X-Ray Structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase Core and Its Complex with DNA

Dürr, Harald; Körner, Christian; Müller, Marisa; Hickmann, Volker; Hopfner, Karl‐Peter

doi:10.1016/j.cell.2005.03.026

Cited by 239 publications

(358 citation statements)

References 54 publications

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“…These models were intuitive and provided important initial concepts. However, all remodeler ATPases are classified as members of the SF2 family of DEAD/H-box helicase/translocases, and a significant advance was the demonstration that remodelers are indeed ATP-dependent DNA translocases 4,5,[35][36][37][38] . This indicated a possible motor force for breaking histone-DNA contacts and moving DNA on the octamer surface.…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

“…This indicated a possible motor force for breaking histone-DNA contacts and moving DNA on the octamer surface. Notably, remodeler ATPases lack the 'pin' motif required for DNA strand separation and are therefore DNA translocases but not helicases 5,39 . One consistent feature of SF2 translocases is their tracking along the phosphate backbone of one of the two DNA strands, with limited interaction with the bases themselves 39,40 .…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

“…Together, these observations strongly suggest that the translocase domain pumps DNA from this internal position on the nucleosome and that the arrival of a DNA gap or end at this position stops translocation 38,41,43,44 . This model has not been tested for Rad54; as Rad54 lacks specific nucleosome-interaction domains, current models favor the idea that Rad54 perturbs nucleosomes by exerting torsional stress when it encounters a nucleosome while translocating 5,46 .…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

“…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 .…”

Section: Introductionmentioning

confidence: 99%

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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%

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

View full text Add to dashboard Cite

show abstract

“…Gene activation and silencing during this period is largely accomplished through epigenetic modifications of chromatin that involve DNA methylation, histone modification, and the function of ATP-dependent remodeling complexes (de la Serna et al, 2006;Ho and Crabtree, 2010). The ATP-dependent remodeling enzymes are a class of ATPases that contain a SNF2 domain (sucrose non-fermenting, originally identified in Saccharomyces cerevisiae) (Durr et al, 2005;Eisen et al, 1995). SNF2-containing ATPases are the catalytic subunits of multi-protein chromatin remodeling complexes that are also known as chromatin remodelers (for review see e.g., Clapier and Cairns (2009)).…”

Section: Introductionmentioning

confidence: 99%