scholarly journals Dynamic regulation of transcription factors by nucleosome remodeling

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Ming Li ◽  
Arjan Hada ◽  
Payel Sen ◽  
Lola Olufemi ◽  
Michael A Hall ◽  
...  
Keyword(s):  
Direct Evidence ◽  
Nucleosome Positioning ◽  
Regulation Of Transcription ◽  
Dynamic Regulation ◽  
Major Barrier ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Promoter Architecture ◽  
Sequence Elements ◽  
Dna Template

The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.

scholarly journals Dynamic Regulation of Transcription Factors by Nucleosome Remodeling

2014 ◽  
Vol 106 (2) ◽  
pp. 76a ◽  
Author(s):  
Ming Li ◽  
Payel Sen ◽  
Lola Olufemi ◽  
Arjan Hada ◽  
Michael A. Hall ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulation Of Transcription ◽  
Dynamic Regulation ◽  
Nucleosome Remodeling

scholarly journals Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Elisa Oberbeckmann ◽  
Vanessa Niebauer ◽  
Shinya Watanabe ◽  
Lucas Farnung ◽  
Manuela Moldt ◽  
...  
Keyword(s):  
Phased Arrays ◽  
Stable Steady State ◽  
Reference Sites ◽  
Chromatin Remodelers ◽  
Sliding Direction ◽  
Nucleosome Dynamics ◽  
Genome Wide ◽  
Sequence Elements ◽  
Nucleosome Array ◽  
Dna Ends

AbstractArrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the ‘ruler’ that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.

scholarly journals Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

2021 ◽  
Vol 22 (11) ◽  
pp. 5578
Author(s):  
Cedric R. Clapier
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Structural Diversity ◽  
Nucleosome Positioning ◽  
Basic Mechanism ◽  
Progressive Increase ◽  
Chromatin Organization ◽  
Dna Translocation ◽  
Dynamic Regulation ◽  
Cooperative Action

The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions—in particular, the regulation of gene expression—and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.

scholarly journals RSC2, Encoding a Component of the RSC Nucleosome Remodeling Complex, Is Essential for 2μm Plasmid Maintenance in Saccharomyces cerevisiae

2002 ◽  
Vol 22 (12) ◽  
pp. 4218-4229 ◽  
Author(s):  
Michael C. V. L. Wong ◽  
Suzanna R. S. Scott-Drew ◽  
Matthew J. Hayes ◽  
Philip J. Howard ◽  
James A. H. Murray
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Plasmid Dna ◽  
Direct Evidence ◽  
Maternal Inheritance ◽  
Alternative Form ◽  
Nucleosome Remodeling ◽  
Daughter Cells ◽  
Chromatin Remodeling Complex ◽  
Stable Maintenance

ABSTRACT The stable maintenance of the 2μm circle plasmid depends on its ability to overcome intrinsic maternal inheritance bias, which in yeast normally results in the failure to transmit DNA molecules efficiently to daughter cells. In addition to the plasmid proteins Rep1 and Rep2 acting on the plasmid DNA locus STB, it is likely that other chromosomally encoded yeast proteins are required. We have isolated mutants of yeast unable to maintain 2μm and found that RSC2 is essential for 2μm to overcome maternal inheritance bias. Rsc2 is part of a multisubunit RSC chromatin remodeling complex, and we show that in the absence of Rsc2 the chromatin structure of the STB region is significantly altered and the Rep1 protein loses its normal localization to subnuclear foci. Rsc1, a closely related homolog of Rsc2 present in an alternative form of the RSC complex, is not required for 2μm maintenance and does not replace the requirement for Rsc2 when overexpressed. This represents the first specific role for Rsc2 that has been related to a change in chromatin structure, as well as the first direct evidence linking chromatin structure to 2μm segregation.

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 Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jee Min Kim ◽  
Pat Visanpattanasin ◽  
Vivian Jou ◽  
Sheng Liu ◽  
Xiaona Tang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Dissociation Kinetics ◽  
Additional Function ◽  
Fast Kinetics ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Genome Wide ◽  
Regulatory Dna ◽  
Temporal Interactions

Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending ‘tug-of-war’ that controls a temporally shifting window of accessibility for the transcription initiation machinery.

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