  
Α Helix ◽  
Subunit Organization ◽  
Structural Insights ◽  
Base Module ◽  
Positively Charged

Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo–electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.

scholarly journals Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Saurabh K. Bhardwaj ◽  
Solomon G. Hailu ◽  
Lola Olufemi ◽  
Sandipan Brahma ◽  
Soumyadipta Kundu ◽  
...  
Keyword(s):  
Transcription Regulation ◽  
Histone Acetyltransferase ◽  
Mutational Analysis ◽  
Higher Order ◽  
Chromatin Organization ◽  
Atpase Domain ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Accessory Subunit

AbstractOver the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a’s dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.

Xenon ion irradiation of superconducting YBa2Cu3O7 thin films

1990 ◽  
Vol 48 (4) ◽  
pp. 92-93
Author(s):  
H. Watanabe ◽  
B. Kabius ◽  
B. Roas ◽  
K. Urban
Keyword(s):  
Defect Formation ◽  
Ion Irradiation ◽  
High Resolution Electron Microscopy ◽  
Structural Disorder ◽  
Flux Lines ◽  
Pinning Effect ◽  
Magnetic Flux Lines ◽  
Resolution Electron ◽  
Radiation Induced ◽  
Induced Defects

Recently it was reported that the critical current density(Jc) of YBa2Cu2O7, in the presence of magnetic field, is enhanced by ion irradiation. The enhancement is thought to be due to the pinning of the magnetic flux lines by radiation-induced defects or by structural disorder. The aim of the present study was to understand the fundamental mechanisms of the defect formation in association with the pinning effect in YBa2Cu3O7 by means of high-resolution electron microscopy(HRTEM).The YBa2Cu3O7 specimens were prepared by laser ablation in an insitu process. During deposition, a substrate temperature and oxygen atmosphere were kept at about 1073 K and 0.4 mbar, respectively. In this way high quality epitaxially films can be obtained with the caxis parallel to the <100 > SrTiO3 substrate normal. The specimens were irradiated at a temperature of 77 K with 173 MeV Xe ions up to a dose of 3.0 × 1016 m−2.

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