SWI/SNF Chromatin Remodeling Requires Changes in DNA Topology

Gavin, Igor M.; Horn, Peter J.; Peterson, Craig L.

doi:10.1016/s1097-2765(01)00158-7

Cited by 110 publications

(82 citation statements)

References 30 publications

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“…The destabilization of chromatin structure and subsequent increase in polymerase access achieved by covalent modifications such as acetylation has been documented (23,24). Chromatinremodeling machines like SWI͞SNF, whose motor subunits are members of the helicase family of proteins, are known to modify the structure of nucleosomes by perturbing DNA-protein interactions and by inducing topological changes in nucleosomal DNA that are conducive to transcriptional activation (25,26). Likewise, other members of the helicase family which, unlike chromatin-remodeling machines, possess a strand-separating activity, also have been found to destabilize nucleosome structure (27,28).…”

Section: Resultsmentioning

confidence: 99%

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Brower-Toland

Smith

Yeh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

442

465

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The dynamic structure of individual nucleosomes was examined by stretching nucleosomal arrays with a feedback-enhanced optical trap. Forced disassembly of each nucleosome occurred in three stages. Analysis of the data using a simple worm-like chain model yields 76 bp of DNA released from the histone core at low stretching force. Subsequently, 80 bp are released at higher forces in two stages: full extension of DNA with histones bound, followed by detachment of histones. When arrays were relaxed before the dissociated state was reached, nucleosomes were able to reassemble and to repeat the disassembly process. The kinetic parameters for nucleosome disassembly also have been determined.

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Section: Resultsmentioning

confidence: 99%

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Brower-Toland

Smith

Yeh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

442

465

View full text Add to dashboard Cite

show abstract

“…(83) This model is also in accord with the general tendency of SNF2 subfamily factors to disrupt nucleosomes. (68,75,76,81,82,86,88,89,96) In addition, the reaction product (Fig. 5, right panel) could form dinucleosome structures, as seen with SNF2 subfamily complexes but not with ISWI complexes, (69,82,85,88,90) by trans-attachment of the long DNA overhang of one remodeled nucleosome with the histone octamer of another remodeled nucleosome.…”

Section: How Might Chromatin Remodeling Occur?mentioning

confidence: 96%

“…(69,80,84,85) (4) SNF2 subfamily complexes catalyze the apparent disassembly of nucleosomes, as assessed by the loss of DNA supercoiling of chromatin templates. (68,75,81,82,(86)(87)(88)(89) [Note that the wrapping of DNA around a core histone octamer results in a change in the linking number of approximately À1. The loss of negative DNA supercoils in circular nucleosomal DNA (in the presence of topoisomerase I to relieve superhelical torsion) thus indicates the loss of canonical nucleosomes.]…”

Section: How Might Chromatin Remodeling Occur?mentioning

confidence: 99%

Chromatin remodeling by ATP‐dependent molecular machines

2003

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SummaryThe eukaryotic genome is packaged into a periodic nucleoprotein structure termed chromatin. The repeating unit of chromatin, the nucleosome, consists of DNA that is wound nearly two times around an octamer of histone proteins. To facilitate DNA-directed processes in chromatin, it is often necessary to rearrange or to mobilize the nucleosomes. This remodeling of the nucleosomes is achieved by the action of chromatin-remodeling complexes, which are a family of ATP-dependent molecular machines. Chromatin-remodeling factors share a related ATPase subunit and participate in transcriptional regulation, DNA repair, homologous recombination and chromatin assembly. In this review, we provide an overview of chromatin-remodeling enzymes and discuss two possible mechanisms by which these factors might act to reorganize nucleosome structure.

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“…Initial models proposed two ways to disrupt histone-DNA contacts: movement of the remodeler around the nucleosome or, alternatively, use of ATP hydrolysis by the remodeler to induce a conformational change in the octamer 29 . The next generation of models were based on a series of elegant experiments showing that remodelers can impart torsion to DNA 30,31 and that remodelers themselves undergo ATPdependent conformational changes to expose DNA [32][33][34] . These studies initially proposed that the ATPase domain interacts with DNA just outside the nucleosome and that a twisting force or a conformational change pushes a DNA loop (or DNA torsion) into the nucleosome [30][31][32][33][34] .…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

225

208

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Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.Many processes involving chromosomes are guided by DNA-binding proteins, and the access of these proteins to DNA is regulated by chromatin. Nucleosomes, the primary repeating unit of chromatin, package DNA by wrapping 147 base pairs (bp) around an octamer of histone proteins in ∼1.7 helical turns 1-3 . This packaging provides topological order but occludes one face of the DNA, which slows or prevents the recognition of DNA sequences by DNA-binding proteins. To maintain topological order, and also to allow rapid and regulated access to the DNA, cells have evolved a set of chromatin-remodeling machines that alter nucleosome position, presence and structure.Remodelers can be separated into several families on the basis of their composition and activities: SWI/SNF, ISWI, NURD/Mi-2/CHD and the 'split ATPases' INO80 and SWR1 (which bear an insertion within their ATPase domains). Rad54 may represent an additional family, as it perturbs chromatin in vitro, but it apparently lacks specific nucleosome-interacting domains 4,5 . The participation of remodelers in various chromosomal processes has been the subject of many reviews 6-9 . The present work focuses solely on remodeler mechanisms, and primarily on the function of their conserved catalytic subunit, a superfamily 2 (SF2) ATPdependent DNA translocase. Recently, single-molecule approaches have been used to examine several remodelers, providing many new insights into their behavior. Here I discuss these recent studies, compare them with previous biochemical studies and suggest refinements to existing models to account for some of the observations. Remodelers slide, eject and restructure nucleosomesRemodelers can affect nucleosomes in at least four ways ( Fig. 1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access

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SWI/SNF Chromatin Remodeling Requires Changes in DNA Topology

Cited by 110 publications

References 30 publications

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Chromatin remodeling by ATP‐dependent molecular machines

Chromatin remodeling: insights and intrigue from single-molecule studies

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