Generation of Superhelical Torsion by ATP-Dependent Chromatin Remodeling Activities

Havas, Kristina M.; Flaus, Andrew; Phelan, Michael L.; Kingston, Robert E.; Wade, Paul A.; Lilley, David M.J.; Owen-Hughes, Tom

doi:10.1016/s0092-8674(00)00215-4

Cited by 246 publications

(193 citation statements)

References 76 publications

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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

227

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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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

227

208

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“…(69,82,85,88,90) (6) A variety of remodeling factors have been observed to generate superhelical torsion in DNA or chromatin. (35,60,91) (7) RSC complex, ISWI and Rad54 have been found to exhibit triplex DNA displacement activity and thus appear to translocate along the DNA. (65,92) [In the triplex DNA displacement assay, a short oligonucleotide that binds in the major groove of a pyrimidine-rich target sequence is displaced by motor proteins that translocate through the sequence.]…”

Section: How Might Chromatin Remodeling Occur?mentioning

confidence: 99%

“…8,15,20,31,35,65,68,77,78,82,83,85,[91][92][93][94]. Most of the proposed mechanisms involve the generation of a DNA loop or bulge (of variable size) that is propagated across the surface of the histone octamer.…”

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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“…The weight of this issue was made particularly conspicuous by a recent study (Havas et al, 2000) that expanded on earlier observations that action by SWI/SNF can lead to nucleosome mobilization (sliding) (Jaskelio et al, 2000;Whitehouse et al, 1999), i.e., the relocalization of the histone octamer in cis to a di erent position on a given DNA molecule. SWI/SNF shares this unusual property with several other ATPases involved in chromatin remodeling, including Mi-2 (Guschin et al, 2000b) and ISWI (Corona et al, 1999;Hamiche et al, 1999).…”

Section: Twist and Writhe: How Chromatin Gets Goingmentioning

confidence: 99%

Chromatin remodeling and transcriptional activation: the cast (in order of appearance)

2001

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The number of chromatin modifying and remodeling complexes implicated in genome control is growing faster than our understanding of the functional roles they play. We discuss recent in vitro experiments with biochemically de®ned chromatin templates that illuminate new aspects of action by histone acetyltransferases and ATPdependent chromatin remodeling engines in facilitating transcription. We review a number of studies that present an`ordered recruitment' view of transcriptional activation, according to which various complexes enter and exit their target promoter in a set sequence, and at speci®c times, such that action by one complex sets the stage for the arrival of the next one. A consensus emerging from all these experiments is that the joint action by several types of chromatin remodeling machines can lead to a more profound alteration of the infrastructure of chromatin over a target promoter than could be obtained by these enzymes acting independently. In addition, it appears that in speci®c cases one type of chromatin structure alteration (e.g., histone hyperacetylation) is contingent upon prior alterations of a di erent sort (i.e., ATP-dependent remodeling of histone-DNA contacts). The striking di erences between the precise sequence of action by various cofactors observed in these studies may be ± at least in part ± due to di erences between the speci®c promoters studied, and distinct requirements exhibited by speci®c loci for chromatin remodeling based on their pre-existing nucleoprotein architecture. Oncogene (2001) 20, 2991 ± 3006.

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Generation of Superhelical Torsion by ATP-Dependent Chromatin Remodeling Activities

Cited by 246 publications

References 76 publications

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin remodeling by ATP‐dependent molecular machines

Chromatin remodeling and transcriptional activation: the cast (in order of appearance)

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